Rationally engineered nucleic acid architectures for biosensing applications

M Xiao, W Lai, T Man, B Chang, L Li… - Chemical …, 2019 - ACS Publications
Development of biosensing platforms plays a key role in research settings for identification
of biomarkers and in clinical applications for diagnostics. Biosensors based on nucleic acids …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

B Hellenkamp, S Schmid, O Doroshenko… - Nature …, 2018 - nature.com
Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to
determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However …

Identification of slow molecular order parameters for Markov model construction

G Pérez-Hernández, F Paul, T Giorgino… - The Journal of …, 2013 - pubs.aip.org
A goal in the kinetic characterization of a macromolecular system is the description of its
slow relaxation processes via (i) identification of the structural changes involved in these …

Markov models of molecular kinetics: Generation and validation

JH Prinz, H Wu, M Sarich, B Keller, M Senne… - The Journal of …, 2011 - pubs.aip.org
Markov state models of molecular kinetics (MSMs), in which the long-time statistical
dynamics of a molecule is approximated by a Markov chain on a discrete partition of …

Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging

T Ha, P Tinnefeld - Annual review of physical chemistry, 2012 - annualreviews.org
Single-molecule fluorescence spectroscopy and super-resolution microscopy are important
elements of the ongoing technical revolution to reveal biochemical and cellular processes in …

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

E Lerner, A Barth, J Hendrix, B Ambrose, V Birkedal… - Elife, 2021 - elifesciences.org
Single-molecule FRET (smFRET) has become a mainstream technique for studying
biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by …

Sequential requirements for distinct Polθ domains during theta-mediated end joining

C Fijen, LD Beckham, D Terino, Y Li, DA Ramsden… - Molecular Cell, 2024 - cell.com
DNA polymerase θ (Polθ) plays a central role in a DNA double-strand break repair pathway
termed theta-mediated end joining (TMEJ). TMEJ functions by pairing short-sequence" …

Alternating-laser excitation: single-molecule FRET and beyond

J Hohlbein, TD Craggs, T Cordes - Chemical Society Reviews, 2014 - pubs.rsc.org
The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of
fluorescence-based assays to study biological entities and interactions. Especially the …

Combining MFD and PIE for accurate single‐pair Förster resonance energy transfer measurements

V Kudryavtsev, M Sikor, S Kalinin… - …, 2012 - Wiley Online Library
Single‐pair Förster resonance energy transfer (spFRET) experiments using single‐molecule
burst analysis on a confocal microscope are an ideal tool to measure inter‐and …