Premium
Conformations of DNA strands containing GAGT, GACA, or GAGC tetranucleotide repeats
Author(s) -
Kypr Jaroslav,
Kejnovská Iva,
Vorlíčková Michaela
Publication year - 2007
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20822
Subject(s) - chemistry , duplex (building) , aqueous solution , protonation , dna , ionic strength , cytosine , ionic bonding , stereochemistry , crystallography , biochemistry , ion , organic chemistry
The (GA) n microsatellite has been known from previous studies to adopt unusual, ordered, cooperatively melting secondary structures in neutral aqueous solutions containing physiological concentrations of salts, at acid pH values or in aqueous ethanol solutions. To find more about the primary structure specificity of these structures, we performed parallel comparative studies of related tetranucleotide repeats (GAGC) 5 , (GAGT) 5 , and (GACA) 5 . The general conclusion following from these comparative studies is that the primary structure specificity is fairly high, indicating that not only guanines but also adenines play a significant role in the stabilization of these unusual structures. (GAGC) 5 is a hairpin or a duplex depending on DNA concentration. Neither acid pH nor ionic strength or the presence of ethanol changed the secondary structure of (GAGC) 5 in a significant way. (GACA) 5 forms a weakly stable hairpin in neutral aqueous solutions but forms a duplex at acid pH where cytosine is protonated. (GAGT) 5 behaves most similar to (GAGA) 5 . Salt induces its hairpin to duplex transition at neutral pH and an isomerization into another, probably parallel stranded, duplex takes place at acid pH. (GAGT) 5 is the only of the three present 20‐mers that responds to ethanol like (GAGA) 5 . © 2007 Wiley Periodicals, Inc. Biopolymers 87: 218–224, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com