A study of the interactions that stabilize DNA frayed wires

Biophysical Chemistry
Rashid M Abu-GhazalahR B Macgregor

Abstract

Oligodeoxyribonucleotides (ODNs) with long, terminal runs of consecutive guanines, and either a dA or dT tract at the other end form higher-order structures called DNA frayed wires. These aggregates self-assemble into species consisting of 2, 3, 4, 5, ... associated strands. Some of the remarkable features of these structures are their extreme thermostability and resistance to chemical denaturants and nucleases. However, the nature of the molecular interactions that stabilize these structures remains unclear. Based on dimethyl sulfate (DMS) methylation results, our group previously proposed DNA frayed wires to be a unique set of nucleic-acid assemblies in which the N7 of guanine does not participate in the guanine-guanine interactions. To probe the hydrogen bonding involved in the stabilization of d(A(15)G(15)) frayed wires, we used Raman spectroscopy in which the DNA sample is held in photonic crystal fibers. This technique significantly enhances the signals thus allowing the use of very low laser power. Based on our results for d(A(15)G(15)) and those of incorporating the isoelectronic guanine analog pyrazolo[3,4,-d]pyrimidine or PPG, into a frayed wire-forming sequence, we provide evidence that these structures are based on ...Continue Reading

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Citations

Nov 20, 2015·Journal of Chemical Theory and Computation·Yevgen P YurenkoRadek Marek
Jan 18, 2014·Methods : a Companion to Methods in Enzymology·Jun ZhouJean Louis Mergny
Aug 31, 2012·Biochemistry·Rashid M Abu-GhazalahAmr S Helmy
Sep 21, 2013·Biochemistry·Katarína TlučkováViktor Viglasky
Jan 4, 2019·Chemical Reviews·Jean-Louis Mergny, Dipankar Sen

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