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Studies on the Extension of Sequence‐independence and the Enhancement of DNA Triplex Formation
Author(s) -
Wei MingTsai,
Walter Axel,
Gabrielian Anna,
Schütz Holger,
BirchHirschfeld Eckhard,
Lin ShwuBin,
Lin WeiChen,
Fritzsche Hartmut,
Kan LouSing
Publication year - 2005
Publication title -
journal of the chinese chemical society
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.329
H-Index - 45
eISSN - 2192-6549
pISSN - 0009-4536
DOI - 10.1002/jccs.200500056
Subject(s) - chemistry , triple helix , dna , duplex (building) , recombination , base pair , pyrimidine , crystallography , cytidine , stereochemistry , d loop , oligonucleotide , biochemistry , gene , enzyme , mitochondrial dna
A more elaborate sequence‐independent triple‐helix formation viability study was carried out and extended from a recombination‐like triple‐helical DNA motif of a previous study (J. Mol. Recognition 14, 122–139 (2001)). The intended triple‐helix was formed by mixing one part of a DNA hairpin duplex and one part of a single (or third) strand identical to one of the duplex strands and complementary to the other strand. In contrast to the common purine and pyrimidine motifs in triple‐stranded DNA, the strands of the recombination‐like motif are not monotonously built from pyrimidine only, or purine only, in the sequence. The stability of the recombination‐like motif triplexes with varying sequences was monitored by UV thermal melting curves. The results showed that the order of the stability of the R‐form DNA base triads (J. Mol. Biol., 239, 181–200 (1994)) is G*(G ○ C) > C*(C ○ G) > A*(A ○ T) >T*(T ○ A) (the Watson‐Crick base pair is denoted in the parentheses) in 200 mM NaCl, at pH 7. In an attempt to increase the stability of the triplex in the recombination‐like motif, we replaced cytidine by 5‐methylcytidine ( m C) of the third strand. There is a general trend that m C modification stabilizes the complex (<2 °C per m C). The complex is furthermore stabilized by Mg 2+ ion. The Tm increases from 7 to 2 °C from less stable to highly stable triplex by 20 mM Mg 2+ ion in solution.