Detection of single-base mutation in RNA using T4 RNA ligase-based nick-joining or DNAzyme-based nick-generation

Kkothanahreum Park; Bo-Ra Choi; Yea Seul Kim; Seonmi Shin; Sang Soo Hah; Woong Jung; Sangtaek Oh; Dong-Eun Kim

doi:10.1016/j.ab.2011.03.028

Detection of single-base mutation in RNA using T4 RNA ligase-based nick-joining or DNAzyme-based nick-generation

Anal Biochem. 2011 Jul 15;414(2):303-5. doi: 10.1016/j.ab.2011.03.028. Epub 2011 Mar 29.

Authors

Kkothanahreum Park¹, Bo-Ra Choi, Yea Seul Kim, Seonmi Shin, Sang Soo Hah, Woong Jung, Sangtaek Oh, Dong-Eun Kim

Affiliation

¹ Department of Bioscience and Biotechnology, and WCU and BRL Program, Konkuk University, Seoul, Republic of Korea.

PMID: 21453671
DOI: 10.1016/j.ab.2011.03.028

Abstract

A single nucleotide polymorphism (SNP) is a common genetic variation when a single nucleotide differs between members of a species or paired chromosome. Due to its association with disease susceptibility and drug resistance, SNP detection is of great value in studying the variation in drug responses. Here we present two quantitative SNP detection methods for a single-base mismatch in RNA, based on nick-joining and nick-generating activities of T4 RNA ligase and DNAzyme, respectively. T4 RNA ligase successfully discriminated a one-base mismatch in the ligation junction, and the designed DNAzyme cleaved RNA by discerning a single-base mismatch in the cleaving site.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Pair Mismatch*
DNA, Catalytic / metabolism*
Electrophoresis, Agar Gel / methods
Molecular Probe Techniques*
Oligonucleotide Probes / chemistry
Polymorphism, Single Nucleotide
RNA / chemistry*
RNA Ligase (ATP) / metabolism*
Viral Proteins / metabolism*

Substances

DNA, Catalytic
Oligonucleotide Probes
Viral Proteins
RNA
RNA Ligase (ATP)
bacteriophage T4 RNA ligase 2