Methods and kits for nucleic acid amplification

Abstract

Compositions and methods are provided for amplifying nucleic acid molecules. The nucleic acid molecules can be used in various research and diagnostic applications, such as gene expression studies involving nucleic acid microarrays.

1 . A method for synthesizing at least one asRNA molecule directly from at least one sRNA molecule, comprising: 
 a) providing at least one sRNA molecule having a 5′ end and a 3′ end, said 3′ end comprising a first nucleotide sequence corresponding to the partial 5′ end of the template strand of a RNA polymerase recognition sequence;    b) annealing to the 3′ end of said sRNA molecule a primer having a 5′ end and a 3′ end, said primer comprising a second nucleotide sequence corresponding to at the 5′ end of the non-template strand of said RNA polymerase recognition sequence sufficient in length to anneal to said first nucleotide sequence corresponding to the partial 5′ end of the template strand of said RNA polymerase recognition sequence;    c) extending the 3′ end of said primer such that a double stranded RNA/DNA duplex is formed;    d) degrading at least the 3′ portion of the RNA strand of said double stranded RNA/DNA duplex, thereby providing at least a partially single stranded DNA molecule having a single stranded 5′ end, said 5′ end comprising a third nucleotide sequence corresponding to the complete non-template strand of said RNA polymerase recognition sequence;    e) synthesizing at least a partially double stranded DNA molecule from said at least partially single stranded DNA molecule such that said third nucleotide sequence corresponding to the complete non-template strand of said RNA polymerase recognition sequence is converted into a double stranded RNA polymerase promoter; and    f) initiating RNA transcription using an RNA polymerase which recognizes said double stranded RNA polymerase promoter,    thereby synthesizing at least one asRNA molecule directly from at least one sRNA molecule.    
     
     
         2 . The method of  claim 1 , wherein in step e) the double stranded RNA polymerase promoter is a bacteriophage promoter.  
     
     
         3 . The method of  claim 1 , wherein in step d) the RNA strand of the double stranded RNA/DNA duplex is substantially completely degraded using a RNase enzyme separate from reverse transcriptase.  
     
     
         4 . The method of  claim 3 , wherein step e) comprises addition of an exogenous primer.  
     
     
         5 . The method of  claim 4 , the exogenous primer comprises a nucleotide sequence of sufficient complementarity such that it anneals to the at least partially single stranded DNA molecule.  
     
     
         6 . The method of  claim 5 , wherein the exogenous primer anneals to the 3′ most nucleotides of the at least partially single stranded DNA molecule.  
     
     
         7 . The method of  claim 5 , wherein the exogenous primer is complementary to a complementary to naturally occurring gene-specific sequence on the at least partially single stranded DNA molecule.  
     
     
         8 . The method of  claim 5 , wherein the exogenous primer is complementary to a complementary to an engineered sequence on the at least partially single stranded DNA molecule.  
     
     
         9 . The method of  claim 1 , wherein in step d) the RNA strand of the double stranded RNA/DNA duplex is partially degraded using a reverse transcriptase having RNAse activity without the addition of a separate RNase enzyme.  
     
     
         10 . The method of  claim 9 , wherein in step e) a remaining portion of the RNA strand serves as a primer for second strand DNA synthesis.  
     
     
         11 . The method of  claim 1 , wherein step f) comprises initiating RNA transcription in the presence of fluorescently labeled nucleotides.  
     
     
         12 . The method of  claim 1 , wherein step f) comprises RNA transcription initiating in the presence of amino allyl nucleotides.  
     
     
         13 . The method of  claim 1 , wherein step a) comprises: 
 g) providing at least one RNA molecule having a 5′ end and a 3′ end; and synthesizing at least one single stranded cDNA molecule from said RNA molecule or molecules using a primer having a 5′ extension comprising a fourth nucleotide sequence corresponding to the partial 3′ end of the non-template strand of the RNA polymerase recognition sequence.    
     
     
         14 . The method of  claim 13 , wherein the primer is a random primer, an oligodT primer or a combination thereof.  
     
     
         15 . The method of  claim 13 , further comprising: 
 (h) attaching an oligodeoxynucleotide tail having a 5′ end and 3′ end onto the 3′ end of the cDNA molecule or molecules;    (i) annealing to said oligodeoxynucleotide tail a single stranded RNA/DNA composite bridge oligonucleotide comprising a 5′ RNA portion and a 3′ DNA sequence portion, such that the RNA portion remains single stranded;    (j) extending the 3′ end of said oligodeoxynucleotide tail, such that said single stranded RNA portion becomes a double stranded RNA/DNA duplex;    (k) degrading the RNA portion of said RNA/DNA duplex, thereby exposing a 3′ single stranded DNA tail;    (l) annealing to said 3′ single stranded DNA tail a single stranded promoter template comprising at least one RNA polymerase recognition sequence;    (m) extending said 3′ single stranded DNA tail such that said at least one single stranded RNA polymerase recognition sequence is converted into at least one RNA polymerase promoter;    (n) and initiating RNA transcription using a RNA polymerase which recognizes said at least one RNA polymerase promoter,    thereby providing at least one sRNA molecule having a 5′ end and a 3′ end, said 3′ end comprising a first nucleotide sequence corresponding to the partial 5′ end of the template strand of a RNA polymerase recognition sequence.    
     
     
         16 . The method of  claim 15 , wherein steps  1 ) through m) are performed substantially at the same time.  
     
     
         17 . The method of  claim 15 , wherein in step  1 ) the single stranded promoter template comprises a first RNA polymerase recognition sequence and a second RNA polymerase recognition sequence 3′ to said first recognition sequence, wherein said first and second RNA polymerase recognition sequence are different.  
     
     
         18 . The method of  claim 17 , wherein the first and second RNA polymerase recognition sequences are bacteriophage RNA polymerase recognition sequences.  
     
     
         19 . The method of  claim 17 , wherein in step n) RNA transcription is initiated using a RNA polymerase which recognizes said the first RNA polymerase recognition sequence.  
     
     
         20 . The method of  claim 19 , further comprising: 
 (o) synthesizing at least one cDNA molecule having a 5′ end and 3′ end from the sRNA molecule or molecules using a primer having a nucleotide sequence corresponding to the fourth nucleotide sequence of the 5′ extension of the primer in step g), thereby forming a double stranded sRNA/cDNA duplex;    (p) degrading the sRNA portion of said sRNA/cDNA duplex, thereby providing a single stranded cDNA molecule;    (q) annealing to said single stranded cDNA molecule a single stranded promoter oligonucleotide complementary to the second different RNA polymerase recognition sequence such that a second different RNA polymerase promoter is formed; and    (r) initiating RNA transcription using an RNA polymerase which recognizes said second different RNA polymerase promoter,    thereby providing at least one sRNA molecule having a 5′ end and a 3′ end, said 3′ end comprising a first nucleotide sequence corresponding to the partial 5′ end of the template strand of a RNA polymerase recognition sequence.    
     
     
         21 . The method of  claim 20 , wherein the first and second RNA polymerase recognition sequences are bacteriophage RNA polymerase recognition sequences.  
     
     
         22 . A method for synthesizing at least one cDNA molecule directly from at least one sRNA molecule, comprising: 
 a) providing at least one sRNA molecule having a 5′ end and a 3′ end, said 3′ end comprising a first nucleotide sequence corresponding to the partial 5′ end of the template strand of a RNA polymerase recognition sequence;    b) annealing to the 3′ end of said sRNA molecule a primer having a 5′ end and a 3′ end, said primer comprising a second nucleotide sequence corresponding to at the 5′ end of the non-template strand of said RNA polymerase recognition sequence sufficient in length to anneal to said first nucleotide sequence corresponding to the partial 5′ end of the template strand of said RNA polymerase recognition sequence; and    c) extending the 3′ end of said primer with reverse transcriptase,    thereby synthesizing at least one cDNA molecule directly from at least one sRNA molecule.    
     
     
         23 . The method of  claim 22 , wherein step c) comprises extending the 3′ end of the primer in the presence of detectably labeled nucleotides.  
     
     
         24 . The method of  claim 23 , wherein the detectable labeled nucleotides are fluorescently labeled nucleotides.  
     
     
         25 . The method of  claim 23 , wherein the detectable labeled nucleotides are amino allyl nucleotides.  
     
     
         26 . The method of  claim 22 , wherein the primer in step b) further comprises a capture nucleotide sequence at its 5′ end.  
     
     
         27 . The method of  claim 26 , further comprising indirectly labeling the cDNA molecule or molecules with a molecule comprising a nucleotide sequence complementary to the capture nucleotide sequence.  
     
     
         28 . The method of  claim 27 , wherein the molecule is a nucleic acid dendrimer.  
     
     
         29 . A method for probing a nucleic acid microarray, comprising: contacting a nucleic acid microarray with at least one asRNA molecule synthesized by the method of  claim 1 .  
     
     
         30 . A method for probing a nucleic acid microarray, comprising: contacting a nucleic acid microarray with at least one cDNA molecule synthesized by the method of  claim 22 .  
     
     
         31 . A kit for synthesizing asRNA molecules and/or cDNA molecules directly from a sRNA molecule, comprising: one or more first primers comprising a nucleotide sequence corresponding to at least a portion of the 5′ end of the non-template strand of a RNA polymerase recognition sequence; and instructional materials for synthesizing asRNA and/or molecules directly from sRNA molecules using said first primer.  
     
     
         32 . The kit of  claim 31 , further comprising one or more reagents and instructional materials for synthesizing sRNA molecules from which asRNA and/or cDNA molecules can be directly synthesized.  
     
     
         33 . The kit of claim,  32  comprising: one or more second primers having a 5′ extension comprising a nucleotide sequence corresponding to the partial 3′ end of the non-template strand of a RNA polymerase recognition sequence.  
     
     
         34 . The kit of  claim 33 , further comprising a single stranded promoter template comprising at least one RNA polymerase recognition sequence; and a single stranded RNA/DNA composite bridge oligonucleotide comprising a RNA sequence 5′ of a DNA sequence.  
     
     
         35 . The kit of  claim 34 , further comprising one or more third primers comprising a nucleotide sequence corresponding to the nucleotide sequence of the 5′ extension of the second primer or primers; and a single stranded promoter oligonucleotide complementary to a second RNA polymerase recognition sequence of the promoter template.