Physics of base-pairing dynamics in DNA

M Manghi, N Destainville - Physics Reports, 2016 - Elsevier
As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of
investigations with the help of biological, chemical and physical techniques. From a physical …

What do we know about DNA mechanics so far?

A Aggarwal, S Naskar, AK Sahoo… - Current opinion in …, 2020 - Elsevier
Highlights•DNA molecules are often bent, twisted, and stretched.•DNA mechanics has been
studied using many theoretical models.•DNA mechanics crucially depends on physiological …

High flexibility of DNA on short length scales probed by atomic force microscopy

PA Wiggins, T Van Der Heijden… - Nature …, 2006 - nature.com
The mechanics of DNA bending on intermediate length scales (5–100 nm) plays a key role
in many cellular processes, and is also important in the fabrication of artificial DNA …

Generalized theory of semiflexible polymers

PA Wiggins, PC Nelson - Physical Review E—Statistical, Nonlinear, and Soft …, 2006 - APS
DNA bending on length scales shorter than a persistence length plays an integral role in the
translation of genetic information from DNA to cellular function. Quantitative experimental …

Statistics of loop formation along double helix DNAs

J Yan, R Kawamura, JF Marko - Physical Review E—Statistical, Nonlinear, and …, 2005 - APS
We compute relative position distributions of distant sites along discretized semiflexible
polymers, focusing on encounter statistics for pairs of sites along a double-stranded DNA …

Probing the elastic limit of DNA bending

TT Le, HD Kim - Nucleic acids research, 2014 - academic.oup.com
Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome
structure and function. However, the elastic limit of dsDNA bending remains controversial …

Mechanical properties of DNA and DNA nanostructures: Comparison of atomistic, Martini and oxDNA models

S Naskar, PK Maiti - Journal of Materials Chemistry B, 2021 - pubs.rsc.org
The flexibility and stiffness of small DNA molecules play a fundamental role ranging from
several biophysical processes to nano-technological applications. Here, we estimate the …

DNA elasticity from short DNA to nucleosomal DNA

A Garai, S Saurabh, Y Lansac… - The journal of physical …, 2015 - ACS Publications
Active biological processes like transcription, replication, recombination, DNA repair, and
DNA packaging encounter bent DNA. Machineries associated with these processes interact …

DNA flexibility on short length scales probed by atomic force microscopy

AK Mazur, M Maaloum - Physical review letters, 2014 - APS
Unusually high bending flexibility has been recently reported for DNA on short length scales.
We use atomic force microscopy (AFM) in solution to obtain a direct estimate of DNA …

End-to-end distance vector distribution with fixed end orientations for the wormlike chain model

AJ Spakowitz, ZG Wang - Physical Review E—Statistical, Nonlinear, and Soft …, 2005 - APS
We find exact expressions for the end-to-end distance vector distribution function with fixed
end orientations for the wormlike chain model. This function in Fourier-Laplace space …