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| Open AccessSingle-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model
Multiple models have been proposed for how diffusion is regulated to shape morphogen gradients. Here they use single molecule tracking of an activator-inhibitor signaling pair in a developing tissue to show how effective diffusivity is modulated in the extracellular space.
- Timo Kuhn
- , Amit N. Landge
- & J. Christof M. Gebhardt
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Article
| Open AccessSearch and processing of Holliday junctions within long DNA by junction-resolving enzymes
Locating a four-way junction in a high background of genomic DNA is likely to be the rate-limiting step of the resolution process. This study captures the entire reaction trajectory of a nuclease targeting and resolving a DNA junction at single-molecule level.
- Artur P. Kaczmarczyk
- , Anne-Cécile Déclais
- & David S. Rueda
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Article
| Open AccessMutS functions as a clamp loader by positioning MutL on the DNA during mismatch repair
MutS and MutL homologs are thought to form a stable complex to execute mismatch repair. This work shows that E. coli MutS only acts as a mismatch-dependent clamp-loader that assembles the MutL sliding clamp.
- Xiao-Wen Yang
- , Xiao-Peng Han
- & Jiaquan Liu
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Article
| Open AccessFtsN maintains active septal cell wall synthesis by forming a processive complex with the septum-specific peptidoglycan synthases in E. coli
FtsN promotes the inward synthesis of septal peptidoglycan (sPG) through the FtsWI complex during bacterial cell division. Here, Lyu et al. apply single-molecule microscopy on E. coli to show that FtsN proteins (I) move processively at a speed similar to that of FtsWI molecules. (II) can be divided into two populations based on their speeds, and (III) their movement is driven exclusively by peptidoglycan synthesis
- Zhixin Lyu
- , Atsushi Yahashiri
- & Jie Xiao
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Article
| Open AccessStress induced TDP-43 mobility loss independent of stress granules
Amyotrophic Lateral Sclerosis related TDP-43 protein translocates to stress granules with a concomitant reduction in mobility. Here, the authors use single molecule tracking and find a stress-induced reduction in TDP-43 mobility also in the cytoplasm potentially relevant for TDP-43 aggregation.
- Lisa Streit
- , Timo Kuhn
- & Karin M. Danzer
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Article
| Open AccessA blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories
The ability to infer quantitative kinetic information from single-molecule FRET (smFRET) data can be challenging. Here the authors perform a blind benchmark study assessing different analysis tools used to infer kinetic rate constants from smFRET trajectories, testing on simulated and experimental data.
- Markus Götz
- , Anders Barth
- & Sonja Schmid
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Article
| Open AccessMultiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila
Here the authors applied their recently developed multiplexed DNA-FISH Hi-M method to dissect the sources of heterogeneity in topologically associating domain (TAD)-like organization during Drosophila embryogenesis. This single-nucleus analysis allows them to reveal that multiple parameters contribute to shaping the trace of the chromatin path from a single nucleus.
- Markus Götz
- , Olivier Messina
- & Marcelo Nollmann
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Article
| Open AccessA multi-state dynamic process confers mechano-adaptation to a biological nanomachine
Combining experiments with modeling, Wadhwa et al. propose a model for mechano-adaptation in the bacterial flagellar motor, finding that load-dependent transitions between multiple internal states govern the binding and unbinding of subunits.
- Navish Wadhwa
- , Alberto Sassi
- & Yuhai Tu
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Article
| Open AccessComprehensive structural assignment of glycosaminoglycan oligo- and polysaccharides by protein nanopore
Glycosaminoglycans (GAGs) are highly anionic functional polysaccharides with subtle structural variations that are very difficult to differentiate. Here the authors demonstrate proof-of-concept single-molecule detection by nanopore, taking a first step towards the ultimate goal of GAG sequencing.
- Parisa Bayat
- , Charlotte Rambaud
- & Régis Daniel
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Article
| Open AccessPerforin-2 clockwise hand-over-hand pre-pore to pore transition mechanism
Direct visualization of the structural transformation from pre-pore to pore of the mammalian immune defense complex perforin-2 (PFN2) reveals a clockwise hand-over-hand mechanism that propagates at ~15 subunits per second.
- Fang Jiao
- , François Dehez
- & Simon Scheuring
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Article
| Open AccessNucleosome-directed replication origin licensing independent of a consensus DNA sequence
Most eukaryotes do not use a consensus DNA sequence as binding sites for the origin recognition complex (ORC) to initiate DNA replication, however budding yeast do. Here the authors show S. cerevisiae ORC can bind nucleosomes near nucleosome-free regions and recruit replicative helicases to form a pre-replication complex independent of the DNA sequence.
- Sai Li
- , Michael R. Wasserman
- & Shixin Liu
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Article
| Open AccessExtraction of accurate cytoskeletal actin velocity distributions from noisy measurements
Dynamic remodeling of the actin cytoskeleton underlies cell movement, but is challenging to characterize at the molecular level. Here, the authors present a method to extract actin filament velocities in living cells, and compare their results to current models of cytoskeletal dynamics.
- Cayla M. Miller
- , Elgin Korkmazhan
- & Alexander R. Dunn
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Article
| Open AccessStructural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β
The authors revealed novel roles of catalytic residues and divalent metal ions for hsTOP3B, the human RNA topoisomerase, and demonstrated the structural elements that kinetically modulate the DNA and RNA topoisomerase activities of TOP3B.
- Xi Yang
- , Sourav Saha
- & Yves Pommier
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Article
| Open AccessMolecular mechanism for the synchronized electrostatic coacervation and co-aggregation of alpha-synuclein and tau
Here, the authors report that α-synuclein phase-separates into liquid condensates with positively charged polypeptides such as Tau. The condensates undergo different maturation processes, including the formation of α-synuclein/Tau amyloid hetero-aggregates inside the condensates.
- Pablo Gracia
- , David Polanco
- & Nunilo Cremades
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Article
| Open AccessStructural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter
Tripartite ATP-independent periplasmic (TRAP) transporters are widespread in bacteria and archaea. Here, the authors used cryo-EM and a range of biophysical techniques to study the structure of function of the sialic acid TRAP transporter HiSiaQM.
- Martin F. Peter
- , Jan A. Ruland
- & Gregor Hagelueken
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Article
| Open AccessCross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET
Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are used to determine conformational changes and probe distances in biological macromolecules. Here the authors compare the methods on a large set of samples.
- Martin F. Peter
- , Christian Gebhardt
- & Gregor Hagelueken
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Article
| Open AccessAltered tRNA dynamics during translocation on slippery mRNA as determinant of spontaneous ribosome frameshifting
Slippery sequences in mRNA can cause the ribosome to change its reading frame. Using smFRET, Poulis et al. show how reversible fluctuations of peptidyl-tRNA slow down translocation, alter ribosome dynamics, and favor spontaneous ribosome frameshifting.
- Panagiotis Poulis
- , Anoshi Patel
- & Sarah Adio
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Article
| Open AccessChromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA
Here the authors used single-molecule imaging and manipulation to study the mechanical effects of transcription factor Sox2 co-condensation with DNA and chromatin. They found that Sox2 condensates exert a high level of mechanical stress on DNA, but this stress is dramatically attenuated by nucleosomes assembled on the DNA.
- Tuan Nguyen
- , Sai Li
- & Shixin Liu
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Article
| Open AccessLigand-induced transmembrane conformational coupling in monomeric EGFR
EGFR regulates cellular processes across the animal kingdom. Here, the authors show that transmembrane conformational coupling is the first step in EGFR signaling, providing evidence for the existence of transmembrane intramolecular conformational changes in a single pass membrane protein.
- Shwetha Srinivasan
- , Raju Regmi
- & Gabriela S. Schlau-Cohen
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Article
| Open AccessSingle-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2
Single-molecule FRET measurements provide detailed insights into the conformational states and dynamics of human Argonaute 2 that are required for its function at the core of the eukaryotic RNA silencing pathway.
- Sarah Willkomm
- , Leonhard Jakob
- & Dina Grohmann
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Article
| Open AccessThe force required to remove tubulin from the microtubule lattice by pulling on its α-tubulin C-terminal tail
Tubulin, the building blocks of microtubules, can be removed from the microtubule wall by mechanical forces. Using single-molecule methods, the authors show that tubulin partially unfolds prior to its removal and determined the tubulin-extraction force.
- Yin-Wei Kuo
- , Mohammed Mahamdeh
- & Jonathon Howard
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Article
| Open AccessMapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers
Quantitative characterization of kinase conformational dynamics remains challenging. Here, the authors show that protein nanopore tweezers allow analyzing the conformational energy landscape and ligand binding of the Abl kinase domain.
- Fanjun Li
- , Monifa A. Fahie
- & Min Chen
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Article
| Open AccessDynamic interaction of BRCA2 with telomeric G-quadruplexes underlies telomere replication homeostasis
G-quadruplex (G4) can be formed in telomeric DNA. Here the authors show that BRCA2 interacts with telomere G4 structure generated during telomere replication, protecting telomere from nuclease attack.
- Junyeop Lee
- , Keewon Sung
- & Hyunsook Lee
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Article
| Open AccessImaging translational control by Argonaute with single-molecule resolution in live cells
Guided by miRNA, Argonaute proteins silence mRNA in multiple ways that are not well understood. Here, the authors develop live-cell biosensors to image the impact tethered regulatory factors, such as Argonaute, have on single-mRNA translation dynamics.
- Charlotte A. Cialek
- , Gabriel Galindo
- & Timothy J. Stasevich
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Article
| Open AccessOn the origins of conductive pulse sensing inside a nanopore
Conductive events during nanopore sensing, are seen typically under low salt conditions and widely thought to arise from counterions brought into the pore via analyte. Here, authors show that an imbalance of ionic fluxes lead to conductive events.
- Lauren S. Lastra
- , Y. M. Nuwan D. Y. Bandara
- & Kevin J. Freedman
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Article
| Open AccessGasdermin-A3 pore formation propagates along variable pathways
Gasdermin-A3 pore formation propagates along diverse pathways. It begins with membrane attachment and oligomeric pre-assembly. Once inserted in the membrane, the oligomers re-assemble into various shapes and sizes, which open their lytic pores.
- Stefania A. Mari
- , Kristyna Pluhackova
- & Daniel J. Müller
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Article
| Open AccessAtaluren binds to multiple protein synthesis apparatus sites and competitively inhibits release factor-dependent termination
Ataluren is the only nonsense suppressor drug currently approved for clinical use. Here, the authors determine where ataluren binds to the ribosome and how it inhibits termination at nonsense codons.
- Shijie Huang
- , Arpan Bhattacharya
- & Barry S. Cooperman
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Article
| Open AccessDiversity of bacterial small RNAs drives competitive strategies for a mutual chaperone
Bacterial sRNAs compete for limited copies of an RNA chaperone. Here, real-time single-molecule imaging shows that pairwise interactions of sRNAs with Hfq determine if the sRNAs are actively exchanged or stably coexist on the shared protein.
- Jorjethe Roca
- , Andrew Santiago-Frangos
- & Sarah A. Woodson
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Article
| Open AccessMre11-Rad50 oligomerization promotes DNA double-strand break repair
The Mre11-Rad50 (MR) complex has key functions in the detection, signaling and repair of DNA breaks. Here the authors use transmission electron microscopy to show MR oligomerization is governed by a small beta-sheet protruding from the head domain of Rad50 at the base of the MR structure, and reveal MR head domain oligomerization is required for efficient DNA end resection.
- Vera M. Kissling
- , Giordano Reginato
- & Matthias Peter
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Article
| Open AccessEvanescent scattering imaging of single protein binding kinetics and DNA conformation changes
Single molecule detection based on evanescent illumination usually require specially designed nanomaterials. Here, the authors show that single molecule detection can be realised on a plain glass surface via interference between the evanescent lights scattered by molecules and the natural roughness of the glass.
- Pengfei Zhang
- , Lei Zhou
- & Shaopeng Wang
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Article
| Open AccessBloom helicase mediates formation of large single–stranded DNA loops during DNA end processing
Bloom syndrome is a genetic disorder associated with increased cancer risk and is caused by mutations in Bloom helicase. This study investigates the mechanisms used by BLM helicase as initiates the repair of broken chromosomes.
- Chaoyou Xue
- , Sameer J. Salunkhe
- & Eric C. Greene
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Article
| Open AccessMechanism of sensitivity modulation in the calcium-sensing receptor via electrostatic tuning
Tuning of receptor sensitivity is often thought to rely on direct ligand-receptor interactions. Here, Schamber, et al. demonstrate the ability of a dimer interface to allosterically regulate calcium-sensing receptor (CaSR) sensitivity.
- Michael R. Schamber
- & Reza Vafabakhsh
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Article
| Open AccessDirect measurements of mRNA translation kinetics in living cells
Metelev et al. use single-molecule tracking to study kinetics of translation directly in E. coli cells, and how it is affected by translation inhibitors and rRNA mutations. Their results support widespread 70S re-initiation on mRNAs.
- Mikhail Metelev
- , Erik Lundin
- & Magnus Johansson
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Article
| Open AccessUltraviolet optical horn antennas for label-free detection of single proteins
The authors introduce optical horn antennas, a nanophotonic platform combining plasmonic enhancement, efficient collection and background screening, for detection of UV autofluorescence from single proteins. They demonstrate label-free monitoring of protein unfolding and dissociation upon denaturation.
- Aleksandr Barulin
- , Prithu Roy
- & Jérôme Wenger
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Article
| Open AccessAuxiliary ATP binding sites support DNA unwinding by RecBCD
RecBCD is a remarkably fast DNA helicase. Using a battery of biophysical methods, Zananiri et. al reveal additional, non-catalytic ATP binding sites that increase the ATP flux to the catalytic sites that allows fast unwinding when ATP is scarce.
- Rani Zananiri
- , Sivasubramanyan Mangapuram Venkata
- & Arnon Henn
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Article
| Open AccessSingle-molecule imaging of microRNA-mediated gene silencing in cells
For decades, miRNAs have been studied primarily by ensemble methods, where a bulk collection of molecules is measured outside cells. Here, Kobayashi and Singer report methods to image miRNA function at the single-molecule level inside cells.
- Hotaka Kobayashi
- & Robert H. Singer
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Article
| Open Accessα-catenin switches between a slip and an asymmetric catch bond with F-actin to cooperatively regulate cell junction fluidity
By using laser tweezers, the authors show that a single α-catenin molecule does not resist force on F-actin. However, clustering of multiple molecules and force applied toward F-actin pointed end engage a molecular switch in α-catenin, which unfolds and strongly binds F-actin.
- C. Arbore
- , M. Sergides
- & M. Capitanio
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Article
| Open AccessMulti-parameter photon-by-photon hidden Markov modeling
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. The utility of mpH2MM in identifying and quantifying dynamic biomolecular sub-populations is demonstrated in three different systems.
- Paul David Harris
- , Alessandra Narducci
- & Eitan Lerner
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Article
| Open AccessCooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core
Simulations reveal concerted interactions between the SARS-CoV-2 spike trimers and ACE2 receptors that result in cooperative spike binding and shedding, and further suggest that variant efficacy is promoted by increased RBD opening or S1/S2 cleavage efficiency.
- Alexander J. Pak
- , Alvin Yu
- & Gregory A. Voth
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Article
| Open AccessDisentangling the recognition complexity of a protein hub using a nanopore
Nanopores are powerful tools for sampling protein-peptide interactions. Here, the authors convert a protein-based nanopore into a sensitive biosensor to characterize the complex binding of WDR5 protein to a 14-residue ligand.
- Lauren Ashley Mayse
- , Ali Imran
- & Liviu Movileanu
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Article
| Open AccessSpecific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation
This study shows that rather than high thermodynamic stability, specific length and structure enable regulatory mRNA stem-loops to pause translation. These findings aid identification of new regulatory mRNA stem-loops.
- Chen Bao
- , Mingyi Zhu
- & Dmitri N. Ermolenko
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Article
| Open AccessDuplex DNA and BLM regulate gate opening by the human TopoIIIα-RMI1-RMI2 complex
Here the authors probe the cleavage and gate opening of single-stranded DNA by the human topoisomerase TRR using a unique single-molecule strategy to reveal structural plasticity in response to both double-stranded DNA and the helicase BLM.
- Julia A. M. Bakx
- , Andreas S. Biebricher
- & Erwin J. G. Peterman
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Article
| Open AccessHeterotrimeric Gq proteins act as a switch for GRK5/6 selectivity underlying β-arrestin transducer bias
GPCR kinases (GRKs) phosphorylate active-form G-protein-coupled receptors (GPCRs). Here, the authors reveal that Gq heterotrimer coupled with the angiotensin II type-1 receptor (AT1R) determines the GRK subtypes recruited to the complex in a microdomain, thus defining subsequent AT1R phosphorylation patterns, β-arrestin conformation and functionality.
- Kouki Kawakami
- , Masataka Yanagawa
- & Asuka Inoue
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Article
| Open AccessSingle-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C
The authors used novel single-molecule technology to measure the affinity of interactions between the ubiquitin ligase APC/C and its substrates, providing insights into the control of APC/C substrate destruction during mitosis.
- Nairi Hartooni
- , Jongmin Sung
- & David O. Morgan
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Article
| Open AccessAn anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch
A single molecule fluorescence study revealed three dynamically interconverting conformations of the fluoride riboswitch from Bacillus cereus, where an anionic ligand snap-locks a docked conformation through a long-range interaction necessary for downstream gene regulation.
- Rajeev Yadav
- , Julia R. Widom
- & Nils G. Walter
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Article
| Open AccessChirality transmission in macromolecular domains
Chiral communication can propagate in secondary structures within the effective intermolecular force (IMF) range but it is not known whether long-range chiral communication exists between tertiary peptide structures. Here, the authors use single-molecule force spectroscopy to investigate chiral interaction between DNA duplexes/triplexes and peptide coiled-coils and demonstrate chiral communication beyond the IMF distance.
- Shankar Pandey
- , Shankar Mandal
- & Hanbin Mao
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Article
| Open AccessResonator nanophotonic standing-wave array trap for single-molecule manipulation and measurement
Applications of nanophotonic tweezers have been limited by the low trapping force. Here, the authors present enhanced force generation in a nanophotonic standing-wave array trap by integrating a critically-coupled resonator design and demonstrate common single-molecule experiments.
- Fan Ye
- , James T. Inman
- & Michelle D. Wang
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Article
| Open AccessSingle molecule kinetics of bacteriorhodopsin by HS-AFM
Here, the authors use high-speed atomic force microscopy (HS-AFM) methods to characterize the single molecule kinetics of wild-type bacteriorhodopsin (bR) with millisecond temporal resolution, providing new insights into the bR conformational cycle.
- Alma P. Perrino
- , Atsushi Miyagi
- & Simon Scheuring
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Article
| Open AccessKinetic and structural mechanism for DNA unwinding by a non-hexameric helicase
UvrD is a model helicase from the non-hexameric Superfamily 1. Here, the authors use optical tweezers to measure directly the stepwise translocation of UvrD along a DNA hairpin, and propose a mechanism in which UvrD moves one base pair at a time, but sequesters the nascent single strands, releasing them after a variable number of ATP hydrolysis cycles.
- Sean P. Carney
- , Wen Ma
- & Yann R. Chemla