Junction resolving enzymes use multivalency to keep the Holliday junction dynamic [PDF]
, 2019 Holliday junction (HJ) resolution by resolving enzymes is essential for chromosome segregation and recombination-mediated DNA repair. HJs undergo two types of structural dynamics that determine the outcome of recombination: conformer exchange between two
Cho, Yunje +8 more
core +2 more sources
High-Resolution smFRET in a Microfluidic Gas Exchange Platform [PDF]
Biophysical Journal, 2010 Single-molecule Forster Resonance Energy Transfer (smFRET) is a powerful technique providing new insights in the physics and chemistry of bio-molecules. The smFRET signal quality depends on the photon-flux that can be harvested from the fluorescent dyes.
Gambin, Yann +4 more
openaire +1 more source
Analyzing conformational changes in single FRET-labeled A1 parts of archaeal A1AO-ATP synthase
, 2018 ATP synthases utilize a proton motive force to synthesize ATP. In reverse, these membrane-embedded enzymes can also hydrolyze ATP to pump protons over the membrane.
Börsch, Michael +3 more
core +1 more source
Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET [PDF]
, 2016 Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their ...
Alexandrov, Y +11 more
core +1 more source
Graphical models for inferring single molecule dynamics
BMC Bioinformatics, 2010 Background The recent explosion of experimental techniques in single molecule biophysics has generated a variety of novel time series data requiring equally novel computational tools for analysis and inference. This article describes in general terms how
Gonzalez Ruben L +4 more
doaj +1 more source
Multi-parameter photon-by-photon hidden Markov modeling
Nature Communications, 2022 In this work, the authors demonstrate the application of multi-parameter photon-by-photon hidden Markov modeling (mpH2MM) on alternating laser excitation (ALEX)-based smFRET measurements.
Paul David Harris +5 more
doaj +1 more source
Single-Molecule Analysis of i-motif Within Self-Assembled DNA Duplexes and Nanocircles [PDF]
, 2019 The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif–forming sequences have shown increasing evidence of their roles in gene regulation.
Cox, Bobby D. +6 more
core +1 more source
Structural snapshots of Xer recombination reveal activation by synaptic complex remodeling and DNA bending [PDF]
, 2016 Bacterial Xer site-specific recombinases play an essential genome maintenance role by unlinking chromosome multimers, but their mechanism of action has remained structurally uncharacterized. Here, we present two high-resolution structures of Helicobacter
Adams +71 more
core +4 more sources
Advances in Double‐Stranded DNA Targeting Technologies
Exploration, EarlyView.Double‐stranded DNA (dsDNA) plays a crucial role in genetic information storage and disease management, but its inherent stability limits access to internal bases. To overcome this challenge, various high‐specificity molecular targeting technologies have been developed to destabilize the DNA structure.
Zuhao Shen +8 more
wiley +1 more source
Protein-Folding Studies using Hybrid TIRF SmFRET-Magnetic Tweezers [PDF]
Biophysical Journal, 2014 Optical tweezers are a useful research tool for applying forces to single proteins and measuring the resulting end-to-end extension increases that accompany unfolding and other force-induced conformational changes. They do, however, have a few limitations: they can only observe changes in extension along the axis of force application; the accompanying ...
Leachman, Samuel M. +3 more
openaire +1 more source