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High fidelity reverse transcriptases and uses thereof

a reverse transcriptase, high-fidelity technology, applied in the field of molecular and cellular biology, can solve the problems of low fidelity of rts, inability to copy rna templates, inefficient use of unmodified rts to catalyze reverse transcription, etc., and achieve high fidelity

Inactive Publication Date: 2006-05-04
LIFE TECH CORP
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0012] The present invention provides reverse transcriptase enzymes, compositions comprising such enzymes and methods useful in overcoming the efficiency limitations of reverse transcription. In general, the invention provides compositions for use in high fidelity reverse transcription of a nucleic acid m

Problems solved by technology

However, the use of unmodified RT to catalyze reverse transcription is inefficient for at least two reasons.
First, RT sometimes renders an RNA template unable to be copied before reverse transcription is initiated or completed, primarily due to the intrinsic RNase H activity present in RT.
Second, RTs generally have low fidelity.
That is, RTs incorporate mismatched bases during cDNA synthesis thus producing cDNA products having sequence errors.
However such RTs (“RNase H-” forms) do not address the second problem of improving the fidelity of reverse transcription.

Method used

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  • High fidelity reverse transcriptases and uses thereof
  • High fidelity reverse transcriptases and uses thereof
  • High fidelity reverse transcriptases and uses thereof

Examples

Experimental program
Comparison scheme
Effect test

example 1

Mutation Frequency of M-MLV High Fidelity Mutants

[0144] Mutation frequency Data and Calculation of Error Rates. Mutation frequency (MF) is determined by dividing the number of mutant plaques (light blue or white) by the total number of plaques and then subtracting the background mutation frequency of the starting DNA.

[0145] All mutant reverse transcriptases tested also contained the point mutations to remove RNase H activity, as in SuperScript II (SS II, U.S. Pat. Nos. 5,244,797; 5,405,776; 5,668,005 and 6,063,608). Point mutations were made in the M-MLV RT gene to remove RNase H activity. The point mutations include D524G, D583N, and E562Q. Briefly, the RT gene from pRT601 was inserted into a pUC plasmid and then the above point mutations were made in the RNase H domain of the RT gene. pRT601 is described in U.S. Pat. Nos. 5,244,797; 5,405,776; 5,668,005 and 6,063,608 and was deposited at the ATCC under Accession No. 67007 (See U.S. Pat. No. 5,017,492). This RNase H— mutant is re...

example 2

Misinsertion Assays with DNA Template

[0147] Misinsertion assay of Y64W, R116M, K152R, Q190F, T197A, V223H M-MLV RNase H− RT with DNA template. This assay was employed to compare the misincorporation capability of the mutants to Superscript II (M-MLV RNase H− RT). The assay is a primer extension assay using synthetic DNA template-primer and biased dNTP pools containing only three of the four dNTPs. The reactions are displayed on a gel in FIGS. 1-3. In this assay, higher efficiency of primer extension in the absence of one dNTP denotes lower fidelity. As shown in FIGS. 1-3, in the presence of all 4 dNTPs, SuperScript II and all the selected mutants were able to extend the primer approximately equally, with some variance in the addition of non-template nucleotides at the end of the primer. However when incubated with biased pools of nucleotides, SS II was able to catalyze substantial extension past template nucleotides for which a complementary dNTP was missing, indicating use of inco...

example 3

TdT Reverse Transcriptase Mutants

[0148] In checking fidelity mutants of reverse transcriptase (RT) for misextension in a 3 dNTP assay, it was observed that SS II RT extended 2-3 bases past the end of the template in the presence of 3 and 4 dNTPs. This non-template directed extension or TdT activity is reduced in many mutants, but in a few such as F309N and T197E it appears that this activity is severely reduced or eliminated. These mutants are probably in close proximity or in contact with the template-primer as determined by homology to HIV reverse transcriptase and its crystal structure with bound template-primer.

Methods

Mutagenesis

[0149] For F309N:

[0150] Primers were designed corresponding to the mutant position F309 with the silent insertion of a NgoMIV restriction site at amino acid positions 310-311. The primers encoded a random NNK sequence for this position generating a random library of F309 mutants, where N is any of the four bases and K is T or G. The primers along w...

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Abstract

The invention relates to reverse transcriptases which have increased fidelity (or reduced misincorporation rate) and / or terminal deoxynucleotidyl transferase activity. In particular, the invention relates to a method of making such reverse transcriptases by modifying or mutating specified positions in the reverse transcriptases. The invention also relates to nucleic acid molecules containing the genes encoding the reverse trancriptases of the invention, to host cells containing such nucleic acid molecules and to methods to make the reverse trancriptases using the host cells. The reverse transcriptases of the invention are particularly suited for nucleic acid synthesis, sequencing, amplification and cDNA synthesis.

Description

CROSS REFERENCE TO RELATED APPLICATIONS [0001] The present application is a continuation of, and claims priority under 35 U.S.C. § 120 to, U.S. application Ser. No. 09 / 808,124, filed Mar. 15, 2001, which claims the benefit of U.S. Provisional Application No. 60 / 189,454, filed Mar. 15, 2000, the contents of each of which are incorporated by reference herein in their entireties.FIELD OF THE INVENTION [0002] The present invention is in the fields of molecular and cellular biology. The invention is generally related to reverse transcriptase enzymes and methods for the reverse transcription of nucleic acid molecules, especially messenger RNA molecules. Specifically, the invention relates to reverse transcriptase enzymes which have been mutated or modified to increase fidelity, and / or decrease terminal deoxynucleotidyl transferase activity, and to methods of producing, amplifying or sequencing nucleic acid molecules (particularly cDNA molecules) using these reverse transcriptase enzymes o...

Claims

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Application Information

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IPC IPC(8): C12Q1/68C12N9/22C12N15/09C12N1/15C12N1/19C12N1/21C12N5/10C12N9/12
CPCC12N9/1276C12Q2521/107
Inventor POTTER, ROBERTROSENTHAL, KIM
Owner LIFE TECH CORP
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