Biophysical characterization of DNA binding from single molecule force measurements

KR Chaurasiya, T Paramanathan, MJ McCauley… - Physics of life …, 2010 - Elsevier
Single molecule force spectroscopy is a powerful method that uses the mechanical
properties of DNA to explore DNA interactions. Here we describe how DNA stretching …

Ultrafast hole relaxation dynamics in quantum dots revealed by two-dimensional electronic spectroscopy

PJ Brosseau, JJ Geuchies, D Jasrasaria… - Communications …, 2023 - nature.com
Elucidating the population dynamics of correlated electron-hole pairs (bound excitons) in
semiconducting quantum dots (QDs) is key for developing our fundamental understanding of …

Mechanical identities of RNA and DNA double helices unveiled at the single-molecule level

E Herrero-Galán, ME Fuentes-Perez… - Journal of the …, 2013 - ACS Publications
Double-stranded (ds) RNA is the genetic material of a variety of viruses and has been
recently recognized as a relevant molecule in cells for its regulatory role. Despite that the …

Optical tweezers experiments resolve distinct modes of DNA‐protein binding

MJ McCauley, MC Williams - Biopolymers: Original Research …, 2009 - Wiley Online Library
Optical tweezers are ideally suited to perform force microscopy experiments that isolate a
single biomolecule, which then provides multiple binding sites for ligands. The captured …

Two distinct overstretched DNA states

H Fu, H Chen, JF Marko, J Yan - Nucleic acids research, 2010 - academic.oup.com
The DNA double helix undergoes an 'overstretching'transition in a narrow force range near
65 pN. Despite numerous studies the basic question of whether the strands are separated or …

[HTML][HTML] Geometric approach to nonequilibrium hasty shortcuts

SS Chittari, Z Lu - The Journal of Chemical Physics, 2023 - pubs.aip.org
Complex and even non-monotonic responses to external control can be found in many
thermodynamic systems. In such systems, nonequilibrium shortcuts can rapidly drive the …

Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching

H Fu, H Chen, X Zhang, Y Qu, JF Marko… - Nucleic acids …, 2011 - academic.oup.com
Recent studies have revealed two distinct pathways for the DNA overstretching transition
near 65 pN:'unpeeling'of one strand from the other, and a transition from B-DNA to an …

Coarse-grained simulations of DNA overstretching

F Romano, D Chakraborty, JPK Doye… - The Journal of …, 2013 - pubs.aip.org
We use a recently developed coarse-grained model to simulate the overstretching of duplex
DNA. Overstretching at 23 C occurs at 74 pN in the model, about 6–7 pN higher than the …

Overstretching DNA at 65 pN does not require peeling from free ends or nicks

DH Paik - Biophysical Journal, 2011 - cell.com
Oct4 and Sox2 are key transcription factors (TFs) essential for maintaining pluripotency as
well as the self-renewal ability of embryonic stem cells (ESC). Oct4 and Sox2 have been …

[HTML][HTML] DNA overstretching in the presence of glyoxal: structural evidence of force-induced DNA melting

L Shokri, MJ McCauley, I Rouzina, MC Williams - Biophysical journal, 2008 - cell.com
When a long DNA molecule is stretched beyond its B-form contour length, a transition occurs
in which its length increases by a factor of 1.7, with very little force increase. A quantitative …