Methods for detecting modification resistant nucleic acids
First Claim
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1. A method for detecting a plurality of mRNA molecules bound to at least one ribosome, said method comprising:
- (i) contacting said plurality of mRNA molecules with an enzymatic degradant or a chemical degradant thereby forming a plurality of RNA fragments, wherein each RNA fragment comprises an RNA portion protected from said enzymatic degradant or said chemical degradant by a ribosome to which the RNA portion is bound;
(ii) amplifying said RNA fragments comprising said RNA portions to form a detectable number of amplified nucleic acid fragments; and
(iii) detecting said detectable number of amplified nucleic acid fragments, thereby detecting an amount of two or more of said RNA portions and correlating said amount of two or more of said RNA portions to a rate of translation of one or more of said plurality of mRNA molecules.
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Abstract
Methods are provided for, inter alia, detecting nucleic acid molecules resistant to degradation, such as a plurality of RNA molecules bound to a ribosome, using various technologies including deep sequencing.
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Citations
28 Claims
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1. A method for detecting a plurality of mRNA molecules bound to at least one ribosome, said method comprising:
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(i) contacting said plurality of mRNA molecules with an enzymatic degradant or a chemical degradant thereby forming a plurality of RNA fragments, wherein each RNA fragment comprises an RNA portion protected from said enzymatic degradant or said chemical degradant by a ribosome to which the RNA portion is bound; (ii) amplifying said RNA fragments comprising said RNA portions to form a detectable number of amplified nucleic acid fragments; and (iii) detecting said detectable number of amplified nucleic acid fragments, thereby detecting an amount of two or more of said RNA portions and correlating said amount of two or more of said RNA portions to a rate of translation of one or more of said plurality of mRNA molecules. - View Dependent Claims (2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 27)
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5. A method for detecting a plurality of mRNA molecules bound to at least one ribosome, said method comprising:
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(i) contacting said plurality of mRNA molecules with an enzymatic degradant or a chemical degradant thereby forming a plurality of RNA fragments, wherein each RNA fragment comprises an RNA portion protected from said enzymatic degradant or said chemical degradant by a ribosome to which the RNA portion is bound; (ii) amplifying said RNA fragments to form a detectable number of amplified nucleic acid fragments; and (iii) detecting said detectable number of amplified nucleic acid fragments, thereby detecting said plurality of mRNA molecules bound to at least one ribosome, wherein said amplifying and detecting comprises; (a) contacting said plurality of RNA fragments with a DNA polymerase and a DNA polymerase primer thereby forming a plurality of linear DNA molecules; (b) contacting said plurality of linear DNA molecules with a ligase thereby forming a plurality of circularized DNA molecules; (c) amplifying said plurality of circularized DNA thereby forming a detectable number of amplified DNA molecules; and (d) detecting said detectable number of amplified DNA molecules thereby detecting said plurality of mRNA molecules bound to at least one ribosome.
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6. A method for detecting a plurality of mRNA molecules bound to at least one ribosome, said method comprising:
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(i) contacting said plurality of mRNA molecules with an enzymatic degradant or a chemical degradant thereby forming a plurality of RNA fragments, wherein each RNA fragment comprises an RNA portion protected from said enzymatic degradant or said chemical degradant by a ribosome to which the RNA portion is bound; (ii) amplifying said RNA fragments to form a detectable number of amplified nucleic acid fragments; and (iii) detecting said detectable number of amplified nucleic acid fragments, thereby detecting said plurality of mRNA molecules bound to at least one ribosome, wherein said plurality of mRNA molecules comprise at least 1,000 different sequence species.
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7. A method for determining translation activity for a plurality of mRNA molecules, comprising:
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(i) treating a plurality of RNA-ribosome complexes, wherein each RNA-ribosome complex comprises an mRNA molecule having an RNA portion that is bound to a ribosome, under conditions sufficient produce a plurality of RNA fragments, wherein each RNA fragment comprises an RNA portion, and wherein each RNA fragment comprises a nucleotide sequence that is longer than the nucleotide sequence of said RNA portion; (ii) sequencing the plurality of RNA fragments to determine the nucleotide sequences of the RNA portions; and (iii) comparing the nucleotide sequences of the plurality of RNA portions to the nucleotide sequences of the mRNA molecules, thereby determining translation activity for the plurality of mRNA molecules, wherein an amount of two or more RNA portions are correlated to a rate of translation of one or more mRNA molecules.
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16. A method for detecting an RNA molecule bound to at least one ribosome, said method comprising:
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(i) contacting said RNA molecule with an enzymatic degradant or chemical degradant thereby forming an RNA fragment, wherein the RNA fragment comprises an RNA portion protected from said enzymatic degradant or said chemical degradant by a ribosome to which the RNA portion is bound; (ii) contacting said RNA fragment with a DNA polymerase and a DNA polymerase primer thereby forming a linear DNA; (iii) contacting said linear DNA with a ligase thereby forming a circularized DNA; (iv) amplifying said circularized DNA thereby forming a detectable number of amplified DNA molecules; and (v) detecting said detectable number of amplified DNA molecules thereby detecting said RNA molecule bound to at least one ribosome.
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17. A method for determining translation activity for a plurality of mRNA molecules, comprising:
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(i) treating a plurality of RNA-ribosome complexes, wherein each RNA-ribosome complex comprises an mRNA molecule having an RNA portion that is bound to a ribosome, under conditions sufficient produce a plurality of RNA fragments, wherein each RNA fragment comprises an RNA portion, and wherein each RNA fragment comprises a nucleotide sequence that is longer than the nucleotide sequence of said RNA portion; (ii) sequencing the plurality of RNA fragments to determine the nucleotide sequences of the RNA portions; and (iii) comparing the nucleotide sequences of the plurality of RNA portions to the nucleotide sequences of the mRNA molecules, thereby determining translation activity for the plurality of mRNA molecules. - View Dependent Claims (18, 19, 20, 21, 22, 23, 24, 25, 26)
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28. A method for detecting a plurality of RNA molecules bound to at least one ribosome, said method comprising:
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(i) contacting said plurality of RNA molecules with an enzymatic degradant or a chemical degradant thereby forming a plurality of RNA fragments, wherein each RNA fragment comprises an RNA portion protected from said enzymatic degradant or said chemical degradant by a ribosome to which the RNA portion is bound; (ii) amplifying said RNA fragments to form a detectable number of amplified nucleic acid fragments; and (iii) detecting said detectable number of amplified nucleic acid fragments, thereby detecting said plurality of RNA molecules bound to at least one ribosome; wherein said amplifying and detecting comprises; (a) contacting said plurality of RNA fragments with a DNA polymerase and a DNA polymerase primer thereby forming a plurality of linear DNA molecules; (b) contacting said plurality of linear DNA molecules with a ligase thereby forming a plurality of circularized DNA molecules; (c) amplifying said plurality of circularized DNA thereby forming a detectable number of amplified DNA molecules; and (d) detecting said detectable number of amplified DNA molecules thereby detecting said plurality of RNA molecules bound to at least one ribosome.
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Specification