High-resolution AFM structure of DNA G-wires in aqueous solution

Nature Communications
Krishnashish BoseAnh Tuân Phan

Abstract

We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G4T2G4] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface. A minor species shows primarily left-handed periodic features of 2.2 nm. In addition to 4.3 and 2.2 nm ridges, background features with periodicity of 0.9 nm are also observed. Using molecular modeling and simulation, we identify a molecular structure that can explain both the periodicity and handedness of the major G-wire species. Our results demonstrate the potential structural diversity of G-wire formation and provide valuable insight into the structure of higher-order intermolecular G-quadruplexes. Our results also demonstrate how AFM can be combined with simulation to gain insight into biomolecular structure.

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Citations

Sep 15, 2020·Biomicrofluidics·Zhengcheng LuDayou Li
Apr 24, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Prabesh GyawaliHamza Balci
Aug 28, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Sofia Kolesnikova, Edward A Curtis
Jun 18, 2020·International Journal of Molecular Sciences·Chiara Reina, Vincenzo Cavalieri
Nov 22, 2019·Nature Communications·Vasantha BasavalingappaEhud Gazit
Jan 28, 2021·Nucleic Acids Research·Poulomi DasAnh Tuân Phan
Mar 21, 2021·NPJ Biofilms and Microbiomes·Thomas SeviourStaffan Kjelleberg
May 1, 2021·International Journal of Molecular Sciences·Melani PotrčLea Spindler
Jul 22, 2021·APL Bioengineering·Kavit H S MainAlice L B Pyne
Aug 23, 2019·ACS Chemical Biology·Sofia KolesnikovaEdward A Curtis
Jan 4, 2019·Chemical Reviews·Jean-Louis Mergny, Dipankar Sen
Aug 18, 2021·Nature Chemistry·Suhua LiK Barry Sharpless
Jul 20, 2019·Journal of the American Chemical Society·Pravin PathakJanarthanan Jayawickramarajah
Aug 31, 2021·RSC Chemical Biology·Jagannath JanaKlaus Weisz

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Methods Mentioned

BETA
atomic force microscopy
AFM
nuclear
circular dichroism
NMR
observed
scanning tunneling microscopy
in
PCR

Software Mentioned

Pymol
MATLAB
XPLOR
Gwyddion
Mathematica
FastScan
Amber
xleap
AFM

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