IP Library › Granted Patent US 12,565,641
Granted Patent B2
US 12,565,641 · App. 18/046,451 · Granted Mar 3, 2026

Engineered terminal deoxynucleotidyl transferase variants

Inventors: Charlene Ching (San Jose, CA); Stephanie Marie Forget (Redwood City, CA); Anders Matthew Knight (Mountain View, CA); Mikayla Jianghongxia Krawczyk (Palo Alto, CA); Niusha Mahmoodi (San Francisco, CA); Melissa Ann Mayo (Foster City, CA); Mathew G. Miller (San Carlos, CA); Jonathan Vroom (South San Francisco, CA)
Assignee: Codexis, Inc.
C12N9/1264C12N15/63C12Y207/07031
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,565,641
App. No.
18/046,451
Granted
Mar 3, 2026
Kind
B2
Abstract

The present invention provides engineered terminal deoxynucleotidyl transferase (TdT) polypeptides useful in template-independent polynucleotide synthesis using a nucleoside triphosphate-3′-O-removable blocking group (NTP-3′-O-RBG), as well as compositions, methods of utilizing these engineered polypeptides, and polynucleotides encoding the engineered terminal deoxynucleotidyl transferases.

Claims (42)

1 . An engineered terminal deoxynucleotidyl transferase comprising a a polypeptide sequence having at least 90% sequence identity to SEQ ID NO: 5296, wherein the engineered terminal deoxynucleotidyl transferase comprises C68R in its polypeptide sequence, and wherein said engineered terminal deoxynucleotidyl transferase has terminal deoxynucleotidyl transferase activity and wherein the amino acid positions of the polypeptide sequence are numbered with reference to SEQ ID NO: 5296.

2 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 14, 17, 19, 20, 21, 22, 24, 27, 28/304, 55, 66, 67, 80, 99, 103, 111, 113, 115, 140, 158, 159, 160, 161, 167, 170, 180, 192, 197, 200, 201, 219, 233, 235, 238, 246, 249, 256, 258, 267, 268, 273, 295, 296, 297, 300, 303, 304, 306, 322, 350, 353, 367, and 373, and/or any combinations thereof.

3 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 10, 17, 20, 27, 28, 55, 62, 63, 66, 67, 68/118, 87, 103, 106, 111, 131, 155, 157, 160, 160/296, 177, 181, 200, 219, 246, 256, 263, 292, 295, 296, 297, 315, and 373, and/or any combinations thereof.

4 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 8, 10, 11, 15, 16, 20, 21, 22, 24, 26, 28, 30, 34, 42, 44, 47, 48, 52, 54, 55, 62, 63, 66, 67, 72, 77, 80, 84, 87, 89, 91, 92, 99, 101, 102, 103, 106, 109, 111, 111/346, 113, 115, 116, 118, 122, 123, 131, 140, 144, 147, 156, 157, 160, 160/296, 161, 162, 163, 164, 170, 173, 174, 175, 180, 181, 185, 189, 192, 193, 194, 197, 198, 198/289, 200, 201, 207, 219, 230, 234, 235, 237, 238, 241, 245, 246, 249, 256, 257, 258, 262, 263, 264, 267, 268, 272, 273, 280, 284, 286, 289, 290, 291, 292, 295, 296, 297, 299, 300, 302, 304, 307, 308, 310, 311, 321, 322, 325, 350, 353, 355, 365, 366, 368, 371, 373, and 388, and/or any combinations thereof.

5 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 60, 60/259, 60/278, and 65/259, and/or any combinations thereof.

6 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 20, 20/21/68/103/200/238/297, 20/21/68/111/235, 20/21/68/160, 20/21/68/160/180/200/246, 20/21/68/160/246, 20/21/68/180, 20/21/68/180/235, 20/21/68/200/235/297, 20/21/68/233/246/297, 20/21/103/233, 20/21/111, 20/21/111/160/200, 20/21/111/200/238, 20/21/180/297, 20/21/233, 20/68/103/160/200, 20/68/103/180/200, 20/68/160, 20/68/160/180, 20/68/160/180/233/235/246, 20/68/160/235/297, 20/68/160/246, 20/68/200/238/246, 20/68/235/297, 20/103/160/180/200/235, 20/103/233, 20/111, 20/111/180/235/246/297, 21, 21/68, 21/68/103/111, 21/68/111/200, 21/68/160/180/200/205/297, 21/68/160/180/200/297, 21/68/160/238, 21/68/160/238/246, 21/68/180, 21/68/180/235, 21/68/180/246, 21/68/200, 21/68/235, 21/103/233, 21/233/297, 68/103/160/235, 68/103/200/235/246/297, 68/111/200/238, 68/111/233/236/297, 68/160/233/246, 68/200/235/297, 103, 103/160/180, 103/160/297, 103/233, 111, and 111/160/233/235/297, and/or any combinations thereof.

7 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 9, 9/28/156/158/173/190/193/303/364, 9/28/156/158/290/364, 9/28/190/193/303/364, 9/28/290/303/364, 9/156/158/193/290/303/364, 9/156/364, 9/290/364, 9/364, 14, 14/58/84/147/162/224/296/297/298/299, 14/58/84/147/162/224/296/297/299, 14/58/84/224/298, 14/84/147/193/197/224/296, 14/84/162/224/297/299, 14/84/224/296/299, 14/162/224/298/299, 14/224/296/298, 23/28/156/158/190/193/290/364, 28/156/173/364, 28/158/173/190/193/290/364, 28/190/193, 28/296/303/364, 28/364, 58/147/162/197/224/296/297/298/299, 58/162/224/296/298, 58/224, 58/224/299, 84/147, 147/224, 147/224/297/298, 156/158/190/193/364, 158/193/290/303, 193/290, 224/296/298, 224/297/299, 290/303/364, 303, and 364, and/or any combinations thereof.

8 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 9, 34, 48, 69, 78, 237/271, 249, 302, 309, 315, 353, 364, and 365, and/or any combinations thereof.

9 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 200, 201, 202, 203, 226, 229, 230, 234, 235, 236, 237, 238, 324, 326, 342, 344, 352, 355, 360, 366, 369, 371, 373, 374, 377, 378, 383, 388, and 390, and/or any combinations thereof.

10 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 200, 203, 226, 234, 237, 342, 350, 360, 366, 369, 373, 377, 378, 380, and 390, and/or any combinations thereof.

11 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 200, 201, 203, 207, 226, 230, 233, 234, 235, 322, 342, 344, 352, 355, 360, 366, 371, 373, 374, 378, and 387, and/or any combinations thereof.

12 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 15, 200, 202, 203, 205, 206, 207, 226, 229, 230, 231, 233, 234, 237, 321, 324, 326, 327, 330, 342, 344, 349, 352, 353, 360, 366, 369, 371, 373, 374, 378, 380, 386, 387, 388, and 390, and/or any combinations thereof.

13 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 55/80/174/268/355/366, 55/80/268/315/366, 55/80/268/346, 55/111/156/268/315/324/327/366/373, 55/111/268/346/355, 55/111/268/355/366, 55/111/315/355/373, 55/268, 55/268/315/346, 55/268/324/366, 55/268/346/355, 62/66/69/143/338/353, 62/66/100/101/104/203/235/338, 62/69/80/101/104/143/235/338, 62/203/211/235/338/350, 66/69/143/235/338, 69/80/203/211/278/338, 80/111/268/324/327/346/366/373, 80/111/355/366, 80/143/203/211/338, 80/268/315/346/355, 80/268/327/346/366, 80/268/346, 80/315/346/364/373, 80/346/366, 100/101/211/278/338/350/353, 111/268, 268, 268/315/327/346, 268/315/346, 268/315/346/366, 268/315/355, 268/324, 268/324/327/346, 268/327/346, 268/346, 268/346/355, 268/355/366, 315/324/327/355/366, 324/346/355/366, and 327/346, and/or any combinations thereof.

14 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 29/77/104/234/271, 29/77/104/234/271/279/380, 29/77/182/207/271, 29/77/207/234/279/380, 29/77/234/271/279/368, 29/77/271, 29/104/234/271/279/380, 29/182/207/380, 29/182/234/271/380, 29/182/271/279/380, 29/234/279/380, 29/271/279, 29/271/279/368/380, 32/78/106/200/226/272/373, 32/78/106/200/226/373, 32/78/106/226, 32/78/200/226, 32/78/200/226/235/272, 32/78/200/226/235/321/373, 32/78/226, 32/78/226/321, 32/78/226/373, 32/106/200/226, 32/106/200/226/235/373, 32/200/226, 32/200/226/321/373, 32/226, 77/182/279/380, 77/182/368, 77/234/271/279/380, 78/106, 78/106/226/321/373, 78/106/235/321/373, 78/200/226/321/373, 78/226/321, 104/182, 106/200/226/373, 106/226/235/373, 182/207/279/368, 182/234/380, 182/279/368/380, 200/226, 200/226/321/373, 200/226/373, 207/271/368/380, 207/380, 226, 226/235/272/373, 226/272/373, and 271/380, and/or any combinations thereof.

15 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 32, 32/161/193/237/360, 32/162, 32/162/193/267, 32/162/237/265/266, 32/162/302, 32/302, 53/163/201/325/329, 53/200/201/325/329, 53/201, 53/201/275/280, 154, 154/166, 154/166/210/296, 154/339, 156/210/339, 161/162, 161/237, 162, 162/193/232/267/302/360, 162/237/265/266/267/302, 162/265, 162/267/360, 166/210, 166/296, 166/346/347, 167/210/346/349, 193/267, 201/371, 210/339, 237, 237/265, 237/266/360, 237/360, 339, and 371, and/or any combinations thereof.

16 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 32, 32/162, 32/162/193, 32/162/193/267, 32/162/237/265/266, 32/162/302, 53/163/201/325/329, 53/200/201/325/329, 53/201, 53/201/275/280, 53/201/371, 82/154/296, 154, 154/166, 154/166/210/296, 154/166/346/347, 154/166/347, 154/167/210/347/349, 154/296/347, 154/339, 154/347, 156/166/167, 161/162, 161/237, 162, 162/193/232/267/302/360, 162/237/265/266/267/302, 162/265, 162/267/360, 163/201, 164/275/280, 166/210, 166/296, 166/346/347, 193/267, 201/371, 210/339, 237, 237/265, and 339, and/or any combinations thereof.

17 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 65, 65/184/187, 82/184/220/386, 154, 154/184, 154/187/220/350/386, 154/293, 154/350, 154/386, 184/187, 184/293, 187/220/350, 187/293, 220, 220/293, 293, 293/350, 293/350/386, 350, and 386, and/or any combinations thereof, wherein the amino acid positions are numbered with reference to SEQ ID NO: 5296.

18 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 157, 160, 186, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 206, 209, 210, 211, 227, 229, 230, 233, 234, 235, 236, 237/381, 238, 241, 242, 243, 247, 253, 258, 260, 267, 272, 278, 282, 286, 288, 290, 292, 297, 298, 299, 327, 331, 368, 373, and 381, and/or any combinations thereof, wherein the amino acid positions are numbered with reference to SEQ ID NO: 5296.

19 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 160, 186, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 199, 200, 201, 202, 203, 204, 209, 210, 211, 229, 230, 233, 234, 235, 236, 237/381, 238, 241, 243, 244, 247, 253, 260, 278, 286, 288, 292, 297, 298, 299, 327, 331, 368, 373, and 381, and/or any combinations thereof, wherein the amino acid positions are numbered with reference to SEQ ID NO: 5296.

20 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 65, 65/70/155/209/228, 65/128/209/371/373, 65/151, 65/155/209, 65/155/209/352/353, 65/159, 65/209/219/352/353, 65/209/352/353/371, 65/228/352/353/373, 65/228/371/373, 65/352/353/371, 128/159/209/352/353, 128/209, 128/209/219, 128/209/219/352/353/371, 128/209/228/371, 128/209/371, 128/209/371/373, 128/209/373, 128/338/352/353/373, 151/209, 151/209/371, 151/209/373, 151/228/352/353/373, 151/228/373, 151/352/353, 151/352/353/371/373, 155, 155/209, 155/228/352/353, 159/209/352/353, 208/209, 209, 209/219/352/353/371, 209/219/371, 209/228, 209/352/353/371, 209/371, 209/371/373, 209/373, 219/228, 219/352/353/371/373, 219/371/373, 228, 228/371, 228/371/373, 228/373, 352/353, 352/353/371, 371, 371/373, and 373, and/or any combinations thereof, wherein the amino acid positions are numbered with reference to SEQ ID NO: 5296.

21 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 55/65/151, 65, 65/70/155/209/228, 65/70/228/373, 65/128, 65/128/155/209/371, 65/128/159/209/371/373, 65/128/209/371, 65/128/209/371/373, 65/128/219/373, 65/128/373, 65/151, 65/155/209, 65/155/209/352/353, 65/159, 65/209/219/352/353, 65/209/352/353/371, 65/219/371, 65/228/352/353/373, 65/228/371, 65/228/371/373, 65/352/353, 65/352/353/371, 65/373, 70/155/352/353, 128, 128/155/209, 128/159, 128/159/209/352/353, 128/209, 128/209/219, 128/209/219/352/353/371, 128/209/228/371, 128/209/371, 128/209/371/373, 128/209/373, 128/219/352/353, 128/219/371/373, 128/228/352/353, 128/228/371, 128/228/373, 128/352/353, 128/352/353/373, 128/371, 128/371/373, 128/373, 151, 151/155, 151/155/209, 151/155/209/219/228/371/373, 151/155/209/373, 151/155/219/352/353/371, 151/155/352/353, 151/155/352/353/371/373, 151/155/352/353/373, 151/209, 151/209/371, 151/209/371/373, 151/209/373, 151/219, 151/219/371, 151/228/352/353/373, 151/228/373, 151/352/353, 151/352/353/371/373, 151/371, 151/373, 155, 155/209, 155/219, 155/228/352/353, 155/228/371, 155/228/371/373, 155/352/353/373, 155/371, 155/371/373, 155/373, 159/209/352/353, 209, 209/219/352/353/371, 209/219/371, 209/228, 209/352/353/371, 209/371, 209/371/373, 209/373, 219, 219/228, 219/352/353/371/373, 219/352/353/373, 219/371, 219/371/373, 228/352/353, 228/371, 228/371/373, 228/373, 352/353, 352/353/371, 352/353/373, 371, 371/373, and 373, and/or any combinations thereof, wherein the amino acid positions are numbered with reference to SEQ ID NO: 5296.

22 . The engineered terminal deoxynucleotidyl transferase of claim 1 comprising a polypeptide sequence having at least 90% sequence identity to a sequence of SEQ ID NO: 5628, 5630, 5632, and/or 5636, and wherein the amino acid positions of the polypeptide sequence are numbered with reference to SEQ ID NO: 5628, 5630, 5632, and/or 5636.

23 . The engineered terminal deoxynucleotidyl transferase of claim 1 comprising a polypeptide sequence selected from the even-numbered sequences of SEQ ID NO: 5624-6766.

24 . The engineered terminal deoxynucleotidyl transferase of claim 1 , wherein the engineered terminal deoxynucleotidyl transferase further comprises a residue difference(s) or a residue difference set(s) at an amino acid position selected from 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 34, 36, 38, 40, 42, 44, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 69, 70, 71, 72, 73, 74, 75, 77, 78, 79, 80, 82, 84, 85, 86, 87, 89, 91, 92, 93, 94, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 115, 116, 117, 118, 119, 120, 122, 123, 124, 125, 127, 131, 133, 134, 135, 136, 140, 141, 143, 144, 145, 147, 148, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 170, 173, 174, 175, 176, 177, 180, 181, 182, 184, 185, 186, 187, 189, 190, 192, 193, 194, 196, 197, 198, 200, 201, 202, 203, 204, 205, 206, 207, 209, 210, 211, 217, 219, 220, 224, 226, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 241, 242, 243, 244, 245, 246, 248, 249, 250, 252, 253, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 282, 284, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 315, 319, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 332, 338, 339, 340, 341, 342, 344, 345, 346, 347, 349, 350, 351, 352, 353, 355, 358, 360, 361, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 376, 377, 378, 380, 383, 384, 386, 387, 388, and 390, and/or any combinations thereof, wherein the amino acid positions of the polypeptide sequence are numbered with reference to SEQ ID Nos: 5296, 5628, 5630, 5632, and/or 5636.

25 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at an amino acid position selected from 8, 9, 9/11, 9/14/190/197/364, 9/14/58, 9/14/58/182/190/197/298, 9/28/156/158/173/190/193/303/364, 9/28/156/158/290/364, 9/28/190/193/303/364, 9/28/290/303/364, 9/58/197, 9/156/158/193/290/303/364, 9/156/364, 9/290/364, 9/298, 9/302, 9/364, 10, 10/14/197/364, 11, 12, 14, 14/15/200/230, 14/15/77/200/226/230, 14/15/77/78, 14/15/77/78/200/201/226/230/290, 14/15/77/78/200/203/230/290, 14/15/77/78/203/226/230/290, 14/15/78, 14/15/78/226/230, 14/28/224/296/298, 14/28/58/162/190/193/224, 14/28/58/224, 14/28/58/84/173/297, 14/58/147/162/190/193/224/296/303, 14/58/158/224, 14/58/162, 14/58/182/197/298/364, 14/58/84/147/162/224/296/297/298/299, 14/58/84/147/162/224/296/297/299, 14/58/84/224/298, 14/77/201/230, 14/77/78/200/226/230/257, 14/77/78/226/230/257, 14/78/200/201/226/290, 14/78/200/201/339, 14/78/200/226/230/339, 14/78/200/226/290/339, 14/78/200/230/339, 14/84/147/193/197/224/296, 14/84/162/224/297/299, 14/84/224/296/299, 14/147, 14/147/158/162/224, 14/147/173, 14/147/224, 14/158/162/197/224/296/298/299, 14/162/224/298/299, 14/173/193/197/296/297/298/299, 14/190/197/298, 14/193/197/224/297/298/299/300, 14/197/298/364, 14/200/203/226/230, 14/200/203/226/230/257/339, 14/200/203/230/339, 14/201/203/226, 14/224/296/298, 14/224/296/303, 14/298/364, 15, 15/77, 15/77/200/201/203/226/230/290/339, 15/77/200/230, 15/77/200/230/290/339, 15/77/201/226/230/339, 15/77/226/230/290/339, 15/77/78, 15/77/78/200/201/203/226/230, 15/78/201, 15/78/201/203/230, 15/78/201/230/290, 15/78/203/226/230, 15/200, 15/201/203/226/230/257/339, 15/226/230/339, 15/230, 16, 17, 18, 18/28/147/303, 19, 20, 20/21, 20/21/103/233, 20/21/111, 20/21/111/157/315, 20/21/111/160/200, 20/21/111/200/238, 20/21/111/246, 20/21/180/297, 20/21/233, 20/21/315, 20/21/52/67/68/87/111/157/160/173/180/200/235/246/315, 20/21/55/67/68/87/111/157/160/180/181/200/235/246/256/315/350, 20/21/55/67/68/87/111/157/160/180/200/246/256/315, 20/21/60/72/160/180/200/246/259/338/358, 20/21/67, 20/21/67/160, 20/21/67/68/87/111/157/160/180/200/235/246/315, 20/21/67/68/87/111/157/160/180/200/246/315, 20/21/67/87, 20/21/67/87/111, 20/21/67/87/111/200, 20/21/67/87/111/315, 20/21/67/87/157/180, 20/21/67/87/246/315, 20/21/68/103/200/238/297, 20/21/68/111/235, 20/21/68/160, 20/21/68/160/180/200/246, 20/21/68/160/246, 20/21/68/180, 20/21/68/180/235, 20/21/68/200/235/297, 20/21/68/233/246/297, 20/21/87/111/246/315, 20/21/87/157/200, 20/21/87/180/246/315, 20/21/87/315, 20/67/87/111/180, 20/67/87/157/160/180/315, 20/68/103/160/200, 20/68/103/180/200, 20/68/111/157/160, 20/68/160, 20/68/160/180, 20/68/160/180/233/235/246, 20/68/160/200/246, 20/68/160/235/297, 20/68/160/246, 20/68/200/238/246, 20/68/235/297, 20/87/111/180, 20/87/157/160, 20/100, 20/100/104/111/242, 20/100/104/120/197/367, 20/100/104/197/203/242/292, 20/100/104/203/350/353, 20/100/111, 20/100/120/197/232/235/315/366/367, 20/100/197/292/315, 20/100/203, 20/100/232/292/366/367, 20/100/235/315/367, 20/103/160/180/200/235, 20/103/233, 20/104/111/120/203, 20/111, 20/111/180/235/246/297, 20/120/197/292, 20/120/235, 20/160/315, 20/200, 20/292, 21, 21/67/180/315, 21/67/200, 21/67/87/111/200, 21/67/87/157/246, 21/68, 21/68/103/111, 21/68/111/200, 21/68/160/180/200/205/297, 21/68/160/180/200/297, 21/68/160/238, 21/68/160/238/246, 21/68/180, 21/68/180/235, 21/68/180/246, 21/68/200, 21/68/235, 21/87/157/160, 21/87/160/200/315, 21/87/160/315, 21/87/200, 21/87/246/315, 21/103/233, 21/111, 21/157/160, 21/160/315, 21/200/315, 21/233/297, 21/246, 22, 23, 23/28/156/158/190/193/290/364, 23/186/256/309, 24, 26, 26/60/200, 26/60/200/203/229/234/267, 26/60/200/203/229/267, 26/60/200/203/229/267/290, 26/60/200/203/234/267, 26/60/200/203/292, 26/60/200/234/290, 26/60/203/229/234/290, 26/60/229/267, 26/60/29026/200, 26/200/203, 26/200/203/229, 26/200/290, 26/203/234/290/292, 26/229/234/360, 27, 28, 29, 29/77/104/234/271, 29/77/104/234/271/279/380, 29/77/182/207/271, 29/77/207/234/279/380, 29/77/234/271/279/368, 29/77/271, 29/98/143/266, 29/98/185/197/266, 29/98/185/266/296/299, 29/104/234/271/279/380, 29/143, 29/143/162, 29/143/170/193/197/266, 29/143/185/193/266, 29/158/266, 29/170/185/193/266/299, 29/182/207/380, 29/182/234/271/380, 29/182/271/279/380, 29/185/296, 29/193/197/296/297, 29/234/279/380, 29/271/279, 29/271/279/368/380, 30, 32, 32/72/339, 32/72/339/360, 32/78/106/200/226/272/373, 32/78/106/200/226/373, 32/78/106/226, 32/78/200/226, 32/78/200/226/235/272, 32/78/200/226/235/321/373, 32/78/226, 32/78/226/321, 32/78/226/373, 32/103, 32/103/106/111/322/324, 32/103/106/207/210/235/321/368, 32/103/207/210/344/349, 32/103/207/228/232/373, 32/103/207/321/344, 32/103/210/273/321/373, 32/103/273, 32/103/321/344, 32/106, 32/106/200/226, 32/106/200/226/235/373, 32/106/207/210/232, 32/106/210, 32/106/210/373, 32/106/235/321, 32/106/235/368, 32/106/273/321/373, 32/106/280, 32/111/235, 32/111/235/271/272/339, 32/111/235/339, 32/111/235/339/386, 32/111/235/386, 32/140/141/261/360, 32/140/339, 32/140/360, 32/141/180/244, 32/161/193/237/360, 32/162, 32/162/193, 32/162/193/267, 32/162/237/265/266, 32/162/302, 32/180/261/339, 32/200/226, 32/200/226/321/373, 32/207/210/273, 32/207/210/279, 32/207/210/368/373, 32/207/235, 32/207/273/279/321, 32/207/279, 32/207/344, 32/210/232/235/368, 32/210/232/273/321, 32/210/232/273/368/373, 32/210/273, 32/226, 32/235, 32/235/271/339, 32/235/272, 32/235/272/339, 32/235/272/386, 32/235/273, 32/235/339/386, 32/235/386, 32/244/261, 32/271/339, 32/272, 32/273/279/344/349, 32/273/344/373, 32/279, 32/279/321, 32/302, 32/321/324/360, 32/322/324/383/386, 32/324, 32/339, 34, 34/48/133/158/182/230/233/271/345, 34/48/147, 34/48/147/158/182/220/233/307, 34/48/147/182/230/233/249/307, 34/48/147/271, 34/48/182/233/249, 34/48/339, 34/48/78/133/147/182, 34/48/78/147/158, 34/48/78/147/182/220/233/249/307/315/339, 34/48/78/158/182/220/249/307, 34/48/78/158/182/233/315/345, 34/48/78/182/220/230/315, 34/48/78/182/220/233, 34/78, 34/78/147/182/220/249, 34/78/147/182/233/249/315, 34/78/147/182/233/271/339, 34/78/158, 34/78/158/182/315/345, 34/78/158/249, 34/78/182/233/307, 34/78/204/220/339, 34/78/220/271, 34/78/220/307/339, 34/78/315, 34/78/84/147/158/182/220, 34/78/84/158/230, 34/133/147/158/230/233/249, 34/147, 34/147/155/233/339, 34/147/158, 34/147/158/182/233, 34/147/158/182/249/271, 34/147/182, 34/147/182/220, 34/147/182/220/230/249/315/339, 34/147/182/220/230/339, 34/147/182/220/271/315, 34/147/182/233/271/339, 34/147/182/249/307/315/339, 34/147/182/315, 34/147/182/345, 34/147/220/271, 34/147/230/273/315/345, 34/147/233, 34/147/249, 34/147/315/339, 34/158/182/315/339/345, 34/158/220, 34/158/307, 34/182, 34/182/230/315, 34/182/307/339, 34/182/345, 34/220, 34/220/307, 34/220/307/345, 34/220/315/339, 34/220/339, 34/233, 34/271/339, 34/315/345, 34/339, 36, 38, 40, 42, 44, 44/193, 47, 48, 48/53/237/239, 48/78/147/158/182/220/230/307, 48/78/147/158/182/230/249/271/315, 48/78/147/158/233/249, 48/78/147/182/220/233/249/339/345, 48/78/147/182/220/315, 48/78/147/182/230/233/249, 48/78/158/182/220/233/249, 48/78/158/230/339, 48/78/233/315/339, 48/147/158/182/220/230/249/271/307/315/339, 48/147/158/182/220/249/307/339, 48/147/158/182/220/315, 48/147/158/182/230/233, 48/147/158/182/233/345, 48/147/158/233, 48/147/158/307/345, 48/147/233, 48/147/233/345, 48/147/271/307/339, 48/158/182/230/233/249, 48/182, 48/182/307/315, 48/256/261, 48/339, 49, 50, 51, 52, 52/55/106/256, 52/55/181/235/256, 52/55/181/256, 52/99/181/235, 52/106/181/235/256, 52/106/235/256, 52/106/256, 52/173/235, 52/180, 52/180/200/235/315/349, 52/180/200/349, 52/180/349, 52/200, 52/200/315, 52/200/349, 52/200/349/350, 52/235, 52/235/256, 52/315, 52/315/349, 52/349, 52/349/350, 53, 53/73/75/237/239, 53/157/278/327/331, 53/162/327/331/368, 53/163/201/325/329, 53/200/201/325/329, 53/201, 53/201/275/280, 53/201/371, 53/219/358, 53/237, 54, 55, 55/58, 55/58/256, 55/58/256/350/373, 55/58/256/355, 55/58/350/351, 55/58/69/350/351, 55/58/99/256/351/373, 55/58/99/256/355, 55/58/99/351, 55/67, 55/67/106/111/157, 55/67/106/315, 55/67/111, 55/67/111/315, 55/67/315, 55/67/87, 55/67/87/106/111/315, 55/67/87/157/315, 55/80/174/268/355/366, 55/80/268/315/366, 55/80/268/346, 55/87, 55/87/106, 55/87/106/111/315, 55/87/106/315, 55/87/157, 55/87/157/207, 55/99/103, 55/99/181/256, 55/99/219/358/373, 55/99/256/350, 55/103/181, 55/103/219, 55/103/338, 55/106/111, 55/106/157, 55/111, 55/111/156/268/315/324/327/366/373, 55/111/268/346/355, 55/111/268/355/366, 55/111/315, 55/111/315/355/373, 55/157, 55/181/219, 55/181/235/256/350, 55/181/246, 55/181/358, 55/219/246/358, 55/219/256/338, 55/256, 55/256/259, 55/268, 55/268/315/346, 55/268/324/366, 55/268/346/355, 55/315, 56, 56/75/154/156/192/239/280/282, 56/75/192/239, 56/192/282/350, 57, 57/367, 58, 58/69/256/373, 58/72/211/315, 58/72/220/224, 58/84/211/220/224, 58/99, 58/99/351/355, 58/99/355, 58/147/162/197/224/296/297/298/299, 58/147/162/296/298, 58/162/224/296/298, 58/186/270, 58/197, 58/197/364, 58/224, 58/224/299, 58/256, 58/256/350/355, 58/350/355, 58/364, 59, 59/62/63/68, 59/62/63/68/103/234, 59/62/63/68/147, 60, 60/62/68/91/111/234/289, 60/106/111/235/360, 60/200/203/290, 60/200/229/234, 60/200/234, 60/200/234/267/290/292, 60/200/234/290, 60/203, 60/259, 60/278, 60/280/360, 61, 62, 62/63/68, 62/63/68/91/109/210, 62/63/68/91/147/205/210/234, 62/66/100/101/104/203/235/338, 62/66/69/143/338/353, 62/68/103, 62/68/111, 62/68/91/111/289, 62/69/100/235/268/346, 62/69/353, 62/69/80/101/104/143/235/338, 62/111/235/315/355, 62/111/235/324/346, 62/203/211/235/338/350, 62/235/268/327/346/350/353/355, 62/235/346/350/355, 62/315/327/353, 62/323/346/353/355, 63, 64, 65, 65/70/155/209/228, 65/128/209/371/373, 65/140, 65/140/192/193, 65/140/192/193/302, 65/151, 65/155/209, 65/155/209/352/353, 65/159, 65/184/187, 65/193, 65/209/219/352/353, 65/209/352/353/371, 65/220/339, 65/228/352/353/373, 65/228/371/373, 65/259, 65/352/353/371, 66, 66/69/143/235/338, 66/100/235/315/327/353/355, 66/111/346/353/355, 66/220/224, 66/235/268/346, 66/235/346, 66/235/373, 67, 67/87, 67/87/106/157, 67/87/111/157/160/315, 67/87/111/157/315, 67/87/157, 67/87/315, 67/106, 67/106/111, 67/106/111/315, 67/106/157, 67/111, 67/111/315, 67/157, 67/157/160/180, 67/157/160/315, 67/157/315, 67/160, 67/180/200, 67/180/200/315, 67/315, 68, 68/87, 68/103/160/235, 68/103/200/235/246/297, 68/106/200, 68/106/321/322, 68/111/200/238, 68/111/233/236/297, 68/118, 68/157/160/200/315, 68/160/233/246, 68/200, 68/200/235/297, 68/200/270/321, 68/270/321/322, 68/344, 68/344/383, 69, 69/80/203/211/278/338, 69/100, 69/100/111/298/353/355, 69/100/235, 69/100/353/366, 69/111/235, 69/111/235/300/353/355, 69/111/235/315, 69/220, 69/235/315, 69/235/353, 69/268, 69/268/324/327/353/355, 69/268/346, 69/268/346/353, 69/315/353, 69/324/327/346, 69/324/346/350, 69/324/353, 69/339, 69/353/355, 70, 70/71, 70/71/353, 70/72, 70/72/140/244/261/339, 70/72/141/244, 70/72/180/360, 70/134/353, 70/140/141/339, 70/261/339/360, 70/353, 70/360, 71, 71/77/133/353, 71/77/353, 71/353, 72, 72/74/200/272/339/347, 72/84/220/224/315, 72/84/86/224, 72/86/220, 72/180/244/339, 72/220/224, 72/220/315, 72/256/360, 72/360, 73, 74, 74/106/270/344, 74/200/339, 74/272, 75, 75/207/373/378, 75/233/344, 75/233/366, 75/237/350, 77, 77/78/200/226/339, 77/78/201/226/257/339, 77/78/203, 77/78/203/230/339, 77/133/353, 77/134/353, 77/182/279/380, 77/182/368, 77/200/201, 77/200/201/226/230/339, 77/200/203/230/257/339, 77/200/230, 77/234/271/279/380, 77/353, 78, 78/106, 78/106/226/321/373, 78/106/235/321/373, 78/127, 78/133/147/158/182/220/271/339, 78/135/182/233/249/315/345, 78/147/158/182, 78/147/158/182/230/249, 78/147/158/182/233/271/307/345, 78/147/158/182/339/345, 78/147/158/220/230/233/249/271/307/315/345, 78/147/158/249/307/315, 78/147/182/230/233/249, 78/147/182/249/307, 78/147/182/339/345, 78/147/230/307, 78/147/233, 78/147/249/271/339, 78/158/182, 78/158/182/233/271/315, 78/158/182/307/315/345, 78/182/220/339, 78/182/271/315/339, 78/200/226/321/373, 78/200/230, 78/203/230/290, 78/226/230, 78/226/290, 78/226/321, 78/233, 78/339, 79, 80, 80/111/268/324/327/346/366/373, 80/111/355/366, 80/143/203/211/338, 80/268/315/346/355, 80/268/327/346/366, 80/268/346, 80/315/346/364/373, 80/346/366, 82, 82/154/296, 82/184/220/386, 84, 84/92/173, 84/147, 84/147/197/296/297, 84/147/297/298/303, 84/156/173/204, 84/173/204/303, 84/173/224, 84/220/315, 84/224/297/298/299, 85, 86, 87, 87/106, 87/106/111/315, 87/111, 87/111/157/315, 87/111/200, 87/111/200/246, 87/157, 87/157/180/200, 87/157/315, 87/315, 89, 91, 91/109/111, 91/109/147/205/210/234, 92, 92/173/204/290/303, 93, 94, 96, 97, 98, 98/143/158/170/185/296/297, 98/143/162/266, 98/143/185/266, 98/162/193, 98/170/193/197, 98/185, 98/185/193/197/266/297, 99, 99/103/219, 99/235, 99/256/351/355, 100, 100/101/211/278/338/350/353, 100/111, 100/111/353, 100/120/197/242, 100/235/268/315/346, 100/235/268/346/355, 100/235/268/366/373, 100/235/346/350/353, 100/268/346, 100/268/366, 101, 102, 103, 103/106/207/321, 103/106/210, 103/106/360, 103/111/235/280/360, 103/111/235/321/324, 103/160/180, 103/160/297, 103/207/210/235/321, 103/210/232/235, 103/219/256, 103/219/338/358, 103/232/273, 103/233, 103/256, 103/259, 103/324, 104, 104/106, 104/106/111/200/201/235/268/368, 104/106/111/200/201/268, 104/106/111/201/235/368, 104/106/200/201/268, 104/120/232/353, 104/182, 104/200/207/237/344/373/387, 104/207/344/387, 105, 106, 106/111, 106/111/157, 106/111/200/201, 106/111/200/201/268/368, 106/111/200/235/368, 106/111/201, 106/111/201/368, 106/111/322/324/386, 106/111/322/383/386, 106/173/200/235/315, 106/173/388, 106/182/203/226/235/342/346, 106/200/201, 106/200/201/209/368, 106/200/201/235, 106/200/201/368, 106/200/226/373, 106/200/321/322/383, 106/201/235, 106/201/268, 106/207/210/232/235/321/368/373, 106/207/235/321/368, 106/226/235/373, 106/235, 106/235/273/373, 106/235/383/386, 106/270/344, 106/273, 106/315, 106/324, 107, 108, 109, 109/111/205/210/234/289, 110, 111, 111/157/180/200/315, 111/160/233/235/297, 111/173, 111/173/235/315, 111/197/242, 111/200/201/268, 111/200/368, 111/226, 111/226/321/344/346/369/387, 111/235, 111/235/268/327/346, 111/235/268/346, 111/235/271/339, 111/235/272/339/386, 111/235/280, 111/235/339, 111/235/346/350, 111/268, 111/272/339/386, 111/322/360, 111/327, 111/346, 112, 113, 113/355, 115, 116, 117, 118, 119, 120, 122, 123, 124, 125, 128, 128/159/209/352/353, 128/209, 128/209/2, 128/209/219, 128/209/219/352/353/371, 128/296, 131, 133, 133/135/307/315, 133/220/233/271, 133/307, 134, 134/353, 135, 136, 140, 140/141/256/261/339, 140/180/244/261/339/360, 140/192/193/302, 140/193/302, 141, 141/244/261/360, 141/244/360, 141/256/339/360, 141/261, 141/261/339, 141/360, 143, 143/158/197/266, 143/266/296/297, 144, 144/220, 145, 147, 147/158/162/190/224/296/297/299/303, 147/158/182/220/233, 147/158/182/230/233/249/271/339, 147/158/182/233/249, 147/158/182/233/271/307/339, 147/158/182/233/307/339, 147/158/182/233/315/345, 147/158/182/271/315, 147/158/182/315, 147/158/220/230/233/249/345, 147/158/220/249/315, 147/158/233/249, 147/182/220/233/345, 147/182/230/307/315/339, 147/182/233, 147/182/233/249, 147/182/249/271/307, 147/182/345, 147/210/234, 147/220, 147/224, 147/224/297/298, 147/232/233/271/315/339, 147/233/345, 147/249, 147/290/303/307, 147/339, 148, 149, 150/244/261/360, 151, 153, 154, 154/156/282/350, 154/166, 154/166/210/296, 154/166/346/347, 154/166/347, 154/167/210/347/349, 154/184, 154/187/220/350/386, 154/293, 154/296/347, 154/339, 154/347, 154/350, 154/386, 155, 155/220/325/339, 156, 156/158/190/193/364, 156/166/167, 156/210/339, 157, 157/160, 157/162, 157/162/241/242/260, 157/162/241/242/327/331, 157/162/241/278/331/368, 157/162/241/331, 157/162/242/260/331, 157/162/331, 157/315, 157/327/331, 157/368, 158, 158/182/220/230/249/307/339, 158/193/290/303, 158/233, 158/307, 158/315, 158/315/339, 159, 160, 160/296, 161, 161/162, 161/237, 162, 162/193/232/267/302/360, 162/224, 162/237/265/266/267/302, 162/241/278/327/331, 162/241/331, 162/242/368, 162/265, 162/267/360, 162/367/371, 163, 163/201, 164, 164/275/280, 165, 166, 166/210, 166/296, 166/346/347, 167, 167/210/346/349, 168, 169/390, 170, 170/193/197, 173, 173/204, 173/204/303, 173/297, 174, 175, 176, 177, 180, 180/339, 181, 182, 182/186/256/360, 182/197, 182/201/203/226/234/235/346, 182/201/203/226/234/342/346, 182/201/203/226/235, 182/201/203/226/235/346, 182/201/203/226/342/346, 182/201/203/268/346, 182/201/226/234/342/346, 182/201/226/235/346, 182/201/226/268/346, 182/201/342, 182/203/226, 182/207/279/368, 182/220/345, 182/226/234/268/342/346, 182/226/234/346, 182/226/235, 182/226/235/268/346, 182/226/235/342, 182/226/235/346, 182/226/268/342/346, 182/226/342, 182/226/346, 182/230, 182/230/233, 182/234/380, 182/256, 182/279/368/380, 182/298/364, 182/342/346, 182/345, 184, 184/187, 184/188/200/203/211/242, 184/188/200/203/242/297, 184/188/200/203/290/297/368, 184/188/203/290/297, 184/188/211/242/290/368, 184/189, 184/189/206/297/368, 184/189/297, 184/200, 184/206/242/290/297, 184/211, 184/242, 184/242/297/368, 184/290/297, 184/290/368, 184/293, 185, 186, 186/256, 186/256/270, 187, 187/220/350, 187/293, 188, 188/211, 188/211/242/290/297/368, 189, 189/200, 190, 190/193/197, 191, 192, 192/193, 192/193/211/242/297/368, 192/193/290/297/368, 193, 193/194, 193/197/296/303, 193/267, 193/290, 194, 194/242, 194/242/290, 195, 196, 197, 197/298, 198, 198/289, 199, 200, 200/202/203, 200/203, 200/203/226/230/339, 200/203/229/234, 200/203/290, 200/203/290/368, 200/206, 200/226, 200/226/321/373, 200/226/373, 200/230/257, 200/234/290, 200/235/368, 200/270, 200/270/275/339, 200/270/322/383, 200/271, 200/290/292/360, 200/344, 200/368, 201, 201/202, 201/202/272/360, 201/203, 201/203/226/234, 201/203/226/234/342/346, 201/203/226/234/346, 201/203/226/268/342, 201/203/226/346, 201/203/268/342, 201/203/268/346, 201/226/234/342/346, 201/226/234/346, 201/226/235/342, 201/226/268/346, 201/226/346, 201/230/257, 201/230/290, 201/235/268/342/346, 201/368, 201/371, 202, 202/233, 202/235/360/367/371, 203, 203/206/368, 203/226, 203/226/230, 203/226/230/257, 203/226/234/235, 203/226/234/235/346, 203/226/235/268/346, 203/226/235/342, 203/226/235/346, 203/226/342/346, 203/226/346, 203/229, 203/242/290/297/368, 203/297, 204, 204/264/340, 205, 206, 206/290, 206/297, 207, 207/210/273/279/344, 207/210/273/279/344/349/373, 207/210/273/321/344/349, 207/233/237/344/387, 207/235, 207/235/327/360/371, 207/235/368, 207/271/368/380, 207/273, 207/279/349, 207/368/373, 207/373, 207/380, 207/387, 209, 209/211, 210, 210/211, 210/211/242, 210/273/279, 210/273/279/349, 210/279, 210/339, 211, 211/368, 217, 219, 219/300, 219/358, 220, 220/224/315, 220/249, 220/293, 220/307/339, 220/315, 220/339, 220/349, 224, 224/296/298, 224/297/299, 224/298/299, 226, 226/234/235/346, 226/234/342, 226/235/268, 226/235/268/342/346, 226/235/268/346, 226/235/272/373, 226/235/342, 226/235/346, 226/268, 226/268/342, 226/268/342/346, 226/268/346, 226/272/373, 226/321/369, 226/342, 226/342/346, 226/346, 226/366, 226/366/369/387, 227, 228, 229, 229/325, 229/360, 230, 231, 232, 232/235, 232/235/273/368, 232/235/321, 232/346/350/355, 233, 233/271, 233/315, 233/367/371, 233/371, 234, 235, 235/268/327/346, 235/268/346, 235/271/272/339, 235/271/272/339/386, 235/271/339, 235/271/339/386, 235/272, 235/272/339, 235/272/386, 235/273, 235/280, 235/280/321/322/324, 235/280/321/324/383/386, 235/315, 235/315/353/355, 235/339, 235/339/386, 235/346, 235/346/350, 235/353, 235/353/355, 236, 237, 237/265, 237/266/360, 237/271, 237/360, 237/381, 238, 239, 241, 241/242/368, 242, 242/244, 242/290, 242/290/297, 242/331, 243, 244, 244/256/261/339/360, 245, 246, 247, 248, 249, 249/315/339, 250, 252, 253, 256, 256/259, 256/360, 257, 258, 259, 259/276/387, 260, 260/327, 260/331, 260/368, 261, 262, 262/325/349, 263, 264, 265, 265/346, 266, 266/297/299, 267, 267/270/275/339/347, 267/272/275, 268, 268/315/327/346, 268/315/346, 268/315/346/366, 268/315/355, 268/324, 268/324/327/346, 268/327/346, 268/346, 268/346/350/353/355, 268/346/355, 268/353, 268/355/366, 269, 270, 270/309, 270/322/344/383, 271, 271/339, 271/380, 272, 273, 273/279, 273/279/373, 274, 275, 275/291, 276, 277, 278, 279, 280, 280/383, 282, 284, 286, 287, 288, 289, 290, 290/303/364, 291, 292, 293, 293/350, 293/350/386, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 313, 314, 315, 315/324/327/355/366, 315/327/346, 319, 321, 321/324, 322, 324, 324/327/346, 324/346/350, 324/346/355/366, 324/355, 325, 325/339, 326, 327, 327/346, 328, 330, 331, 332, 338, 339, 341, 342, 342/363, 344, 344/370, 345, 346, 347, 348, 349, 350, 351, 352, 353, 353/355, 355/373, 354, 355, 356, 358, 360, 360/383, 361, 362, 363, 364, 365, 366, 367, 367/371, 368, 369, 370, 371, 372, 373, 374, 376, 377, 378, 380, 381, 382, 383, 384, 385, 386, 387, 388, 390, and 391, and/or any combinations thereof, wherein the amino acid positions of the polypeptide sequence are numbered with reference to SEQ ID NOs: 5296, 5628, 5630, 5632, and/or 5636.

26 . The engineered terminal deoxynucleotidyl transferase of claim 1 , having at least one improved property, as compared to a wild-type terminal deoxynucleotidyl transferase or a reference engineered terminal deoxynucleotidyl transferase.

27 . The engineered terminal deoxynucleotidyl transferase of claim 26 , having at least one improved property, as compared to wild-type terminal deoxynucleotidyl transferase or a reference engineered terminal deoxynucleotidyl transferase, wherein said improved property is selected from increased thermostability, increased activity at elevated temperatures, increased soluble expression, decreased by-product formation, and increased conversion of substrates to products.

28 . The engineered terminal deoxynucleotidyl transferase of claim 27 , wherein said engineered terminal deoxynucleotidyl transferase comprises increased soluble expression as compared to a wild-type terminal deoxynucleotidyl transferase or a reference engineered terminal deoxynucleotidyl transferase.

29 . The engineered terminal deoxynucleotidyl transferase of claim 27 , wherein said engineered terminal deoxynucleotidyl transferase comprises increased activity at elevated temperatures as compared to a wild-type terminal deoxynucleotidyl transferase or a reference engineered terminal deoxynucleotidyl transferase.

30 . The engineered terminal deoxynucleotidyl transferase of claim 27 , wherein said engineered terminal deoxynucleotidyl transferase comprises decreased by-product formation as compared to a wild-type terminal deoxynucleotidyl transferase or a reference engineered terminal deoxynucleotidyl transferase.

31 . The engineered terminal deoxynucleotidyl transferase of claim 27 , wherein said engineered terminal deoxynucleotidyl transferase comprises increased conversion of substrates to products as compared to a wild-type terminal deoxynucleotidyl transferase or a reference engineered terminal deoxynucleotidyl transferase.

32 . The engineered terminal deoxynucleotidyl transferase of claim 27 , wherein said engineered terminal deoxynucleotidyl transferase comprises increased thermostability as compared to a wild-type terminal deoxynucleotidyl transferase or a reference engineered terminal deoxynucleotidyl transferase.

33 . The engineered terminal deoxynucleotidyl transferase of claim 32 , wherein the improved property is increased thermostability of 2-fold, 5-fold, 10-fold, 15-fold, or more, as compared to a reference terminal deoxynucleotidyl transferase.

34 . The engineered terminal deoxynucleotidyl transferase of claim 27 , wherein the improved property is increased activity of the engineered terminal deoxynucleotidyl transferase by 2-fold, 5-fold, 10-fold, 15-fold, or more at 40° C., 45° C., 50° C., 55° C., 60° C., 65° C., 70° C., or 75° C., as compared to a reference terminal deoxynucleotidyl transferase.

35 . The engineered terminal deoxynucleotidyl transferase of claim 32 , wherein the engineered terminal deoxynucleotidyl transferase comprises at least one residue difference at an amino acid position selected from 80, 87, 111, 143, 147, 157, 160, 180, 203, 209, 226, 256, 261, 266, 279, 327, 339, 349, 353, and 364.

36 . The engineered terminal deoxynucleotidyl transferase of claim 35 , wherein the engineered terminal deoxynucleotidyl transferase comprises at least one residue difference selected from 143A, 157V, 203D, 209E and 353N.

37 . The engineered terminal deoxynucleotidyl transferase of claim 27 , wherein the improved property is increased conversion of the substrate to product by the engineered TdT at a rate of 5%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more.

38 . The engineered terminal deoxynucleotidyl transferase of claim 31 , wherein the engineered terminal deoxynucleotidyl transferase comprises at least one residue difference at an amino acid position selected from 53, 65, 159, 211, 217, 224, 271, 272, 273, 275,278, 331, 341, and 391.

39 . The engineered terminal deoxynucleotidyl transferase of claim 38 , wherein the engineered terminal deoxynucleotidyl transferase comprises at least one residue difference selected from 53T, 159R, 211V, 217R, 271H, 272A, 275Q, 278G, 331K and 391L.

40 . The engineered terminal deoxynucleotidyl transferase of claim 1 , further comprising a residue difference(s) or a residue difference set(s) at amino acid positions selected from 53, 65, 80, 87, 111, 143, 147, 157,159, 160, 180, 203, 209, 211, 217, 224, 226, 256, 261, 266, 271, 272, 273, 275, 278, 279, 327, 331, 339, 341, 349, 364, and 391, and/or any combinations thereof, wherein the amino acid positions are numbered with reference to SEQ ID NO: 5296.

41 . The engineered terminal deoxynucleotidyl transferase of claim 1 , wherein said engineered terminal deoxynucleotidyl transferase is purified.

42 . A composition comprising at least one engineered terminal deoxynucleotidyl transferase of claim 1 .

Assignments (4)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 6, 2024
From: CHING, CHARLENE; FORGET, STEPHANIE MARIE; KNIGHT, ANDERS MATTHEW; KRAWCZYK, MIKAYLA JIANGHONGXIA; MAHMOODI, NIUSHA; MAYO, MELISSA ANN; MILLER, MATHEW G.; VROOM, JONATHAN
To: CODEXIS, INC.
Reel/Frame 069158/0484 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Apr 11, 2024
From: CHING, CHARLENE; FORGET, STEPHANIE MARIE; KNIGHT, ANDERS MATTHEW; KRAWCZYK, MIKAYLA JIANGHONGXIA; MAYO, MELISSA ANN; MILLLER, MATTHEW G.; VROOM, JONATHAN
To: CODEXIS, INC.
Reel/Frame 067073/0073 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Apr 11, 2024
From: CHING, CHARLENE; FORGET, STEPHANIE MARIE; KNIGHT, ANDERS MATTHEW; KRAWCZYK, MIKAYLA JIANGHONGXIA; MAYO, MELISSA ANN; MAHMOODI, NIUSHA; MILLER, MATTHEW G.; VROOM, JONATHAN
To: CODEXIS, INC.
Reel/Frame 067073/0234 →
SECURITY INTEREST Recorded Feb 15, 2024
From: CODEXIS, INC.
To: INNOVATUS LIFE SCIENCES LENDING FUND I, LP, AS COLLATERAL AGENT
Reel/Frame 066600/0650 →
Continuity (3)
Provisional Application 63329777 · Apr 11, 2022
Provisional Application 63256353 · Oct 15, 2021
Related Publication 20230183663A1 · Jun 15, 2023
References Cited (295)
US 5605793A · Stemmer · 1997 [cited by applicant]
US 5763594A · Hiat et al. · 1998 [cited by applicant]
US 5811238A · Stemmer et al. · 1998 [cited by applicant]
US 5830721A · Stemmer et al. · 1998 [cited by applicant]
US 5834252A · Stemmer et al. · 1998 [cited by applicant]
US 5837458A · Minshull et al. · 1998 [cited by applicant]
US 5928905A · Stemmer et al. · 1999 [cited by applicant]
US 6096548A · Stemmer · 2000 [cited by applicant]
US 6117679A · Stemmer · 2000 [cited by applicant]
US 6132970A · Stemmer · 2000 [cited by applicant]
US 6165793A · Stemmer · 2000 [cited by applicant]
US 6180406B1 · Stemmer · 2001 [cited by applicant]
US 6251674B1 · Tobin et al. · 2001 [cited by applicant]
US 6265201B1 · Wackett et al. · 2001 [cited by applicant]
US 6277638B1 · Stemmer · 2001 [cited by applicant]
US 6287861B1 · Stemmer et al. · 2001 [cited by applicant]
US 6287862B1 · delCardayre et al. · 2001 [cited by applicant]
US 6291242B1 · Stemmer · 2001 [cited by applicant]
US 6297053B1 · Stemmer · 2001 [cited by applicant]
US 6303344B1 · Patten et al. · 2001 [cited by applicant]
US 6309883B1 · Minshull et al. · 2001 [cited by applicant]
US 6319713B1 · Patten et al. · 2001 [cited by applicant]
US 6319714B1 · Crameri et al. · 2001 [cited by applicant]
US 6323030B1 · Stemmer · 2001 [cited by applicant]
US 6326204B1 · delCardayre et al. · 2001 [cited by applicant]
US 6335160B1 · Patten et al. · 2002 [cited by applicant]
US 6335198B1 · delCardayre et al. · 2002 [cited by applicant]
US 6337186B1 · Krebber · 2002 [cited by applicant]
US 6344356B1 · Stemmer · 2002 [cited by applicant]
US 6352859B1 · delCardayre et al. · 2002 [cited by applicant]
US 6355484B1 · Patten et al. · 2002 [cited by applicant]
US 6358740B1 · Patten et al. · 2002 [cited by applicant]
US 6358742B1 · Stemmer · 2002 [cited by applicant]
US 6365377B1 · Patten et al. · 2002 [cited by applicant]
US 6365408B1 · Stemmer · 2002 [cited by applicant]
US 6368861B1 · Crameri et al. · 2002 [cited by applicant]
US 6372497B1 · Stemmer · 2002 [cited by applicant]
US 6376246B1 · Crameri et al. · 2002 [cited by applicant]
US 6379964B1 · delCardayre et al. · 2002 [cited by applicant]
US 6387702B1 · Stemmer · 2002 [cited by applicant]
US 6391552B2 · Stemmer · 2002 [cited by applicant]
US 6391640B1 · Minshull et al. · 2002 [cited by applicant]
US 6395547B1 · Stemmer · 2002 [cited by applicant]
US 6406855B1 · Patten et al. · 2002 [cited by applicant]
US 6406910B1 · Patten et al. · 2002 [cited by applicant]
US 6413745B1 · Patten et al. · 2002 [cited by applicant]
US 6413774B1 · Stemmer · 2002 [cited by applicant]
US 6420175B1 · Stemmer · 2002 [cited by applicant]
US 6423542B1 · Crameri et al. · 2002 [cited by applicant]
US 6426224B1 · Crameri et al. · 2002 [cited by applicant]
US 6436675B1 · Welch et al. · 2002 [cited by applicant]
US 6444468B1 · Stemmer et al. · 2002 [cited by applicant]
US 6455253B1 · Patten et al. · 2002 [cited by applicant]
US 6479652B1 · Crameri et al. · 2002 [cited by applicant]
US 6482647B1 · Stemmer · 2002 [cited by applicant]
US 6483011B1 · Stemmer et al. · 2002 [cited by applicant]
US 6484105B2 · Zhang · 2002 [cited by applicant]
US 6489146B2 · Stemmer et al. · 2002 [cited by applicant]
US 6500617B1 · Stemmer et al. · 2002 [cited by applicant]
US 6500639B2 · Subramanian · 2002 [cited by applicant]
US 6506602B1 · Stemmer · 2003 [cited by applicant]
US 6506603B1 · Stemmer · 2003 [cited by applicant]
US 6518065B1 · Stemmer · 2003 [cited by applicant]
US 6519065B1 · Colbourne et al. · 2003 [cited by applicant]
US 6521453B1 · Crameri et al. · 2003 [cited by applicant]
US 6528311B1 · delCardayre et al. · 2003 [cited by applicant]
US 6537746B2 · Arnold et al. · 2003 [cited by applicant]
US 6573098B1 · Stemmer · 2003 [cited by applicant]
US 6576467B1 · Stemmer · 2003 [cited by applicant]
US 6579678B1 · Patten et al. · 2003 [cited by applicant]
US 6586182B1 · Patten et al. · 2003 [cited by applicant]
US 6602986B1 · Stemmer et al. · 2003 [cited by applicant]
US 6605430B1 · Affholter et al. · 2003 [cited by applicant]
US 6613514B2 · Patten et al. · 2003 [cited by applicant]
US 6630581B2 · Dellinger et al. · 2003 [cited by applicant]
US 6653072B1 · Patten et al. · 2003 [cited by applicant]
US 6686515B1 · Lassner et al. · 2004 [cited by applicant]
US 6703240B1 · Stemmer et al. · 2004 [cited by applicant]
US 6716631B1 · delCardayre et al. · 2004 [cited by applicant]
US 6825001B2 · Wackett et al. · 2004 [cited by applicant]
US 6902922B2 · Ness et al. · 2005 [cited by applicant]
US 6917882B2 · Selifonov et al. · 2005 [cited by applicant]
US 6946296B2 · Patten et al. · 2005 [cited by applicant]
US 6961664B2 · Selifonov et al. · 2005 [cited by applicant]
US 6995017B1 · Stemmer · 2006 [cited by applicant]
US 7024312B1 · Selifonov et al. · 2006 [cited by applicant]
US 7057026B2 · Barnes et al. · 2006 [cited by applicant]
US 7058515B1 · Selifonov et al. · 2006 [cited by applicant]
US 7105297B2 · Minshull et al. · 2006 [cited by applicant]
US 7148054B2 · delCardayre et al. · 2006 [cited by applicant]
US 7193077B2 · Dellinger et al. · 2007 [cited by applicant]
US 7220566B2 · Ness et al. · 2007 [cited by applicant]
US 7271258B2 · Dellinger et al. · 2007 [cited by applicant]
US 7288375B2 · Stemmer et al. · 2007 [cited by applicant]
US 7384387B1 · Raillard et al. · 2008 [cited by applicant]
US 7421347B2 · Selifonov et al. · 2008 [cited by applicant]
US 7430477B2 · Selifonov et al. · 2008 [cited by applicant]
US 7462469B2 · Bass et al. · 2008 [cited by applicant]
US 7534564B2 · Patten et al. · 2009 [cited by applicant]
US 7544794B1 · Brenner · 2009 [cited by applicant]
US 7620500B2 · Mundorff et al. · 2009 [cited by applicant]
US 7620502B2 · Selifonov et al. · 2009 [cited by applicant]
US 7629157B2 · Davis et al. · 2009 [cited by applicant]
US 7629170B2 · delCardayre et al. · 2009 [cited by applicant]
US 7702464B1 · Emig et al. · 2010 [cited by applicant]
US 7747391B2 · Gustafsson et al. · 2010 [cited by applicant]
US 7747393B2 · Fox · 2010 [cited by applicant]
US 7751986B2 · Gustafsson et al. · 2010 [cited by applicant]
US 7776598B2 · Patten et al. · 2010 [cited by applicant]
US 7783428B2 · Gustafsson et al. · 2010 [cited by applicant]
US 7795030B2 · Minshull et al. · 2010 [cited by applicant]
US 7807356B2 · Sampson et al. · 2010 [cited by applicant]
US 7853410B2 · Selifonov et al. · 2010 [cited by applicant]
US 7868138B2 · Stemmer et al. · 2011 [cited by applicant]
US 7873477B1 · Gustafsson et al. · 2011 [cited by applicant]
US 7873499B2 · Selifonov et al. · 2011 [cited by applicant]
US 7904249B2 · Selifonov et al. · 2011 [cited by applicant]
US 7957912B2 · Selifonov et al. · 2011 [cited by applicant]
US 7981614B2 · Stemmer et al. · 2011 [cited by applicant]
US 8014961B2 · Bass et al. · 2011 [cited by applicant]
US 8029988B2 · Crameri et al. · 2011 [cited by applicant]
US 8030466B2 · Shin et al. · 2011 [cited by applicant]
US 8048674B2 · Minshull et al. · 2011 [cited by applicant]
US 8058001B2 · Crameri et al. · 2011 [cited by applicant]
US 8076138B2 · delCardayre et al. · 2011 [cited by applicant]
US 8108150B2 · Mundorff et al. · 2012 [cited by applicant]
US 8170806B2 · Selifonov et al. · 2012 [cited by applicant]
US 8224580B2 · Mundorff et al. · 2012 [cited by applicant]
US 8309706B2 · Dellinger et al. · 2012 [cited by applicant]
US 8377681B2 · delCardayre et al. · 2013 [cited by applicant]
US 8383346B2 · Colbeck et al. · 2013 [cited by applicant]
US 8457903B1 · Emig et al. · 2013 [cited by applicant]
US 8504498B2 · Fox · 2013 [cited by applicant]
US 8589085B2 · Selifonov et al. · 2013 [cited by applicant]
US 8762066B2 · Fox · 2014 [cited by applicant]
US 8768871B2 · Fox · 2014 [cited by applicant]
US 8808989B1 · Efcavitch et al. · 2014 [cited by applicant]
US 9279149B2 · Efcavitch et al. · 2016 [cited by applicant]
US 9410197B2 · Bergmann et al. · 2016 [cited by applicant]
US 9593326B2 · Clark et al. · 2017 [cited by applicant]
US 9695470B2 · Efcavitch et al. · 2017 [cited by applicant]
US 9771613B2 · Efcavitch et al. · 2017 [cited by applicant]
US 10041110B2 · Efcavitch et al. · 2018 [cited by applicant]
US 10059929B2 · Efcavitch et al. · 2018 [cited by applicant]
US 10059986B2 · Zhou et al. · 2018 [cited by applicant]
US 10407721B2 · Liu et al. · 2019 [cited by applicant]
US 10745727B2 · Chen et al. · 2020 [cited by applicant]
US 10752887B2 · Champion · 2020 [cited by examiner]
US 20080220990A1 · Fox · 2008 [cited by applicant]
US 20090312196A1 · Colbeck et al. · 2009 [cited by applicant]
US 20120276074A1 · Scharenberg et al. · 2012 [cited by applicant]
US 20160244787A1 · Chen et al. · 2016 [cited by applicant]
US 20180023108A1 · Chen et al. · 2018 [cited by applicant]
US 20200190491A1 · Efcavitch et al. · 2020 [cited by applicant]
US 20210164008A1 · Chen et al. · 2021 [cited by applicant]
CN 112746063A · 2021 [cited by applicant]
EP 0641862B1 · 1995 [cited by applicant]
GB 2598152A · 2022 [cited by applicant]
WO 9522625A1 · 1995 [cited by applicant]
WO 9533836A1 · 1995 [cited by applicant]
WO 9600787A1 · 1996 [cited by applicant]
WO 9607669A1 · 1996 [cited by applicant]
WO 9623807A1 · 1996 [cited by applicant]
WO 970078A1 · 1997 [cited by applicant]
WO 9735966A1 · 1997 [cited by applicant]
WO 9827230A1 · 1998 [cited by applicant]
WO 0042651A1 · 2000 [cited by applicant]
WO 0125247A1 · 2001 [cited by applicant]
WO 0155451A1 · 2001 [cited by applicant]
WO 0175767A2 · 2001 [cited by applicant]
WO 0229003A2 · 2002 [cited by applicant]
WO 03048387A2 · 2003 [cited by applicant]
WO 04018493A1 · 2004 [cited by applicant]
WO 04018497A2 · 2004 [cited by applicant]
WO 2009008908A2 · 2009 [cited by applicant]
WO 2009151921A1 · 2009 [cited by applicant]
WO 2009152336A1 · 2009 [cited by applicant]
WO 2010110775A1 · 2010 [cited by applicant]
WO 2010144103A1 · 2010 [cited by applicant]
WO 2012177639A2 · 2012 [cited by applicant]
WO 2014139596A1 · 2014 [cited by applicant]
WO 2015159023A1 · 2015 [cited by applicant]
WO 2015168310A1 · 2015 [cited by applicant]
WO 2015168461A1 · 2015 [cited by applicant]
WO 2016064880A1 · 2016 [cited by applicant]
WO 2016128731A1 · 2016 [cited by applicant]
WO 2016139477A1 · 2016 [cited by applicant]
WO 2017216472A2 · 2017 [cited by applicant]
WO 2018085156A1 · 2018 [cited by applicant]
WO 2018138508A1 · 2018 [cited by applicant]
WO 2018215803A1 · 2018 [cited by applicant]
WO 2018217689A1 · 2018 [cited by applicant]
WO 2019135007A1 · 2019 [cited by applicant]
WO 2020072715A1 · 2020 [cited by applicant]
WO 2020077227A2 · 2020 [cited by applicant]
WO 2020081985A1 · 2020 [cited by applicant]
WO 2020099451A1 · 2020 [cited by applicant]
WO 2020120442A2 · 2020 [cited by applicant]
WO 2020141143A1 · 2020 [cited by applicant]
WO 2020161480A1 · 2020 [cited by applicant]
WO 2020165137A1 · 2020 [cited by applicant]
WO 2020229831A1 · 2020 [cited by applicant]
WO 2020239737A1 · 2020 [cited by applicant]
WO 2021018919A1 · 2021 [cited by applicant]
WO 2021018921A1 · 2021 [cited by applicant]
WO 2021058438A1 · 2021 [cited by applicant]
WO 2021094251A1 · 2021 [cited by applicant]
WO 2021116270A1 · 2021 [cited by applicant]
WO 2021122539A1 · 2021 [cited by applicant]
WO 2021170524A1 · 2021 [cited by applicant]
WO 2021213903A1 · 2021 [cited by applicant]
WO 2021247851A2 · 2021 [cited by applicant]
WO 2021254934A1 · 2021 [cited by applicant]
WO 2022013094A1 · 2022 [cited by applicant]
WO 2022063835A1 · 2022 [cited by applicant]
WO 2022090323A1 · 2022 [cited by applicant]
WO 2023041931A1 · 2023 [cited by applicant]
WO 2023083997A2 · 2023 [cited by applicant]
WO 2023083999A2 · 2023 [cited by applicant]
WO 2023240202A2 · 2023 [cited by applicant]
R; Yang, B.; Gathy, K.N.; Coleman, M.S. Nucleic Acids Res. 23, 2041-2048, 1995. [cited by examiner]
Ngo et al. in The Protein Folding Problem and Tertiary Structure Prediction, 1994, Merz et al. (ed.), Birkhauser, Boston, MA, pp. 433 and 492-495. [cited by examiner]
Koiwai et al., Nuc Acids Res, vol. 14, No. 14, pp. 5777-5792, 1986. [cited by examiner]
UniProt Accession No. A0A674H6A5, Jun. 2025. [cited by examiner]
Tiwari, S., et al., “Prediction of probable genes by Fourier analysis of genomic sequences,” Comput. Appl. Biosci. 13 (3):263-270 [1997]. [cited by applicant]
Truppo, M.D., et al., “Development of an Improved Immobilized CAL-B for the Enzymatic Resolution of a Key Intermediate to Odanacatib,” Organic Process Research & Development, 15:1033-1035 (2011). [cited by applicant]
Uberbacher, E.C., et al., “Discovering and Understanding Genes in Human DNA Sequence Using GRAIL,” Methods Enzymol., 266:259-281 [1996]. [cited by applicant]
Villa-Komaroff, L., et al., “A bacterial clone synthesizing proinsulin,” Proc. Natl Acad. Sci. USA, 75:3727-3731 (1978). [cited by applicant]
Wada, K., et al., “Codon usage tabulated from the GenBank genetic sequence data,” Nucl. Acids Res., 20:2111-2118 [1992]. [cited by applicant]
Wells, J.A., et al., “Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites,” Gene, 34:315-323 (1985). [cited by applicant]
Wetmur, J. G., “DNA Probes: Applications of the Principles of Nucleic Acid Hybridization,” Crit Rev Biochem Mol Biol, 26(3/4):227-259 (1991). [cited by applicant]
Wright, F., “The ‘effective number of codons’ used in a gene,” Gene 87:23-29 [1990]. [cited by applicant]
Yi, S., et al., “Covalent immobilization of omega-transaminase from Vibrio fluvialis JS17 on chitosan beads,” Process Biochemistry 42(5): 895-898 (2007). [cited by applicant]
Zhang, J-H., et al., “Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening ,” Proc. Nat. Acad. Sci., U.S.A., 94:4504-4509 (1997). [cited by applicant]
Zhao, H., et al., “Molecular evolution by staggered extension process (StEP) in vitro recombination,” Nat. Biotechnol., 16:258-261 (1998). [cited by applicant]
NCBI Accession No. XM_027908988.1 dated Jan. 24, 2019 “Predicted: Empidonax Traillil DNA nucleotidylaxotransferase (NDTT), mRNA”; https//www.ncbi.nim.nih.gov/nucleotide/XM_027908988.1. [cited by applicant]
Knight, Anders, “Engineering Enzymes to Produce High Purity Synthetic DNA,” Enzyme Engineering (conference), May 23, 2022. [cited by applicant]
Miller, Matt and Efcavitch, Bill, “Breaking the Barrier to Long, High Purity Synthetic DNA,” SynBio Beta Built with Biology (conference), Apr. 14, 2022. [cited by applicant]
Lutz, Stefan, “Engineering Enzyme Products,” Canadian Chemistry Conference & Exhibition, Jun. 14, 2022. [cited by applicant]
Krawczyk, Mikayla, et al., “Engineering Terminal Deoxynucleotidyl Transferase to Produce Long, High Purity Synthetic DNA,” Gordon Research Conference, Jul. 8, 2022. [cited by applicant]
Zhe, Rui, “Engineering Enzymes to Produce High Purity Synthetic DNA,” Biochemical and Molecular Engineering (conference), Jun. 26, 2022. [cited by applicant]
Lutz, Stefan, “Making Complex Molecules—Engineering Biocatalysts for Use in Sustainable Manufacturing,” Biocatalysis (conference), Aug. 30, 2022. [cited by applicant]
Codexis, Inc., Q2 2021 Earnings Press Release, Aug. 5, 2021. [cited by applicant]
Codexis, Inc., Codexis Corporate Presentation Mar. 2022, available at www.codexis.com. Published Mar. 8, 2022. [cited by applicant]
Codexis, Inc., Codexis Corporate Presentation Nov. 2021, available at www.codexis.com. Published Nov. 15, 2021. [cited by applicant]
Altschul, S., et al., “Basic local alignment search tool,” J. Mol. Biol., 215: 403-410 (1990). [cited by applicant]
Altschul, S.F., et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Res., 25(17):3389-3402 (1997). [cited by applicant]
Baldino, Jr., F., et al., “High-Resolution in Situ Hybridization Histochemistry,” Methods Enzymology, 168:761-777 (1989). [cited by applicant]
Batzer, M.A., “Erratum: Structure and variability of recently inserted Alu family members”, Nucleic Acids Res 19:698-699 [1991]. [cited by applicant]
Beaucage, S.L., et al., “Deoxynucleoside phosphoamidites—A new class of key intermediates for deoxypolynucleotide synthesis,” Tetrahedron Letters, 22(20):1859-62 (1981). [cited by applicant]
Bentolila, L.A., et al., “The two isoforms of mouse terminal deoxynucleotidyl transferase differ in both the ability to add N regions and subcellular localization,” EMBO, 14(17):4221-4229 (1995). [cited by applicant]
Black, M.E., et al., “Creation of drug-specific herpes simplex virus type 1 thymidine kinase mutants for gene therapy,” Proc Natl Acad Sci USA, 93:3525-3529 (1996). [cited by applicant]
Bollum, F.J., “Oligodeoxyribonucleotide-primed Reactions Catalyzed by Calf Thymus PolymeraseM,” J. Biol. Chem., 237(6):1945-1949 [1962]. [cited by applicant]
Bolton, E.T., et al., “A General Method for the lisolation of RNA Complementary to DNA,” Proc. Natl. Acad. Sci. USA 48:1390 ( 1962). [cited by applicant]
Botstein, D., et al., “Strategies and applications of in vitro mutagenesis,” Science, 229(4719):1193-1201 [1985]. [cited by applicant]
Breslauer, K.J., et al., “Predicting DNA duplex stability from the base sequence,” Proc. Natl. Acad. Sci. USA, 83:3746-3750 (1986). [cited by applicant]
Caldwell, R.C., et al., “Mutagenic PCR,” PCR Methods Appl., 3:S136-S140 (1994). [cited by applicant]
Carter, P., “Site-directed mutagenesis,” Biochem. J., 237:1-7 (1986). [cited by applicant]
Christians, F.C., et al., “Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling,” Nat. Biotechnol., 17:259-264 (1999). [cited by applicant]
Chua, J.P.S., et al., “Evolving a Thermostable Terminal Deoxynucleotidyl Transferase,” ACS Synth. Biol., 9:1725-1735 [2020]. [cited by applicant]
Crameri, A., et al., “DNA shuffling of a family of genes from diverse species accelerates directed evolution”, Nature, 391:288-291 (1998). [cited by applicant]
Crameri, A., et al., “Improved green fluorescent protein by molecular evolution using DNA shuffling,” Nat. Biotechnol., 14(3):315-319 (1996). [cited by applicant]
Crameri, A., et al., “Molecular evolution of an arsenate detoxification pathway by DNA shuffling,” Nat. Biotechnol., 15 (5):436-438 (1997). [cited by applicant]
Dale, S.J., et al., “Oligonucleotide-directed random mutagenesis using the phosphorothioate method,” Methods Mol. Biol., 57:369-74 (1996). [cited by applicant]
De Boer, H.A., et al., “The tac promoter: A functional hybrid derived from the trp and lac promoters,” Proc. Natl Acad. Sci. USA, 80: 21-25 (1983). [cited by applicant]
Dominguez, O., et al., “DNA polymerase mu (Pol μ), homologous to TdT, could act as a DNA mutator in eukaryotic cells,” EMBO, 19(7):1731-1742 (2000). [cited by applicant]
Fasman, G.D., CRC Practical Handbook of Biochemistry and Molecular Biology, CRC Press, Boca Raton, FL, pp. 3-70 [1989]. [cited by applicant]
Freier, S.M., et al., “Improved free-energy parameters for predictions of RNA duplex stability,” Proc. Natl. Acad. Sci USA, 83:9373-9377 (1986). [cited by applicant]
Guo, Z., et al., “3′-End-Forming Signals of Yeast mRNA,” Mol. Cell. Biol., 15(11):5983-5990 [1995]. [cited by applicant]
Henaut and Danchin in Neidhardt et al. [eds.], [cited by applicant]
Henikoff, S., et al., “Amino acid substitution matrices from protein blocks,” Proc. Natl. Acad. Sci., 89:10915-10919 (1992). [cited by applicant]
Kierzek, R., et al., “Polymer-Supported RNA Synthesis and Its Application To Test the Nearest-Neighbor Model for Duplex Stability,” Biochemistry, 25:7840-7846 (1986). [cited by applicant]
Koszelewski, D., et al., “Immobilization of omega-transaminases by encapsulation in a sol-gel/celite matrix,” Journal of Molecular Catalysis B: Enzymatic, 63: 39-44 (2010). [cited by applicant]
Kramer, B., et al., “Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of [cited by applicant]
Ling, M., et al., “Approaches to DNA Mutagenesis:An Overview,” Anal. Biochem., 254:157-78 (1997). [cited by applicant]
Lu, X., et al., “Enzymatic DNA Synthesis by Engineering TerminalDeoxynucleotidyl Transferase,” ACS Catalysis, 12:2988-2997 [2022]. [cited by applicant]
Martin, A.R., et al., “Characterization of free and immobilized (S)-aminotransferase for acetophenone production,” Applied Microbiology and Biotechnology, 76(4): 843-851 (2007). [cited by applicant]
Mateo, C., et al., “Epoxy sepabeads: a novel epoxy support for stabilization of industrial enzymes via very intense multipoint covalent attachment,” Biotechnology Progress 18(3):629-34 (2002). [cited by applicant]
Matthes, H.W.D., et al., “Simultaneous rapid chemical synthesis of over one hundred oligonucleotides on a microscale,” EMBO J., 3(4):801-05 (1984). [cited by applicant]
McInerney, J.O., “GCUA: general codon usage analysis,” Bioinformatics, 14(4):372-73 [1998]. [cited by applicant]
Minshull, J., et al., “Protein evolution by molecular breeding,” Curr. Op. Chem. Biol., 3(3):284-290 (1999). [cited by applicant]
Nakamura, Y., et al., “Codon usage tabulated from international DNA sequence databases: status for the year 2000,” Nucl. Acids Res., 28:292 [2000]. [cited by applicant]
Needleman, S., et al., “A general method applicable to the search for similarities in the amino acid sequence of two proteins,” J. Mol. Biol. 48:443-453 (1970). [cited by applicant]
Pearson, W.R., “Improved tools for biological sequence comparison,” Proc. Nat'l. Acad. Sci. USA, 85:2444-2448 (1988). [cited by applicant]
Romanos, M.A., et al., “Foreign gene expression in yeast: a review,” Yeast 8:423-488 [1992]. [cited by applicant]
Rychlik, W., et al., “Optimization of the annealing temperature for DNA amplification in vitro,” Nucleic Acids Res, 18 (21):6409-6412 (1990). [cited by applicant]
Schaudy, E., et al., “Sequence Preference and Initiator Promiscuity for De Novo DNA Synthesis by Terminal Deoxynucleotidyl Transferase,” ACS Synth. Biol., 10:1750-1760 [2021]. [cited by applicant]
Simonen, M., et al., “Protein Secretion in Bacillus Species,” Microbiological Reviews, 57:109-137 (1993). [cited by applicant]
Smith, M., “In vitro mutagenesis,” Ann. Rev. Genet., 19:423-462 (1985). [cited by applicant]
Smith, T., et al., “Comparison of Biosequences,” Adv. Appl. Math, 2:482-489 (1981). [cited by applicant]
Stellwagen, E., “Dye Affinity Chromatography,” Current Protocols in Protein Science, Chapter 9, Unit 9.2-9.2.16 [2001]. [cited by applicant]
Stemmer, W., “DNA Shuffling by Random Fragmentation and Reassembly: In vitro Recombination for Molecular Evolution,” Proc. Natl. Acad. Sci. USA, 91:10747-10751 (1994). [cited by applicant]
Stemmer, W.P.C., “Rapid evolution of a protein in vitro by DNA shuffling”, Nature, 370:389-391 (1994). [cited by applicant]
Stenico, M., et al., “Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases,” Nucl. Acids Res. 22(13):2437-46 [1994]. [cited by applicant]
Suggs, S.V., et al., “Use of synthetic oligodeoxyribonucleotides for the isolation of specific cloned DNA sequences,” In Developmental Biology Using Purified Genes (Brown et al., eds.), pp. 683-693, Academic Press (1981… [cited by applicant]