Massively parallel signature sequencing by ligation of encoded adaptors

Abstract

The invention provides a method of nucleic acid sequence analysis based on the ligation of one or more sets of encoded adaptors to the terminus of a target polynucleotide. Encoded adaptors whose protruding strands form perfectly matched duplexes with the complementary protruding strands of the target polynucleotide are ligated, and the identity of the nucleotides in the protruding strands is determined by an oligonucleotide tag carried by the encoded adaptor. Such determination, or “decoding” is carried out by specifically hybridizing a labeled tag complement to its corresponding tag on the ligated adaptor.

1. A method of determining a nucleotide sequence at an end of a polynucleotide, the method comprising the steps of:
 ligating one or more encoded adaptors to the ends of identical copies of the polynucleotide, each encoded adaptor being a double stranded deoxyribonucleic acid comprising an oligonucleotide tag selected from a minimally cross-hybridizing set of oligonucleotides between 8 and 20 nucleotides or basepairs in length and a protruding strand complementary to a portion of a strand of the polynucleotide, wherein each oligonucleotide of the minimally cross-hybridizing set differs from every other oligonucleotide of the set by at least two nucleotides; and   identifying one or more nucleotides in each of said portions of the strand of the polynucleotides by specifically hybridizing a tag complement to each oligonucleotide tag of the one or more encoded adaptors ligated thereto.   
     
     
       2. The method of  claim 1  wherein said step of ligating includes ligating a plurality of different encoded adaptors to said end of said polynucleotide such that said protruding strands of the plurality of different encoded adaptors are complementary to a plurality of different portions of said strand of said polynucleotide such that there is a one-to-one correspondence between said different encoded adaptors and the different portions of said strand. 
     
     
       3. The method of  claim 2  wherein said different portions of said strand of said polynucleotide are contiguous. 
     
     
       4. The method of  claim 3  wherein said protruding strand of said encoded adaptors contains from 2 to 6 nucleotides and wherein said step of identifying includes specifically hybridizing said tag complements to said oligonucleotide tags such that the identity of each nucleotide in said portions of said polynucleotide is determined successively. 
     
     
       5. The method of  claim 4  A method of determining a nucleotide sequence at an end of a polynucleotide, the method comprising the steps of:
 ligating one or more encoded adaptors to the ends of identical copies of the polynucleotide, each encoded adaptor being a double stranded deoxyribonucleic acid comprising an oligonucleotide tag selected from a minimally cross-hybridizing set of oligonucleotides between 8 and 20 nucleotides or basepairs in length and a protruding strand complementary to a portion of a strand of the polynucleotide, wherein each oligonucleotide of the minimally cross-hybridizing set differs from every other oligonucleotide of the set by at least two nucleotides; and 
 identifying one or more nucleotides in each of said portions of the strand of the polynucleotides by specifically hybridizing a tag complement to each oligonucleotide tag of the one or more encoded adaptors ligated thereto; 
 wherein said step of ligating includes ligating a plurality of different encoded adaptors to said end of said polynucleotide such that said protruding strands of the plurality of different encoded adaptors are complementary to a plurality of different portions of said strand of said polynucleotide such that there is a one-to-one correspondence between said different encoded adaptors and the different portions of said strand; 
 wherein said different portions of said strand of said polynucleotide are contiguous; 
 wherein said protruding strand of said encoded adaptors contains from 2 to 6 nucleotides and wherein said step of identifying includes specifically hybridizing said tag complements to said oligonucleotide tags such that the identity of each nucleotide in said portions of said polynucleotide is determined successively; and  
 wherein said step of identifying further includes providing a number of sets of tag complements equivalent to the number of nucleotides to be identified in said portions of said polynucleotide. 
 
     
     
       6. The method of  claim 5  wherein said step of identifying further includes providing said tag complements in each of said sets that are capable of indicating the presence of a predetermined nucleotide by a signal generated by a fluorescent signal generating moiety, there being a different fluorescent signal generating moiety for each kind of nucleotide. 
     
     
       7. The method of  claim 5  wherein said oligonucleotide tags of said encoded adaptors are single stranded and said tag complements to said oligonucleotide tags are single stranded such the specific hybridization between an oligonucleotide tag and its respective tag complement occurs through Watson-Crick base pairing. 
     
     
       8. The method of  claim 7  wherein said encoded adaptors have the form: 
       
         
           
                 
                 
               
                     
                   5′-p(N) n (N ) r (N ) s (N ) q (N) t -3′ 
                 
                     
                          z(N′) r (N′) s (N′) q -5′ 
                 
                     
                     
                 
                     
                   or 
                 
                     
                     
                 
                     
                      p(N ) r (N ) s (N ) q (N ) t -3′ 
                 
                     
                   3′-z(N′) n (N′) r (N′) s (N′) q -5′ 
                 
             
                
                
                
                
                
                
                
               
            
           
         
       
       where N is a nucleotide and N′ is its complement, p is a phosphate group, z is a 3′ hydroxyl or a 3′ blocking group, n is an integer between 2 and 6, inclusive, r is an integer between 0 and 18, inclusive, s is an integer which is either between four and six, inclusive, whenever the encoded adaptor has a nuclease recognition site or is 0 whenever there is no nuclease recognition site, q is an integer greater than or equal to 0, and t is an integer greater than or equal to 8. 
     
     
       9. The method of  claim 8  wherein r is between 0 and 12, inclusive, t is an integer between 8 and 20, inclusive, and z is a phosphate group. 
     
     
       10. The method of  claim 9  wherein members of said minimally cross-hybridizing set differ from every other member by at least six nucleotides. 
     
     
       11. The method of  claim 5  wherein said oligonucleotide tags of said encoded adaptors are double stranded and said tag complements to said oligonucleotide tags are single stranded such that specific hybridization between an oligonucleotide tag and its respective tag complement occurs through the formation of a Hoogsteen or reverse Hoogsteen triplex. 
     
     
       12. The method of  claim 11  wherein said encoded adaptors have the form: 
       
         
           
                 
                 
               
                     
                   5′-p(N ) n (N ) r (N ) s (N ) q (N ) t -3′ 
                 
                     
                          z(N′) r (N′) s (N′) q (N′) t -5′ 
                 
                     
                     
                 
                     
                   or 
                 
                     
                     
                 
                     
                           p(N ) r (N ) s (N ) q (N ) t -3′ 
                 
                     
                   3′-z(N′) n (N′) r (N′) s (N′) q (N′) t -5′ 
                 
             
                
                
                
                
                
                
                
               
            
           
         
       
       wherein N is a nucleotide and N′ is its complement, p is a phosphate group, z is a 3′ hydroxyl or a 3′ blocking group, n is an integer between 2 and 6, inclusive, r is an integer between 0 and 18, inclusive, s is an integer which is either between four and six, inclusive, whenever the encoded adaptor has a nuclease recognition site or is 0 whenever there is no nuclease recognition site, q is an integer greater than or equal to 0, and t is an integer greater than or equal to 8. 
     
     
       13. The method of  claim 12  wherein r is between 0 and 12, inclusive, t is an integer between 8 and 24, inclusive, and z is a phosphate group. 
     
     
       14. The method of  claim 13  wherein members of said minimally cross-hybridizing set differ from every other member by at least six nucleotides. 
     
     
       15. A method of determining nucleotide sequences of a plurality of polynucleotides, the method comprising the steps of:
 (a) attaching a first oligonucleotide tag from a repertoire of tags to each polynucleotide in a population of polynucleotides such that each first oligonucleotide tag from the repertoire is selected from a first minimally cross-hybridizing set of oligonucleotides between 12 and 60 nucleotides or basepairs in length and wherein each oligonucleotide of the first minimally cross hybridizing set differs from every other oligonucleotide of the first set by at least two nucleotides; 
 (b) sampling the population of polynucleotides to form a sample of polynucleotides such that substantially all different polynucleotides in the sample have different first oligonucleotide tags attached; 
 (c) sorting the polynucleotides of the sample by specifically hybridizing the first oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical oligonucleotides in spatially discrete regions on the one or more solid phase supports; 
 (d) ligating one or more encoded adaptors to an end of identical copies of the polynucleotides in the sample, each encoded adaptor being a double stranded deoxyribonucleic acid comprising a second oligonucleotide tag selected from a second minimally cross-hybridizing set of oligonucleotides between 8 and 20 nucleotides or basepairs in length and a protruding strand complementary to a protruding strand of a polynucleotide of the population, wherein each oligonucleotide of the second minimally cross hybridizing set differs from every other oligonucleotide of the second set by at least two nucleotides; and 
 (e) identifying a plurality of nucleotides in said protruding strands of the polynucleotides by specifically hybridizing a tag complement to each second oligonucleotide tag of the one or more encoded adaptors. 
 
     
     
       16. The method of  claim 15  further including the steps of (f) cleaving said encoded adaptors from said polynucleotides with a nuclease having a nuclease recognition site separate from its cleavage site so that a new protruding strand is formed on said end of each of said polynucleotides, and (g) repeating steps (d) through (f). 
     
     
       17. A method of identifying a population of mRNA molecules, the method comprising the steps of:
 (a) forming a population of cDNA molecules from the population of mRNA molecules such that each cDNA molecule has a first oligonucleotide tag attached, the first oligonucleotide tags being selected from a first minimally cross-hybridizing set of oligonucleotides between 12 and 60 nucleotides or basepairs in length and wherein each oligonucleotide of the first minimally cross hybridizing set differs from every other oligonucleotide of the first set by at least two nucleotides; 
 (b) sampling the population of cDNA molecules to form a sample of cDNA molecules such that substantially all different cDNA molecules have different first oligonucleotide tags attached; 
 (c) sorting the cDNA molecules by specifically hybridizing the first oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical complements in spatially discrete regions on one or more solid phase supports; 
 (d) ligating one or more encoded adaptors to an end of the cDNA molecules in the population, each encoded adaptor being a double stranded deoxyribonucleic acid comprising a second oligonucleotide tag selected from a second minimally cross-hybridizing set of oligonucleotides between 8 and 20 nucleotides or basepairs in length and a protruding strand complementary to a protruding strand of a cDNA molecule of the sample, wherein each oligonucleotide of the second minimally cross hybridizing set differs from every other oligonucleotide of the second set by at least two nucleotides; and 
 (e) determining the identity and ordering of a plurality of nucleotides in each of said protruding strands of the cDNA molecules by specifically hybridizing a tag complement to each second oligonucleotide tag of the one or more encoded adaptors; 
 wherein the population of mRNA molecules is identified by the frequency distribution of the portions of sequences of the cDNA molecules. 
 
     
     
       18. The method of  claim 17  further including the steps of (f) cleaving said encoded adaptors from said polynucleotides with a nuclease having a nuclease recognition site separate from its cleavage site so that a new protruding strand is formed on said end of each of said cDNA molecules, said (g) repeating steps (d) through (f). 
     
     
       19. A method of determining a nucleotide sequence at an end of a polynucleotide, the method comprising the steps of:
 (a) ligating an encoded adaptor to an end of the polynucleotide, the encoded adaptor being a double stranded deoxyribonucleic acid comprising an oligonucleotide tag selected from a minimally cross-hybridizing set of oligonucleotides between 8 and 20 nucleotides or basepairs in length and a protruding strand complementary to a portion of a strand of the polynucleotide, wherein each oligonucleotide of the second minimally cross hybridizing set differs from every other oligonucleotide of the second set by at least two nucleotides; 
 (b) identifying one or more nucleotides in the portion of the strand of the polynucleotide by specifically hybridizing a tag complement to the oligonucleotide tag of the encoded adaptor ligated thereto; 
 (c) cleaving the encoded adaptor from the end of the polynucleotide with a nuclease having a nuclear recognition site separate from its cleavage site so that a new protruding strand is formed at the end of the polynucleotide; and 
 (d) repeating steps (a) through (c). 
 
     
     
       20. The method of  claim 19  wherein said protruding strand of said encoded adaptor contains from 2 to 6 nucleotides and wherein step of identifying includes specifically hybridizing successive said tag complements to said oligonucleotide tag such that the identity of each nucleotide in said portion of said polynucleotide is determined successively. 
     
     
       21. The method of  claim 20  wherein said step of identifying further includes providing a number of sets of tag complements equivalent to the number of nucleotides to be identified in said portion of said polynucleotide. 
     
     
       22. The method of  claim 21  wherein said step of identifying further includes providing said tag complements in each of said sets that are capable of indicating the presence of a predetermined nucleotide by a signal generated by a fluorescent signal generating moiety, there being a different fluorescent signal generating moiety for each kind of nucleotide. 
     
     
       23. The method of  claim 22  wherein said oligonucleotide tags of said encoded adaptors are single stranded and said tag complements to said oligonucleotide tags are single stranded such that specific hybridization between oligonucleotide tag and its respective tag complement occurs through Watson-Crick base pairing. 
     
     
       24. A composition of matter comprising a plurality of double stranded oligonucleotide adaptors each having the form: 
       
         
           
                 
                 
               
                     
                   5′-p(N) n (N ) r (N ) s (N ) q (N ) t -3′ 
                 
                     
                          z(N′) r (N′) s (N′) q (N′) t -5′ 
                 
                     
                     
                 
                     
                   or 
                 
                     
                     
                 
                     
                           p(N ) r (N ) s (N ) q (N ) t -3′ 
                 
                     
                   3′-z(N′) n (N′) r (N′) s (N′) q -5′ 
                 
             
                
                
                
                
                
                
                
               
            
           
         
       
       where N is a nucleotide and N′ is its complement, p is a phosphate group, z is a 3′ hydroxyl or a 3′ blocking group, n is an integer between 2 and 6, inclusive, r is an integer between 0 and 18, inclusive, s is an integer which is either between four and six, inclusive, whenever the encoded adaptor has a nuclease recognition site or is 0 whenever there is no nuclease recognition site, q is an integer greater than or equal to 0, and t is an integer greater than or equal to 8 such that (N) t  is a single stranded moiety, and said single stranded moiety (N) t  is a member of a minimally cross-hybridizing set of oligonucleotides such that each oligonucleotide of the set differs from every other oligonucleotide of the set by at least two nucleotides, and wherein the minimally cross-hybridizing sets comprise subunits made up of at least three of the four natural nucleotides. 
     
     
       25. The composition of  claim 24  wherein r is between 0 and 12, inclusive, t is an integer between 8 and 20, inclusive, and wherein z is a blocking group and the blocking group is a phosphate group, and said single stranded moiety (N) t  is a member of a minimally cross-hybridizing set of oligonucleotides such that each oligonucleotide of the set differs from every other oligonucleotide of the set by at least two nucleotides. 
     
     
       26. The composition of  claim 25  wherein n equals 4 and wherein members of said minimally cross-hybridizing set differ from every other member by at least six nucleotides. 
     
     
       27. A composition of matter comprising a plurality of double stranded oligonucleotide adaptors each having the form: 
       
         
           
                 
                 
               
                     
                   5′-p(N ) n (N ) r (N ) s (N ) q (N ) t -3′ 
                 
                     
                          z(N′) r (N′) s (N′) q (N′) t -5′ 
                 
                     
                     
                 
                     
                   or 
                 
                     
                     
                 
                     
                           p(N ) r (N ) s (N ) q (N ) t -3′ 
                 
                     
                   3′-z(N′) n (N′) r (N′) s (N′) q (N′) t -5′ 
                 
             
                
                
                
                
                
                
                
               
            
           
         
       
       where N is a nucleotide and N′ is its complement, p is a phosphate group, z is a 3′ hydroxyl or a 3′ blocking group, n is an integer between 2 and 6, inclusive, r is an integer between 0 and 18, inclusive, s is an integer which is either between four and six, inclusive, whenever the encoded adaptor has a nuclease recognition site or is 0 whenever there is no nuclease recognition site, q is an integer greater than or equal to 0, and t is an integer greater than or equal to 8 such that, for each of the plurality of double stranded adaptors,  
       
         
           
                 
                 
               
                     
                   —(N) t   
                 
                     
                   —(N′) t   
                 
             
                
                
               
            
           
         
       
       forms a double stranded moiety selected from a minimally cross-hybridizing set of oligonucleotides such that each oligonucleotide of the set differs from every other oligonucleotide of the set by at least two basepairs. 
     
     
       28. The composition of  claim 27  wherein r is between 0 and 12, inclusive, t is an integer between 8 and 24, inclusive, and z is a blocking group and the blocking group is a phosphate group. 
     
     
       29. The composition of  claim 28  wherein members of said minimally cross-hybridizing set differ from every other member by at least six nucleotides.