Molecular cloning of RNA using RNA ligase and synthetic oligonucleotides
First Claim
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1. A method for the insertion of a single-stranded RNA sequence into a cloning vector, comprising:
- annealing both termini of the single-stranded RNA sequence with a linear double-stranded cloning vector having single-stranded termini complementary to both termini of the single-stranded RNA sequence to form an annealed product, in which the complementary termini of the single-stranded RNA sequence where formed by attaching oligonucleotide linkers to the RNA sequence by means of an RNA ligase.
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Abstract
Methods and compositions for the insertion and molecular cloning of RNA in DNA cloning vectors are described. RNA molecules to be cloned are modified by the ligation of oligonucleotide linkers onto the termini of the RNA molecule using T4 RNA ligase. Such linkers may be composed of DNA, RNA, or mixtures of each and facilitate the insertion and ligation of the RNA species into a DNA cloning vector. The resulting recombinant vectors are used to transform host cells which provide for the generation of multiple DNA copies of the RNA molecule.
123 Citations
39 Claims
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1. A method for the insertion of a single-stranded RNA sequence into a cloning vector, comprising:
- annealing both termini of the single-stranded RNA sequence with a linear double-stranded cloning vector having single-stranded termini complementary to both termini of the single-stranded RNA sequence to form an annealed product, in which the complementary termini of the single-stranded RNA sequence where formed by attaching oligonucleotide linkers to the RNA sequence by means of an RNA ligase.
- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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16. A method for cloning an RNA sequence, comprising:
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(a) inserting the single-stranded RNA sequence into a cloning vector by annealing both termini of the single-stranded RNA sequence with a linear double-stranded cloning vector having single-stranded termini complementary to both termini of the single-stranded RNA sequence to form an annealed product, in which the complementary termini of the single-stranded RNA sequence were formed by attaching oligonucleotide linkers to the RNA sequence by means of an RNA ligase; (b) converting the RNA sequence to a cDNA/RNA hybrid to form a recombinant molecule; (c) introducing the recombinant molecule containing the cDNA/RNA hybrid into a compatible unicellular organism capable of replicating the recombinant molecule to form transformants; and (d) growing the transformants under appropriate nutrient conditions.
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17. A method for the insertion of a single-stranded RNA sequence into a cloning vector, comprising:
- annealing the single-stranded RNA sequence with a linear double-stranded cloning vector having a 5'"'"'-single-stranded terminus complementary to the 5'"'"'-terminus of the single-stranded RNA sequence to form an annealed product, in which the 5'"'"'-complementary terminus of the single-stranded RNA sequence was formed by attaching an oligonucleotide linker to the single-stranded RNA sequence by means of an RNA ligase.
- View Dependent Claims (18, 19, 20, 21, 22, 23)
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24. A method for cloning an RNA sequence, comprising:
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(a) inserting the single-stranded RNA sequence into a cloning vector by annealing the single-stranded RNA sequence with the linear double-stranded cloning vector having a 5'"'"'-single-stranded terminus complementary to the 5'"'"'-terminus of the single-stranded RNA sequence to form an annealed product; (b) forming a covalent bond between the 3'"'"'-terminus of the single-stranded RNA sequence and the cloning vector by means of an RNA ligase, to form a recombinant molecule; (c) converting the RNA sequence of the recombinant molecule to a cDNA/RNA hybrid to form a double-stranded recombinant molecule; (d) introducing the double-stranded recombinant molecule containing the cDNA/RNA hybrid into a compatible unicellular organism capable of replicating the recombinant molecule to form transformants; and (e) growing the transformants under appropriate nutrient conditions.
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25. A method for the insertion of a single-stranded RNA sequence into a cloning vector, comprising:
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(a) annealing the 3'"'"'-terminus of the single-stranded RNA sequence with a linear double-stranded cloning vector having a first 3'"'"'-single-stranded terminus complementary to the 3'"'"'-terminus of the single-stranded RNA sequence and a second 3'"'"'-single-stranded terminus composed of RNA; and (b) forming a covalent bond between the 5'"'"'-terminus of the single-stranded RNA sequence and the second 3'"'"'-terminus of the cloning vector by means of an RNA ligase. - View Dependent Claims (26, 27, 28, 29, 30)
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31. A method for cloning an RNA sequence comprising:
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(a) inserting the single-stranded RNA sequence into a cloning vector by annealing the single-stranded RNA sequence with the cloning vector having a first 3'"'"'-single-stranded terminus complementary to the 3'"'"'-terminus of the single-stranded RNA sequence, and a second 3'"'"'-single-stranded terminus composed of RNA to form an annealed product; (b) forming a covalent bond between the 5'"'"'-terminus of the single-stranded RNA sequence and the second 3'"'"'-terminus of the cloning vector by means of an RNA ligase to form a recombinant molecule; (c) converting the RNA sequence of the recombinant molecule to a cDNA/RNA hybrid to form a double-stranded recombinant molecule; (d) introducing the double-stranded recombinant molecule containing the cDNA/RNA hybrid into a compatible unicellular organism capable of replicating the recombinant molecule to form transformants; and (e) growing the transformants under appropriate nutrient conditions.
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32. A method for the insertion of a single-stranded RNA sequence into a cloning vector, comprising:
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(a) circularizing the RNA sequence by means of an enzyme capable of ligating RNA; (b) synthesizing a cDNA strand which is complementary to the circularized RNA sequence to form a CDNA/RNA circular hybrid molecule; (c) ligating the cDNA strand and removing the RNA portion of the circular hybrid molecule; (d) syntesizing a second DNA strand which is complementary to the cDNA strand to form a circular double-stranded DNA molecule; (e) cleaving the circular double-stranded DNA molecule by means of a restriction endonuclease capable of cleaving said circular DNA to produce a linear double-stranded DNA molecule having single-stranded termini; and (f) annealing the linear double-stranded DNA molecule with a linear double-stranded cloning vector having complementary single-stranded termini to form an annealed product. - View Dependent Claims (33, 34)
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35. A method for cloning an RNA sequence, comprising:
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(a) circularizing the RNA sequence by means of an enzyme capable of ligating RNA; (b) synthesizing a cDNA strand which is complementary to the circularized RNA sequence to form a cDNA/RNA circular hybrid molecule; (c) ligating the cDNA strand and removing the RNA portion of the circular hybrid molecule; (d) synthesizing a second strand of DNA which is complementary to the cDNA strand to form a circular double-stranded DNA molecule; (e) cleaving the circular double-stranded DNA molecule by means of a restriction-endonuclease capable of cleaving said circular DNA to produce a linear double-stranded molecule having single-stranded termini; (f) annealing the linear double-stranded DNA molecule with a linear double-stranded cloning vector having complementary single-stranded termini to form an annealed product; (g) forming a covalent 3'"'"'-5'"'"'phosphodiester bond between the double-stranded DNA molecule and the double-stranded cloning vector to form a recombinant molecule; (h) introducing the recombinant molecule into a compatible unicellular organism capable of replicating the recombinant molecule to form transformants; and (i) growing said transformants under appropriate nutrient conditions.
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36. A method for the insertion of a single-stranded RNA sequence into a cloning vector, comprising:
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(a) attaching to said RNA sequence an oligonucleotide linker by means of an enzyme capable of ligating RNA to form an RNA-linker product, wherein said linker contains a deoxyribonucleotide sequence encoding a restriction endonuclease recognition site and a 3'"'"'-terminal ribonucleotide; (b) circularizing the RNA-linker product by means of an enzyme capable of ligating RNA; (c) synthesizing a cDNA strand which is complementary to the circularized RNA sequence to form a cDNA/RNA circular hybrid molecule containing a duplex DNA site that encodes a restriction enzyme recognition site; (d) cleaving the circular hybrid molecule at said duplex DNA site by means of a restriction endonuclease capable of cleaving said duplex DNA site to form a linear hybrid molecule having single-stranded termini; and (e) annealing the linear hybrid molecule with a linear double-stranded cloning vector having complementary termini to form an annealed product. - View Dependent Claims (37, 38)
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39. A method for cloning an RNA sequence, comprising:
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(a) attaching to said RNA sequence an oligonucleotide linker by means of an enzyme capable of ligating RNA to form an RNA-linker product, wherein said linker contains a deoxyribonucleotide sequence encoding a restriction endonuclease recognition site and a 3'"'"'-terminal ribonucleotide; (b) circularizing the RNA-linker product by means of an enzyme capable of ligating RNA; (c) synthesizing a cDNA strand which is complementary to the circularized RNA sequence to form a cDNA/RNA circular hybrid molecule containing a duplex DNA site that encodes a restriction enzyme recognition site; (d) cleaving the circular hybrid molecule at said duplex DNA site by means of a restriction endonuclease capable of cleaving said duplex DNA site to form a linear hybrid molecule having single-stranded termini; (e) annealing the linear hybrid molecule with a linear double-stranded cloning vector having complementary single-stranded termini to form an annealed product; (f) forming a covalent 3'"'"'-5'"'"'phosphodiester bond between the hybrid molecule and the double-stranded cloning vector to form a recombinant molecule; (g) introducing the recombinant molecule into a compatible unicellular organism capable of replicating the recombinant molecule to form transformants; and (h) growing said transformants under IIIIIIappropriate nutrient conditions.
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Specification