Compositions and methods for improving sample identification in indexed nucleic acid libraries

1. A method, comprising:

providing a first library comprising a first plurality of polynucleotides having a first adapter-target-first adapter sequence, wherein the polynucleotides of the first plurality of polynucleotides are double stranded in a region comprising the target and at least a portion of the first adapter on both ends of the target;

providing a first primer oligonucleotide configured to hybridize with a portion of the first adapter in proximity to a 3′ end of a strand of the first adapter, wherein the 5′ end of the first primer oligonucleotide is modified to prevent digestion by an enzyme having 5′ exonuclease activity;

providing a second primer oligonucleotide configured to hybridize with a complement of a portion of the first adapter in proximity to a 3′ end of a strand of the complement of the first adapter, wherein the 5′ end of the second primer oligonucleotide is modified to prevent digestion by an enzyme having 5′ exonuclease activity;

incubating the first library with the first and second primer oligonucleotides in a solution under conditions suitable to amplify the polynucleotides having a first adapter-target-first adapter sequence to produce an amplified first library of polynucleotides having 5′ ends modified to prevent digestion by an enzyme having 5′ exonuclease activity, wherein the amplified polynucleotides have an amplified first adapter-target-amplified first adapter sequence, and wherein the amplified first adapter sequence comprises a first library-specific sequence;

modifying 3′ ends of the amplified first library of polynucleotides to prevent one or both of (i) digestion by an enzyme having 3′ exonuclease activity, or (ii) addition of nucleotides to the 3′ end by an enzyme having polymerase activity, thereby generating a protected first library of polynucleotides having modified 5′ and 3′ ends.

2. The method according to claim 1 , wherein modifying the 3′ ends of the amplified first library of polynucleotides comprises incorporating a dideoxynucleotide at the 3′ ends of the polynucleotides.

3. The method according to claim 1 , wherein the 5′ ends of the amplified first library of polynucleotides comprise a phosphorothioate bond.

4. The method according to claim 1 , wherein the 5′ ends of the amplified first library of polynucleotides comprise three phosphorothioate bonds.

5. The method according to claim 1 , further comprising incubating the protected first library of polynucleotides having modified 3′ ends with one or more enzymes having 5′ exonuclease activity and 3′ exonuclease activity.

6. The method according to claim 1 , further comprising

providing a substrate having a surface comprising a plurality of attached oligonucleotides having free 3′ ends; and

contacting the surface of the substrate with a composition comprising the protected first library of polynucleotides having modified 3′ ends under conditions that permit hybridization of a portion of a strand of the first adapter of the protected first library of polynucleotides to at least a portion of the oligonucleotides attached to the surface of the substrate.

7. The method according to claim 6 , further comprising extending the oligonucleotides attached to the surface of the substrate from the free 3′ end by incorporating nucleotides complementary to a sequence of the protected first library of polynucleotides having the modified 3′ ends that are hybridized to the attached oligonucleotides to produce a copy of the hybridized polynucleotide such that the copy is attached to the surface of the substrate.

8. The method according to claim 7 , further comprising amplifying the copy attached to the surface of the substrate.

9. The method according to claim 1 , further comprising:

providing a second library comprising a plurality of polynucleotides having a second adapter-target-second adapter sequence, wherein the polynucleotides of the second plurality of polynucleotides are double stranded in a region comprising the target and at least a portion of the second adapter on both ends of the target;

providing a third primer oligonucleotide configured to hybridize with a portion of the second adapter in proximity to a 3′ end of a strand of the second adapter, wherein the 5′ end of the third primer oligonucleotide is modified to prevent digestion by an enzyme having 5′ exonuclease activity;

providing a fourth primer oligonucleotide configured to hybridize with a complement of a portion of the second adapter in proximity to a 3′ end of a strand of the complement of the second adapter, wherein the 5′ end of the fourth primer oligonucleotide is modified to prevent digestion by an enzyme having 5′ exonuclease activity;

incubating the second library with the third and fourth primer oligonucleotides in a solution under conditions suitable to amplify the polynucleotides having a second adapter-target-second adapter sequence to produce an amplified second library of polynucleotides having 5′ ends modified to prevent digestion by an enzyme having 5′ exonuclease activity, wherein the amplified polynucleotides have an amplified second adapter-target-amplified second adapter sequence, and wherein the amplified second adapter sequence comprises a second library-specific sequence;

modifying 3′ ends of the amplified second library of polynucleotides to prevent one or both of (i) digestion by an enzyme having 3′ exonuclease activity, or (ii) addition of nucleotides to the 3′ end by an enzyme having polymerase activity, thereby generating a protected second library of polynucleotides having modified 5′ and 3′ ends.

10. The method according to claim 9 , wherein modifying the 3′ ends of the amplified second library of polynucleotides comprises incorporating a dideoxynucleotide at the 3′ ends of the polynucleotides.

11. The method according to claim 9 , wherein the 5′ ends of the amplified second library of polynucleotides comprise a phosphorothioate bond.

12. The method according to claim 9 , wherein the 5′ ends of the amplified second library of polynucleotides comprise three phosphorothioate bonds.

13. The method according to claim 9 , further comprising incubating the protected second library of polynucleotides having modified 3′ ends with one or more enzymes having 5′ exonuclease activity and 3′ exonuclease activity.

14. The method according to claim 9 , further comprising contacting the surface of the substrate with a composition comprising the protected second library of polynucleotides having modified 3′ ends under conditions that permit hybridization of a portion of a strand of the second adapter of the protected second library of polynucleotides to at least a portion of the oligonucleotides attached to the surface of the substrate.

15. The method according to claim 14 , further comprising extending the oligonucleotides attached to the surface of the substrate from the free 3′ end by incorporating nucleotides complementary to a sequence of the protected second library of polynucleotides having the modified 3′ ends that are hybridized to the attached oligonucleotides to produce a copy of the hybridized polynucleotide such that the copy is attached to the surface of the substrate.

16. The method according to claim 15 , further comprising amplifying the copy attached to the surface of the substrate.

17. The method according to claim 1 , wherein the first adapter sequence comprises the first library-specific sequence.

18. The method according to claim 17 , further comprising:

providing a second library comprising a plurality of polynucleotides having a second adapter-target-second adapter sequence, wherein the polynucleotides of the second plurality are double stranded in a region comprising the target and at least a portion of the second adapter on either end of the target, wherein the second adapter comprises a second library-specific sequence,

wherein the first primer oligonucleotide is configured to hybridize with a portion of the second adapter in proximity to a 3′ end of a strand of the second adapter, and

wherein the second primer oligonucleotide is configured to hybridize with a complement of a portion of the second adapter in proximity to a 3′ end of a strand of the complement of the second adapter; and

incubating the second library in the solution with the first library with the first and second primer oligonucleotides to amplify the polynucleotides having the second adapter-target-second adapter sequence to produce an amplified second library of polynucleotides having 5′ ends modified to prevent digestion by an enzyme having 5′ exonuclease activity,

wherein modifying 3′ ends of the amplified first library of polynucleotides further comprises modifying the amplified second library of polynucleotides to prevent one or both of (i) digestion by an enzyme having 3′ exonuclease activity, or (ii) addition of nucleotides to the 3′ end by an enzyme having polymerase activity, thereby generating a protected second library of polynucleotides having modified 5′ and 3′ ends.

19. The method according to claim 1 , further comprising incubating a composition comprising the protected first library of polynucleotides having modified 5′ and 3′ ends with an exonuclease.