Method and reagent for constructing nucleic acid double-linker single-strand cyclical library

• US 10,479,991 B2
• Filed: 11/26/2014
• Issued: 11/19/2019
• Est. Priority Date: 11/26/2014
• Status: Active Grant

• Current Assignee: MGI Tech Co., Ltd (BGI Genomics Co., Ltd.)
• Original Assignee: MGI Tech Co., Ltd (BGI Genomics Co., Ltd.)
• Inventors: Jiang, Yuan, Li, Qiaoling, Alexeev, Andrei, Hurowitz, Evan, Zhao, Xia, Wang, Tong, Dong, Chao, Li, Dong, Drmanac, Radoje, Zhang, Wenwei, Jiang, Hui
• Primary Examiner(s): Bunker, Amy M
• Application Number:
  US15/529,881
• Publication Number:
  US 20170355981A1
• Time in Patent Office: 1,819 Days
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: C12N 15/1093 General methods of preparing gene libraries, not provided for in other subgroups
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C40B 50/06 Biochemical methods, e.g. using enzymes or whole viable microorganisms
• CPC Class Codes: C40B 50/18 using a particular method of attachment to the solid support

Abstract

A method and reagent for constructing a nucleic acid double-linker single-strand cyclic library. The method comprises: breaking a nucleic acid into nucleic acid fragments; connecting a first linker sequence; producing by amplification a first product provided with the first linker sequence at either end, where a U nucleobase site is provided on primer sequences and a nicking enzyme recognition sequence is either provided or not provided on same, and a first affinity tag is provided on one of the primer sequences; using USER enzyme to cleave the first product; cyclizing the cleaved first product; treating the cyclization product with either a phosphatase or a nicking enzyme; using a solid-phase vector for combination with a cyclized molecule; performing a restrictive gap translation reaction; removing by digestion any portion that did not undergo the restrictive gap translation reaction; connecting a second linker sequence; producing by amplification a second product provided with the second linker sequence at either end; denaturing the second product, and cyclizing a single-strand nucleic acid molecule. The method allows an increase in the length of library insert fragments, a simplified library construction process, reduced library construction time, and reduced library construction costs.

Claims

1. A method for constructing a library of single-stranded cyclic nucleic acid fragments having double adaptors, comprising the following steps carried out in the following order:

(1) disrupting a nucleic acid into nucleic acid fragments for library construction and selecting disrupted fragments using magnetic bead purification or gel recovery;

(2) subjecting the fragments to dephosphorylation and end repairing reactions;

(3) ligating a 5′

adaptor A sequence to the fragments, wherein the 5′

adaptor A sequence comprise a strand with 5′

end phosphorylation modification and the other strand with 3′

end dideoxy modification and uracil (U) base sites;

(4) performing a one-step reaction of Uracil-Specific Excision Reagent enzyme digestion and phosphorylation using Uracil-Specific Excision Reagent (USER) enzyme and T4 polynucleotide kinase;

(5) ligating a first 3′

L-type adaptor sequence to the 5′

end of each strand of the phosphorylated nucleic acid fragments;

(6) performing a first polymerase chain reaction (PCR) amplification to obtain first products having the first adaptor sequence at both ends, wherein the primer sequences used in the first PCR have a U base site and have a nickase recognition sequence, and one of the primers has a biotin label;

followed by purification using magnetic beads;

(7) digesting the first products with a Uracil-Specific Excision Reagent (USER) enzyme to remove the U base site in the primer sequences to generate sticky ends and generate or do not generate a gap;

(8) performing a double-stranded cyclization of the digested first products to generate cyclic nucleic acid molecules, which having a nickase recognition sequence on one strand and a gap on the other strand or having a nickase recognition sequence but not a gap on both strands, such that cyclization occurs due to the complementarity of the sticky ends to generate cyclized nucleic acid molecules;

(9) performing linear digestion by treating the cyclic nucleic acid molecules having a nickase recognition sequence on one strand and a gap on the other strand or having a nickase recognition sequence but not a gap on both strands with a nickase to generate a nick;

(10) performing magnetic purification by binding the treated cyclic nucleic acid molecules to streptavidin magnetic beads via the biotin label on the cyclic nucleic acid molecules; and

allowing a solid phase carrier harboring a second affinity label to bind to the cyclic nucleic acid molecules;

(11) enzymatically digesting the nickase recognition sequence with nickase to get a nick on each single-strand to provide an initiation site for controlled nick translation (CNT), wherein the enzymatic reaction proceeds on the magnetic beads without eluting the nucleic acids from the magnetic beads;

(12) initiating a controlled nick translation reaction from the nick and/or gap by using the cyclic nucleic acid molecules bound to the streptavidin magnetic beads, wherein in the controlled gap translation reaction, the length of the gap translation fragments generated is controlled by controlling at least one factor selected from the group consisting of the molar ratio of deoxynucleotide triphosphates (dNTPs) to the nucleic acid molecules as template, the enzymatic reaction temperature, and the enzymatic reaction time, to generate nucleic acid fragments with a length in the range of 50-250 base pairs (bp);

(13) digesting and removing the portion of the respective cyclic nucleic acid molecules that does not undergo the controlled gap translation reaction to obtain linear nucleic acid molecules;

(14) ligating a second adaptor sequence bubble-type adaptor comprising a top strand and a bottom strand which are complementary to one another to both ends of the linear nucleic acid molecules, wherein the bottom strand having U base sites;

(15) performing Uracil-Specific Excision Reagent (USER) enzyme digestion of the U base site;

(16) performing a second polymerase chain reaction amplification to obtain second products having the second adaptor sequence at both ends;

(17) denaturing the second products to obtain single-stranded nucleic acid molecules, and cyclizing one of the single-stranded nucleic acid molecules with a mediating sequence complementary to both ends of the single-stranded nucleic acid molecule to obtain the library of single-stranded cyclic nucleic acid fragments having double adaptors to produce nucleic acid fragments in a size range of 50 bp to 250 bp, and wherein the steps of the method provide fragments suitable for next-generation sequencing on a Complete Genomics sequencing platform.

2. The method according to claim 1, wherein the first adaptor sequence comprises a first 5′

adaptor sequence and a first 3′

L-type adaptor sequence that respectively ligate to the 3′

end and the 5′

end of each strand of the fragments;

the first 5′

adaptor sequence comprises a 5′

end-phosphorylated long strand and a complementary short strand, the short strand having dideoxy modification at the 3′

end, and the short strand comprising a U base site; and

a portion of the first 3′

L-type adaptor sequence which is adjacent to the ligated fragment is complementary to part of the bases of the first 5′

adaptor sequence; and

said ligating a first adaptor sequence to both ends of the nucleic acid fragments specifically comprises;

dephosphorylating the nucleic acid fragments;

subjecting the dephosphorylated nucleic acid fragments to end repairing;

ligating the first 5′

adaptor sequence to the 3′

end of each strand of the nucleic acid fragments;

digesting the U base site of the short strand of the first 5′

adaptor sequence with a USER enzyme;

phosphorylating the USER enzyme-digested nucleic acid fragments; and

ligating the first 3′

L-type adaptor sequence to the 5′

end of each strand of the phosphorylated nucleic acid fragments.

3. The method according to claim 1, wherein each of the primer sequences used in the first PCR has a U base site and a nickase recognition sequence;

and after digesting the U base site with the USER enzyme, sticky ends are formed at both ends of the nucleic acid fragments, and cyclization occurs due to the complementarity of the sticky ends, generating cyclized nucleic acid molecules;

then a nickase is used to digest the nickase recognition sequence to generate a nick.

4. The method according to claim 1, wherein one of the primer sequences used in the first PCR has two U base sites, while the other primer sequence has a single U base site;

and after digesting the U base sites with the USER enzyme, sticky ends are formed at both ends of the

nucleic acid fragments, and cyclization occurs due to the complementarity of the sticky ends, generating cyclized nucleic acid molecules.

5. The method according to claim 4, wherein following cyclizing the digested first products, the method further comprises:

digesting the nucleic acid molecules that are not cyclized.

6. The method according to claim 4, wherein said digesting and removing the portion of the respective cyclic nucleic acid molecules that does not undergo the controlled gap translation reaction specifically comprises:

first degrading the cyclic nucleic acid molecules with a double strand exonuclease until the gaps at both ends meet; and

then degrading the resulting single strands with a single strand exonuclease;

or directly excising the portion of the respective cyclic nucleic acid molecules that does not undergo the controlled gap translation reaction with an endonuclease.

7. The method according to claim 4, wherein the second adaptor sequence is a bubble-type adaptor sequence, comprising two base sequences which are complementary to each other in terminal portions but not complementary to each other in a middle portion, thus forming a bubble shape in the middle portion;

the middle portion harbors a U base site, and one of the strands of the bubble-type adaptor sequence has an overhanging thymine (T base) at the 5′

end; and

said ligating a second adaptor sequence to both ends of the linear nucleic acid molecules specifically comprises;

subjecting the linear nucleic acid molecules to end repairing and to a reaction of adding adenine (A base) to the 3′

end;

ligating a bubble-type adaptor sequence to each end of the linear nucleic acid molecules by means of pairing of the T base with the A base; and

digesting the U base site in the middle portion by using a USER enzyme.

8. The method according to claim 4, wherein following cyclizing the single-stranded nucleic acid molecules, the method further comprises:

digesting the single-stranded nucleic acid molecules that are not cyclized.

9. A method for constructing a library of single-stranded cyclic nucleic acid fragments having double adaptors, comprising the following steps in the following order:

(1) disrupting of 1 μ

g of genomic DNA using ultrasound in a 96-well polymerase chain reaction (PCR) plate;

(2) selecting nucleic acid fragments by adding magnetic beads to the disrupted DNA and separating the beads on a magnetic rack;

(3) dephosphorylation of the fragments using shrimp alkaline phosphatase;

(4) end-repairing the fragments using deoxyribonucleotide triphosphates (dNTPs), bovine serum albumin and T4 deoxyribonucleic acid polymerase;

(5) ligating a 5′

adaptor A sequence using having SEQ ID NO;

1 and a 5′

blocking sequence having SEQ ID NO;

2;

(6) digesting the products of step (5) in a one-step reaction with Uracil-Specific Excision Reagent (USER) enzyme and phosphorylation using T4 polynucleotide kinase;

(7) ligating a first adaptor 3′

L-type adaptor A sequence having SEQ ID NO;

3 using T4 DNA ligase;

(8) performing a first polymerase chain reaction (PCR) using primer 1 having SEQ ID NO;

4 and primer 2 having SEQ ID NO;

5 followed by purification using magnetic beads;

(9) removal of uracil using USER enzyme;

(10) double strand cyclization;

(11) linear digestion followed by magnetic purification, wherein the initiation site is in the form of a nick, and adaptor A sequence harbors and a nickase recognition sequence;

(12) binding cyclic DNA to streptavidin magnetic beads which bind via a biotin label on the DNA;

(13) enzymatic digestion with nickase;

(14) controlled gap translation reaction using dNTPs and DNA polymerase I;

(15) digestion at the gap by T7 endonuclease I;

(16) filling of sticky ends and addition of A at the 3′

end using Klenow fragment and Klex NTA mix;

(17) ligation of a bubble-type adaptor comprising a top strand and a bottom strand, which are complementary to one another having SEQ ID NO;

6 and SEQ ID NO;

7;

(18) USER enzyme digestion;

(19) performing polymerase chain reaction using primer F and primer R having SEQ ID NO;

8 and SEQ ID NO;

9;

(20) single strand cyclization by nucleic acid single strand O via corresponding complementary sequences, wherein the nucleic acid single strand O having SEQ ID NO;

10; and

(21) linear DNA digestion using Exonuclease 1 and Exonuclease 3, to produce nucleic acid fragments in a size range of 200 bp to 300 bp, and wherein the steps of the method provide fragments suitable for next-generation sequencing on a Complete Genomics sequencing platform.