Single-molecule DNA flexibility in the presence of base-pair mismatch

Abstract

The conformational changes of a 22 base-pair double-stranded DNA, anchored via one end to a quartz substrate, have been characterized using a single-pair fluorescence resonance energy transfer technique. Base-pair mismatch, a major form of DNA damage, has been found to decrease the energy transfer between a fluorescence donor and an acceptor attached to the two ends of DNA molecules with 3 and 7 mismatches, by 4.4% and 10.4%, respectively, as compared to that for perfectly matched DNA. This result suggests that the disruption of the hydrogen bonds in damaged DNA leads to increased contour length and improved flexibility.

Nanofabrication for Molecular Scale Devices

“…The thermodynamical stability of the structure is based on the matching between compatible couples of bases, among four types (adenine, A, thymine T, guanine, G, and cytosine C). Stable links are A-T and C-G; each mismatch is a weak ring in the chain increasing the flexibility of the overall structure (Schallhorn et al, 2005) and decreasing its stability; couples of too mismatched (non-complementary) helices are expected not to bind at all. Since its discovery in the 1950s by Watson and Crick, the progress in DNA manipulation proceeded at astonishing speed: nowadays it is possible to design and synthesize single or double helices with relative simplicity to create even very complicated structures.…”

Impact of Single Basepair Mismatches on Electron‐Transfer Processes at Fc‐PNA⋅DNA Modified Gold Surfaces

“…Regarding the mechanical properties of nucleic acid duplexes with basepair mismatches it is reported, that a mismatch provokes an enlargement of the contour length l c of the strand as well as an enhancement of the mechanical bending elasticity of the strand compared to the fully complementary duplex (persistence length a of DNA·DNA: a = 50 nm). [13] Finally, single basepair mismatches are reported to interrupt the electron transport through a DNA duplex, as it is studied in the context of oxidative DNA damage provoked by free radicals. [14,15] Gold-surface grafted peptide nucleic acid (PNA) strands, which carry a redox-active ferrocene tag, present unique tools to electrochemically investigate their mechanical bending elasticity based on the kinetics of electron-transfer (ET) processes.…”

A kinetic analysis of strand breaks on large DNA induced by cigarette smoke extract

“…Thus DNA damage including DNA-nucleoprotein complexes has been widely studied with biochemical and biophysical approaches. For example, the structure of DNA in the nucleosome core [3], looped protein-DNA complexes [4,5], and DNA flexibility in the presence of base-pair mismatch [6] have been studied. Of course, DNA damage caused by cigarette smoke has been also studied for above reasons [7][8][9].…”