Kinetics and dynamics of DNA hybridization

Y Yin, XS Zhao - Accounts of chemical research, 2011 - ACS Publications
DNA hybridization, wherein strands of DNA form duplex or larger hybrids through
noncovalent, sequence-specific interactions, is one of the most fundamental processes in …

A highly fluorescent nucleobase molecular rotor

A Karimi, R Börner, G Mata… - Journal of the American …, 2020 - ACS Publications
Fluorescent base analogs (FBAs) are powerful probes of nucleic acids' structures and
dynamics. However, previously reported FBAs exhibit relatively low brightness and therefore …

Electrochemical aptamer-based biosensors for measurements in undiluted human saliva

MD Nguyen, KN Nguyen, S Malo, I Banerjee, D Wu… - ACS …, 2023 - ACS Publications
Although blood remains a gold standard diagnostic fluid for most health exams, it involves
an unpleasant and relatively invasive sampling procedure (finger pricking or venous draw) …

Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations

A Soranno, A Holla, F Dingfelder, D Nettels… - Biophysical …, 2017 - cell.com
The dynamics of proteins, which are essential for both folding and function, are known to be
strongly dependent on solvent viscosity or friction. However, an increasing number of …

Non-Markovian polymer reaction kinetics

T Guérin, O Bénichou, R Voituriez - Nature chemistry, 2012 - nature.com
Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in
nucleic acids or polypeptides, is complicated by the structural dynamics of their chains …

Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models

RR Cheng, AT Hawk, DE Makarov - The Journal of Chemical Physics, 2013 - pubs.aip.org
Recent experiments showed that the reconfiguration dynamics of unfolded proteins are often
adequately described by simple polymer models. In particular, the Rouse model with …

Chain dynamics limit electron transfer from electrode-bound, single-stranded oligonucleotides

P Dauphin-Ducharme, N Arroyo-Currás… - The Journal of …, 2018 - ACS Publications
A wide range of new devices aimed at in vivo molecular detection and point-of-care
diagnostics rely on binding-induced changes in electron-transfer kinetics from an electrode …

A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs

T Uzawa, RR Cheng, RJ White… - Journal of the …, 2010 - ACS Publications
Electrode-bound, redox-reporter-modified oligonucleotides play roles in the functioning of a
number of electrochemical biosensors, and thus the question of electron transfer through or …

2‐Aminopurine Fluorescence Spectroscopy for Probing a Glucose Binding Aptamer

C Lu, PJ Jimmy Huang, J Zheng, J Liu - ChemBioChem, 2022 - Wiley Online Library
Glucose is the most important analyte for biosensors. Recently a DNA aptamer was reported
allowing binding‐based detection. However, due to a relatively weak binding affinity, it is …

Interplay of non-Markov and internal friction effects in the barrier crossing kinetics of biopolymers: Insights from an analytically solvable model

DE Makarov - The Journal of chemical physics, 2013 - pubs.aip.org
Conformational rearrangements in biomolecules (such as protein folding or enzyme-ligand
binding) are often interpreted in terms of low-dimensional models of barrier crossing such as …