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Fast detection of quadruplex structure in DNA by the intrinsic fluorescence of a single‐stranded DNA binding protein
Author(s) -
Zhuang Xinying,
Tang Jun,
Hao Yuhua,
Tan Zheng
Publication year - 2007
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.847
Subject(s) - dna , g quadruplex , quenching (fluorescence) , dna sequencing , fluorescence , guanine , biophysics , chemistry , computational biology , biology , biochemistry , microbiology and biotechnology , gene , nucleotide , physics , quantum mechanics
Single‐stranded guanine‐rich (G‐rich) DNA can fold into a four‐stranded G‐quadruplex structure and such structures are implicated in important biological processes and therapeutic applications. So far, bioinformatic analysis has identified up to several hundred thousand of putative quadruplex sequences in the genome of human and other animal. Given such a large number of sequences, a fast assay would be desired to experimentally verify the structure of these sequences. Here we describe a method that identifies the quadruplex structure by a single‐stranded DNA binding protein from a thermoautotrophic archaeon. This protein binds single‐stranded DNA in the unfolded, but not in the folded form. Upon binding to DNA, its fluorescence can be quenched by up to 70%. Formation of quadruplex greatly reduces fluorescence quenching in a K + ‐dependent manner. This structure‐dependent quenching provides simple and fast detection of quadruplex in DNA at low concentration without DNA labelling. Copyright © 2007 John Wiley & Sons, Ltd.