Splint nucleic acid molecule for cyclizing single-stranded nucleic acid molecule and use thereof
Provided in the present invention are a splint nucleic acid molecule for cyclizing a single-stranded nucleic acid molecule and an application therefor. The splint nucleic acid, molecule is composed of a 5′ terminal fragment and a 3′ terminal fragment, the 5′ terminal fragment being adapted to forming a first complementary region with a 5′ terminal of the single-stranded nucleic acid molecule, and the 3′ terminal fragment being suited to forming a second complementary region with a 3′ terminal of the single-stranded nucleic acid molecule, the length of the first complementary region and the second complementary region being different.
1. A method for cyclizing a single-stranded nucleic acid molecule, comprising:
allowing a reaction mixture containing a splint nucleic acid molecule, a single-stranded nucleic acid molecule and a ligase to be under a condition suitable for ligation, so as to obtain a cyclized single-stranded nucleic acid molecule,
wherein the splint nucleic acid molecule is for cyclizing the single-stranded nucleic acid molecule and consists of a 5′ terminal fragment and a 3′ terminal fragment,
wherein the single-stranded nucleic acid molecule comprises:
an insert fragment;
a first adaptor, connected to a 5′ terminal of the insert fragment; and
a second adaptor, connected to a 3′ terminal of the insert fragment,
wherein the 5′ terminal fragment of the splint nucleic acid molecule is adapted to form a first complementary region between the 5′ terminal fragment of the splint nucleic acid molecule and at least a part of the first adaptor, and
the 3′ terminal fragment of the splint nucleic acid molecule is adapted to form a second complementary region between the 3′ terminal fragment of the splint nucleic acid molecule and at least a part of the second adaptor,
wherein the length of the first complementary region is equal to the length of the 5′ terminal fragment of the splint nucleic acid molecule, and the length of the second complementary region is equal to the length of the 3′ terminal fragment of the splint nucleic acid molecule,
wherein the length of the first complementary region is different from the length of the second complementary region, and
the method specifically comprises steps of:
(i) allowing the reaction mixture to be at a first temperature for a first predetermined time, wherein the first temperature is suitable to form the first complementary region;
(ii) allowing the reaction mixture obtained in step (i) to be at a second temperature for a second predetermined time, wherein the second temperature is suitable to form the second complementary region;
(iii) allowing the reaction mixture obtained in step (ii) to be at a third temperature for a third predetermined time, wherein the third temperature is suitable to unwind at least one of the first complementary region and the second complementary region;
(iv) subjecting the reaction mixture obtained in step (iii) to steps (i) and (ii) in sequence, and
(v) subjecting the reaction mixture obtained in step (iv) to steps (iii), (i) and (ii) in sequence for at least one cycle,
wherein the first temperature is higher than the second temperature.
2. The method according to claim 1 , wherein the length of the first complementary region is at least 1.5 or at least 2 times longer than the length of the second complementary region; or
the length of the first complementary region is at least 13 bp longer than the length of the second complementary region.
3. The method according to claim 2 , wherein melting temperature (Tm) values of the first complementary region and the second complementary region differ by 10° C..
4. The method according to claim 1 , wherein the 5′ terminal fragment is of the nucleotide sequence of SEQ ID NO: 1,
the 3′ terminal fragment is of the nucleotide sequence of SEQ ID NO: 2, and
the splint nucleic acid molecule is of the nucleotide sequence of SEQ ID NO: 3.
5. The method according to claim 1 , wherein the first complementary region and the second complementary region each independently comprise 5 mismatched bases or fewer.
6. The method according to claim 1 , wherein the insert fragment is derived from at least a part of a genomic fragment, and the genomic fragment is obtained by fragmenting and denaturing genomic DNA.
7. The method according to claim 1 , wherein the difference between the second temperature and an optimal temperature of the ligase is 10° C. or below.
8. The method according to claim 1 , wherein the second temperature is lower than an optimal temperature of the ligase, and the second temperature is 2 to 8° C. lower than the optimal temperature of the ligase.
9. The method according to claim 1 , wherein the activity of the ligase at the second temperature is 50% or above of the highest activity.
10. The method according to claim 1 , wherein the ligase is a thermostable ligase, and
the thermostable ligase is capable of resisting a temperature of at least 50° C.
11. The method according to claim 10 , wherein the thermostable ligase is Taq DNA ligase, and the optimal temperature of the ligase is 45° C.
12. The method according to claim 1 , wherein
the first temperature is 35 to 65° C.,
the second temperature is 32 to 42° C., and
the third temperature is 94 to 98° C.
13. The method according to claim 1 , wherein
the first temperature is 50° C.,
the second temperature is 37° C., and
the third temperature is 95° C.
14. The method according to claim 12 , wherein the first predetermined time is 2 minutes,
the second predetermined time is 30 minutes, and
the third predetermined time is 30 seconds.