Hairpin structures in synthetic oligodeoxynucleotides: sequence effects on the duplex-to-hairpin transition

Biochimie
L E XodoJ H van Boom

Abstract

We have synthesized and examined a number of fully and partly self-complementary palindromic oligodeoxynucleotides for their ability to assume in solution a unimolecular hairpin structure. The main results obtained by a combined optical and electrophoresis investigation show that: (i) DNA folding needs not be driven by mismatched base pairings over the dyad; fully self-complementary palindromic duplexes, comprising regular (CG)n DNA fragments, possess a considerable intrinsic propensity to make intramolecular base pairings; (ii) The duplex-hairpin interconversion is, in general, a slow process independent of the length and base composition of the palindrome; (iii) The palindromic sequences energetically least favored to form hairpin structures consist of C:G base pairs around the dyad axis and of T:A blocks in the arms of the inverted repeat; (IV) The base composition of the stem strongly influences the hairpin thermal stability. For instance, the substitution of one C:G with one A:T base pair in the stem helix of d(CG)7 diminishes the stability of the hairpin by 9 degrees C. It is found that the stability of the stem helix, in hairpins of defined sequence and with the same loop length, decreases in the order alternating-CG gre...Continue Reading

References

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Citations

Aug 1, 1996·Journal of Biomolecular Structure & Dynamics·E R KandimallaS Agrawal
Oct 11, 1995·Nucleic Acids Research·A Amir-AslaniS Fermandjian
Nov 20, 2001·Nucleic Acids Research·P Fojtík, M Vorlícková
Apr 28, 2011·Organic & Biomolecular Chemistry·Niels BomholtErik B Pedersen
Jun 12, 2012·Biochimica Et Biophysica Acta·Jeu-Ming P YuannMing-Hon Hou
Oct 1, 2021·Chemical Reviews·Eric LargyValérie Gabelica

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