Methods of constructing small RNA libraries and their use for expression profiling of target RNAs
First Claim
1. A method for detecting and quantifying an amount of a target RNA in a sample, the method comprising:
- a) hybridizing the target RNA with a target-specific oligonucleotide (TSO) to produce a TSO-hybridized target RNA;
wherein the TSO is(i) shorter than the target RNA, or as long as or shorter than the target RNA wherein the target RNA is a miRNA; and
(ii) substantially complementary to the target RNA sequence;
b) ligating a 5′
adapter to a 5′
end of the TSO-hybridized target RNA and/or ligating a 3′
adapter to a 3′
end of the TSO-hybridized target RNA, wherein the ligating comprises performing a splint-independent ligation to produce an adapter-ligated TSO-hybridized target RNA, and reverse transcribing the adapter-ligated TSO-hybridized target RNA, or a portion thereof, to produce a reverse transcript thereof;
c) enzymatically amplifying the reverse transcript, or a portion thereof, to produce an amplified polynucleotide comprising a sequence corresponding to or complementary to the target RNA sequence; and
d) quantitatively detecting an amount of the amplified polynucleotide, wherein the amount of the amplified polynucleotide correlates with the amount of the target RNA,wherein the TSO is not immobilized in any step of the method.
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Accused Products
Abstract
Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) are disclosed herein. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used to attach adapters and/or linkers to target RNAs. Methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used in reactions, including, but not limited to, ligation reactions, amplification reactions, and sequencing reactions. Additionally, methods, compositions, and kits comprising target-specific oligonucleotides (TSOs) can be used for reducing and/or preventing the formation of secondary structures in target RNAs. These methods, compositions, and kits can also find use in a number of applications, for example, any application that benefits from stabilizing primary RNA structure, such as detecting and quantifying target RNAs in a sample, in the construction of small RNA libraries, in microarray and RT-qPCR applications, etc.
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Citations
20 Claims
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1. A method for detecting and quantifying an amount of a target RNA in a sample, the method comprising:
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a) hybridizing the target RNA with a target-specific oligonucleotide (TSO) to produce a TSO-hybridized target RNA;
wherein the TSO is(i) shorter than the target RNA, or as long as or shorter than the target RNA wherein the target RNA is a miRNA; and (ii) substantially complementary to the target RNA sequence; b) ligating a 5′
adapter to a 5′
end of the TSO-hybridized target RNA and/or ligating a 3′
adapter to a 3′
end of the TSO-hybridized target RNA, wherein the ligating comprises performing a splint-independent ligation to produce an adapter-ligated TSO-hybridized target RNA, and reverse transcribing the adapter-ligated TSO-hybridized target RNA, or a portion thereof, to produce a reverse transcript thereof;c) enzymatically amplifying the reverse transcript, or a portion thereof, to produce an amplified polynucleotide comprising a sequence corresponding to or complementary to the target RNA sequence; and d) quantitatively detecting an amount of the amplified polynucleotide, wherein the amount of the amplified polynucleotide correlates with the amount of the target RNA, wherein the TSO is not immobilized in any step of the method. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20)
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Specification