Classification of nucleic acid templates

Abstract

Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.

1 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) locking the forward and reverse strands of the nucleic acid sample together to form a circular pair-locked molecule;   b) obtaining sequence data of the circular pair-locked molecule via single molecule sequencing, wherein sequence data comprises sequences of the forward and reverse strands of the circular pair-locked molecule; and   c) determining the sequence of the double stranded nucleic acid sample and the position of the at least one modified base in the sequence of the double stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular pair-locked molecule.   
     
     
         2 . The method of  claim 1 , wherein the double stranded nucleic acid sample comprises at least one modified base chosen from 5-bromouracil, uracil, 5,6-dihydrouracil, ribothymine, 7-methylguanine, hypoxanthine, and xanthine. 
     
     
         3 . The method of  claim 1 , wherein at least one modified base in the double-stranded nucleic acid sample is paired with a base with a base pairing specificity different from its preferred partner base. 
     
     
         4 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) locking the forward and reverse strands of the nucleic acid sample together to form a circular pair-locked molecule;   b) altering the base-pairing specificity of bases of a specific type in the circular pair-locked molecule;   c) obtaining sequence data of the circular pair-locked molecule via single molecule sequencing, wherein sequence data comprises sequences of the forward and reverse strands of the circular pair-locked molecule; and   d) determining the sequence of the double-stranded nucleic acid sample and the position of the at least one modified base in the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular pair-locked molecule.   
     
     
         5 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) locking the forward and reverse strands together to form a circular pairlocked molecule;   b) obtaining sequence data of the circular pair-locked molecule via single molecule sequencing, wherein the sequence data comprises sequences of the forward and reverse strands of the circular pair-locked molecule;   c) determining the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular pair-locked molecule;   d) obtaining sequencing data of the circular pair-locked molecule via single molecule sequencing, wherein at least one nucleotide analog that discriminates between a base and its modified form is used to obtain sequence data comprising at least one position wherein the at least one differentially labeled nucleotide analog was incorporated; and   e) determining the positions of modified bases in the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands.   
     
     
         6 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) locking the forward and reverse strands of the nucleic acid sample together to form a circular pair-locked molecule;   b) obtaining sequence data of the circular pair-locked molecule via single molecule sequencing, wherein at least one nucleotide analog that discriminates between a base and its modified form is used to obtain sequence data comprising at least one position wherein the at least one differentially labeled nucleotide analog was incorporated; and   c) determining the sequence of the double-stranded nucleic acid sample and the position of the at least one modified base in the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular pair-locked molecule.   
     
     
         7 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) locking the forward and reverse strands together to form a circular pairlocked molecule;   b) obtaining sequence data of the circular pair-locked molecule via single molecule sequencing, wherein the sequence data comprises sequences of the forward and reverse strands of the circular pair-locked molecule;   c) determining the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular pair-locked molecule;   d) altering the base-pairing specificity of bases of a specific type in the circular pair-locked molecule to produce an altered circular pair-locked molecule;   e) obtaining the sequence data of the altered circular pair-locked molecule wherein the sequence data comprises sequences of the altered forward and reverse strands; and   f) determining the positions of modified bases in the sequence of the double-stranded nucleic acid sample by comparing the sequences of the altered forward and reverse strands.   
     
     
         8 . The method of  claim 7 , wherein the double-stranded nucleic acid sample is obtained as a primary isolate from a cellular, viral, or environmental source. 
     
     
         9 . The method of  claim 8 , wherein the primary isolate is maintained at or below 25° C. in conditions substantially free of divalent cations and nucleic acid modifying enzymes prior to step (a) of  claim 7 . 
     
     
         10 . The method of  claim 7 , wherein the double-stranded nucleic acid sample is obtained from an in vitro reaction or from extracellular nucleic acid. 
     
     
         11 . The method of  claim 7 , wherein altering the base-pairing specificity of bases of a specific type in the circular pair-locked molecule comprises bisulfite treatment. 
     
     
         12 . The method of  claim 7 , wherein altering the base-pairing specificity of bases of a specific type in the circular pair-locked molecule comprises photochemical transition. 
     
     
         13 . The method of  claim 7 , wherein locking the forward and reverse strands together comprises joining two nucleic acid inserts, which may be identical or non-identical, to the double-stranded nucleic acid sample, one to each end. 
     
     
         14 . The method of  claim 13 , wherein the nucleic acid inserts have lengths ranging from 14 to 200 nucleotide residues. 
     
     
         15 . The method of  claim 13 , wherein the nucleic acid inserts have known sequences. 
     
     
         16 . The method of  claim 13 , wherein the nucleic acid inserts form hairpins overhangs, and the nucleic acid sample has overhangs compatible with the overhangs of the nucleic acid inserts. 
     
     
         17 . The method of  claim 13 , wherein obtaining sequence data comprises annealing a primer complementary to at least part of at least one of the nucleic acid inserts to the template and extending the primer. 
     
     
         18 . The method of  claim 13 , wherein at least one of the nucleic acid inserts comprises a promoter, and obtaining sequence data comprises contacting the promoter with an RNA polymerase that recognizes the promoter followed by synthesizing a product nucleic acid molecule comprising ribonucleotide residues. 
     
     
         19 . The method of  claim 13 , wherein joining is achieved by ligation. 
     
     
         20 . The method of  claim 7 , wherein the double-stranded nucleic acid sample comprises a plurality of samples linked together. 
     
     
         21 . The method of  claim 20 , wherein the samples of said plurality are linked via intervening nucleic acid inserts. 
     
     
         22 . The method of  claim 21 , wherein locking the forward and reverse strands together comprises ligating a complex formed by contacting the overhangs of the nucleic acid inserts with the compatible overhangs of the nucleic acid sample. 
     
     
         23 . The method of  claim 7 , wherein the double-stranded nucleic acid sample is a genomic DNA fragment. 
     
     
         24 . The method of  claim 7 , wherein the double-stranded nucleic acid sample comprises at least one RNA strand. 
     
     
         25 . The method of  claim 7 , wherein said single molecule sequencing comprises sequencing by a method chosen from single molecule sequencing by synthesis, and ligation sequencing. 
     
     
         26 . The method of  claim 7 , wherein said single molecule sequencing comprises real-time single molecule sequencing by synthesis. 
     
     
         27 . The method of  claim 7 , wherein said single molecule sequencing comprises single molecule sequencing by synthesis by a method chosen from pyrosequencing, reversible terminator sequencing, and third-generation sequencing. 
     
     
         28 . The method of  claim 7 , wherein said single molecule sequencing comprises nanopore sequencing. 
     
     
         29 . The method of  claim 7 , wherein:
 the forward and reverse strands of the circular pair-locked molecule are locked together by nucleic acid inserts;   the sequence data obtained in step (b) comprises at least two copies of the sequence of the circular pair-locked molecule, each copy comprising sequences of first and second insert-sample units;   the sequences of the first and second insert-sample units comprise insert sequences, which may be identical or non-identical, and oppositely oriented repeats of the sequence of the nucleic acid sample;   and the method further comprises:   g) calculating scores of the sequences of at least four inserts contained in the sequence data by comparing the sequences of the at least four inserts to the known sequences of the inserts;   h) accepting or rejecting at least four of the repeats of the sequence of the nucleic acid sample contained in the sequence data according to the scores of one or both of the sequences of the inserts immediately upstream and downstream of the sample sequences, subject to the condition that at least one sample sequence in each orientation is accepted;   i) compiling an accepted sequence set comprising the at least one sample sequence in each orientation accepted in step (g); and   j) determining the sequence of the nucleic acid sample using the accepted sequence set.   
     
     
         30 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) linking the forward and reverse strands of the nucleic acid sample together to form a circular template molecule comprising a double-stranded segment joined at both ends by linking oligonucleotides;   b) obtaining sequence data of the circular template molecule via single molecule sequencing, wherein sequence data comprises sequences of the forward and reverse strands of the circular template molecule; and   c) determining the sequence of the double stranded nucleic acid sample and the position of the at least one modified base in the sequence of the double stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular template molecule.   
     
     
         31 . The method of  claim 30 , wherein the double stranded nucleic acid sample comprises at least one modified base chosen from uracil, dihydrouridine, and methyl-7-guanosine. 
     
     
         32 . The method of  claim 30 , wherein at least one modified base in the double-stranded nucleic acid sample is paired with a base with a base pairing specificity different from its preferred partner base. 
     
     
         33 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) linking the forward and reverse strands of the nucleic acid sample together to form a circular template molecule comprising a double-stranded segment joined at both ends by linking oligonucleotides;   b) altering a base of a specific type in the circular template molecule;   c) obtaining sequence data of the circular template molecule via single molecule sequencing, wherein sequence data comprises sequences of the forward and reverse strands of the circular template molecule; and   d) determining the sequence of the double-stranded nucleic acid sample and the position of the at least one modified base in the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular template molecule.   
     
     
         34 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) linking the forward and reverse strands together to form a circular template molecule comprising a double stranded segment joined at both ends by linking oligonucleotides;   b) obtaining sequence data of the circular template molecule via single molecule sequencing, wherein the sequence data comprises sequences of the forward and reverse strands of the circular template molecule;   c) determining the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular template molecule;   d) obtaining sequencing data of the circular template molecule via single molecule sequencing, wherein at least one nucleotide analog that discriminates between a base and its modified form is used to obtain sequence data comprising at least one position wherein at least one nucleotide analog that discriminates between a base and its modified form was incorporated; and   e) determining the positions of modified bases in the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands.   
     
     
         35 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) linking the forward and reverse strands of the nucleic acid sample together to form a circular template molecule comprising a double stranded segment joined at both ends by linking oligonucleotides;   b) obtaining sequence data of the circular template molecule via single molecule sequencing, wherein at least one nucleotide analog that discriminates between a base and its modified form is used to obtain sequence data comprising at least one position wherein at least one analog that discriminates between a base and its modified form was incorporated; and   c) determining the sequence of the double-stranded nucleic acid sample and the position of the at least one modified base in the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular template molecule.   
     
     
         36 . A method of determining a sequence of a double-stranded nucleic acid sample and a position of at least one modified base in the sequence, comprising:
 a) linking the forward and reverse strands together to form a circular template molecule comprising a double stranded segment joined at both ends by linking oligonucleotides;   b) obtaining sequence data of the circular template molecule via single molecule sequencing, wherein the sequence data comprises sequences of the forward and reverse strands of the circular template molecule;   c) determining the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands of the circular template molecule;   d) altering a base of a specific type in the circular template molecule to produce an altered circular template molecule;   e) obtaining the sequence data of the altered circular template molecule wherein the sequence data comprises sequences of the forward and reverse strands; and   f) determining the positions of modified bases in the sequence of the double-stranded nucleic acid sample by comparing the sequences of the forward and reverse strands obtained in e).   
     
     
         37 . The method of  claim 36 , wherein the double-stranded nucleic acid sample is isolated from a biological source. 
     
     
         38 . The method of  claim 36 , wherein the double-stranded nucleic acid sample is synthesized or isolated from a biological source. 
     
     
         39 . The method of  claim 36 , wherein altering a base of a specific type in the circular template molecule comprises bisulfite treatment. 
     
     
         40 . The method of  claim 36 , wherein the linking oligonucleotides are hairpin adaptors, and said linking the forward and reverse strands together comprises joining two hairpin adaptors, which may be identical or non-identical, to the double-stranded nucleic acid sample, one to each end. 
     
     
         41 . The method of  claim 40 , wherein the hairpin adaptors have lengths ranging from 4 to 100 nucleotide residues. 
     
     
         42 . The method of  claim 40 , wherein the nucleic acid inserts have known sequences 
     
     
         43 . The method of  claim 40 , wherein the hairpin adaptors form overhangs, and the nucleic acid sample has overhangs compatible with the overhangs of the hairpin adaptors. 
     
     
         44 . The method of  claim 40 , wherein obtaining sequence data comprises annealing a primer complementary to at least part of at least one of the hairpin adaptors and extending the primer. 
     
     
         45 . The method of  claim 40 , wherein sequence data is obtained by contacting the nucleic acid sample with an RNA polymerase that synthesizes a product nucleic acid molecule comprising ribonucleotide residues. 
     
     
         46 . The method of  claim 40 , wherein joining is achieved by ligation. 
     
     
         47 . The method of  claim 36 , wherein the double-stranded nucleic acid sample comprises multiple copies of a nucleic acid segment of interest. 
     
     
         48 . The method of  claim 36 , wherein the double-stranded nucleic acid sample comprises at least one RNA strand. 
     
     
         49 . The method of  claim 36 , wherein said single molecule sequencing comprises sequencing by synthesis. 
     
     
         50 . The method of  claim 36 , wherein said single molecule sequencing comprises nanopore sequencing.