Searching genomes for sequences with the potential to form intrastrand triple helices

被引:29
作者
Hoyne, PR [1 ]
Edwards, LM
Viari, A
Maher, LJ
机构
[1] Mayo Clin & Mayo Fdn, Dept Biochem & Mol Biol, Rochester, MN 55905 USA
[2] Rochester Mayo High Sch, Rochester, MN USA
[3] INRIA Rhone Alpes, Projet HELIX, F-38330 St Martin Dheres, France
关键词
intrastrand triplexes; Palingol; box C; Escherichia coli; repetitive element;
D O I
10.1006/jmbi.2000.4502
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The canonical double-helix form of DNA is thought to predominate both in dilute solution and in living cells. Sequence-dependent fluctuations in local DNA shape occur within the double helix. Besides these relatively modest variations in shape, more extreme and remarkable structures have been detected in which some bases become unpaired. Examples include unusual three-stranded structures such as H-DNA. Certain RNA and DNA strands can also fold onto themselves to form intrastrand triplexes. Although they have been extensively studied in vitro, it remains unknown whether nucleic acid triplexes play natural roles in cells. If natural nucleic acid triplexes were identified in cells, much could be learned by examining the formation, stabilization, and function of such structures. With these goals in mind, we adapted a pattern-recognition program to search genetic databases for a type of potential tripler structure whose presence in genomes has not been previously investigated. We term these sequences Potential Intrastrand Tripler (PIT) elements. The formation of an intrastrand tripler requires three consecutive sequence domains with appropriate symmetry along a single nucleic acid strand. It is remarkable that we discovered multiple copies of sequence elements with the potential to form one particular class of intrastrand triplexes in the fully sequenced genomes of several bacteria. We then focused on the characterization of the 25 copies of a particular similar to 37 nt PIT sequence detected in Escherichia coli. Through biochemical studies, we demonstrate that an isolated DNA strand from this family of E. coli PIT elements forms a stable intrastrand tripler at physiological temperature and pH in the presence of physiological concentrations of Mg2+ (C) 2000 Academic Press.
引用
收藏
页码:797 / 809
页数:13
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