Oligo(dT) Primer Generates a High Frequency of Truncated CDNAs Through Internal Poly(A) Priming During Reverse Transcription

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2002 Apr 25

PMID 11972056

Citations 90

Authors

Douglas Kyung Nam

Sanggyu Lee

Guolin Zhou

Xiaohong Cao

Clarence Wang

Terry Clark

Jianjun Chen

Janet D Rowley

San Ming Wang

Affiliations

Soon will be listed here.

Abstract

We have analyzed a systematic flaw in the current system of gene identification: the oligo(dT) primer widely used for cDNA synthesis generates a high frequency of truncated cDNAs through internal poly(A) priming. Such truncated cDNAs may contribute to 12% of the expressed sequence tags in the current dbEST database. By using a synthetic transcript and real mRNA templates as models, we characterized the patterns of internal poly(A) priming by oligo(dT) primer. We further demonstrated that the internal poly(A) priming can be effectively diminished by replacing the oligo(dT) primer with a set of anchored oligo(dT) primers for reverse transcription. Our study indicates that cDNAs designed for genomewide gene identification should be synthesized by use of the anchored oligo(dT) primers, rather than the oligo(dT) primers, to diminish the generation of truncated cDNAs caused by internal poly(A) priming.

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