Effect of loop distortion on the stability and structural dynamics of DNA hairpin and dumbbell conjugates

The Journal of Physical Chemistry. B
Martin McCullaghFrederick D Lewis

Abstract

The thermal stability and conformational dynamics of DNA hairpin and dumbbell conjugates having short A-tract base pair domains connected by tri- or hexa(ethylene glycol) linkers is reported. The formation of stable base-paired A-tract hairpins having oligo(ethylene glycol) linkers requires a minimum of four or five A-T base pairs. The formation of base-paired dumbbells having oligo(ethylene glycol) linkers by means of chemical ligation of nicked dumbbells requires a minimum of two A-T base pairs on either side of the nick. Molecular modeling indicates that the hexa(ethylene glycol) linker is sufficiently long to permit formation of strain-free loop regions and B-DNA base pair domains. In contrast, the tri(ethylene glycol) is too short to permit Watson-Crick base pairing between the bases attached to the linker. The shorter linker distorts the duplex, resulting in fluxional behavior in which the base pairs adjacent to the linker and at the open end of the hairpin dissociate on the nanosecond time scale. The loss of interstrand binding energy caused by these fluctuations leads to a difference of approximately 5 degrees C in melting temperature between EG3 and EG6 hairpins. An analysis of the fluxional behavior of the EG3 adjacen...Continue Reading

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Citations

Jul 11, 2013·Journal of the American Chemical Society·Jinquan ChenBern Kohler
Dec 2, 2009·Journal of the American Chemical Society·Sabrina LusvarghiBruce A Armitage
May 1, 2010·Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology·Tarek A ZeidanFrederick D Lewis
Jun 6, 2013·Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society for Photobiology·Johanna BrazardDimitra Markovitsi
Jan 24, 2009·Proceedings of the National Academy of Sciences of the United States of America·Alexander L BurinFrederick D Lewis
Apr 29, 2011·The Journal of Biological Chemistry·Vladimir MeklerKonstantin Severinov
Sep 2, 2016·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·David J SkowronBern Kohler
Mar 2, 2016·Chemistry : a European Journal·Ignacio VayáDimitra Markovitsi
Mar 31, 2015·Journal of the American Chemical Society·Ryan M YoungMichael R Wasielewski
Feb 24, 2011·Journal of the American Chemical Society·Martin McCullaghGeorge C Schatz

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