Publications
Dynamic Single-Molecule
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Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase
Wasserman, M. et al.
2019
Cell
https://www.cell.com/cell/fulltext/S0092-8674(19)30735-4
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Real-Time Assembly of Viruslike Nucleocapsids Elucidated at the Single-Particle Level
Marchetti, M. et al.
2019
Nano Letters
https://pubs.acs.org/doi/pdf/10.1021/acs.nanolett.9b02376?rand=zqflrlav
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Single-Molecule Mechanics in Ligand Concentration Gradient
Kretzer, B. et al.
2020
Micromachines
https://www.mdpi.com/2072-666X/11/2/212/htm
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Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin
Leicher, R. et al.
2019
PNAS
https://www.pnas.org/content/early/2020/11/13/2003395117
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Cooperative DNA looping by PRC2 complexes
Lin, X. et al.
2021
Nucleic Acids Research
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab441/6290079
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Alkyltransferase-like protein clusters scan DNA rapidly over long distances and recruit NER to alkyl-DNA lesions
Rill, N. et al.
2020
PNAS
https://www.pnas.org/content/early/2020/04/08/1916860117.short
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Distinct pre-initiation steps in human mitochondrial translation
Khawaja, A. et al.
2020
Nature Communications
https://www.nature.com/articles/s41467-020-16503-2
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Constructing arrays of nucleosome positioning sequences using Gibson Assembly for single-molecule studies
Spakman, D. et al.
2020
Scientific Reports
https://www.nature.com/articles/s41598-020-66259-4
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Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins
Belan, O. et al.
2021
Molecular Cell
https://www.sciencedirect.com/science/article/abs/pii/S1097276520309394
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Dynamics of Staphylococcus aureus Cas9 in DNA target Association and Dissociation
Zhang, S. et al.
2020
EMBO Rep
https://www.embopress.org/doi/10.15252/embr.202050184
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HP1 proteins compact DNA into mechanically and positionally stable phase separated domains
Keenen, M. M. et al.
2021
eLife
https://elifesciences.org/articles/64563
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Proximal Single-Stranded RNA Destabilizes Human Telomerase RNA G-Quadruplex and Induces Its Distinct Conformers
Ye, S. et al.
2021
J. Phys. Chem. Lett.
https://pubs.acs.org/doi/10.1021/acs.jpclett.1c00250
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Generation of versatile ss-dsDNA hybrid substrates for single-molecule analysis
Belan, O. et al.
2021
STAR Protocols
https://www.sciencedirect.com/science/article/pii/S2666166721002951#undfig1
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Mechanics of CRISPR-Cas12a and engineered variants on λ-DNA
Paul, B. et al.
2021
Nucleic Acids Research
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab1272/6482587
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Force generation by protein–DNA co-condensation
Quail, T. et al.
2021
Nature Physics
https://www.nature.com/articles/s41567-021-01285-1
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Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy
Backer, A. S. et al.
2021
J. Phys. Chem. B
https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.1c02708
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CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS
de Asis Balaguer, F. et al.
2021
eLife
https://elifesciences.org/articles/67554#content
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Efficient DNA interrogation of SpCas9 governed by its electrostatic interaction with DNA beyond the PAM and protospacer
Zhang, Q. et al.
2021
Nucleic Acids Research
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab1139/6439681
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Virus self-assembly proceeds through contact-rich energy minima
Buzón, P. et al.
2021
Science Advances
https://www.science.org/doi/10.1126/sciadv.abg0811
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Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch
Hill, C. H. et al.
2021
Nature Communications
https://www.nature.com/articles/s41467-021-27400-7
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DNA replication origins retain mobile licensing proteins
Sánchez, H. et al.
2021
Nature Communications
https://www.nature.com/articles/s41467-021-22216-x
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Human HELB is a processive motor protein that catalyzes RPA clearance from single-stranded DNA
Hormeno, S. et al.
2022
eLife
https://www.pnas.org/doi/10.1073/pnas.2112376119
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HELQ is a dual-function DSB repair enzyme modulated by RPA and RAD51
Anand, R. et al.
2021
Nature Communications
https://www.nature.com/articles/s41586-021-04261-0
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Cas12a Target Search and Cleavage on Force-Stretched DNA
Losito, M. et al.
2021
PCCP
https://pubs.rsc.org/en/Content/ArticleLanding/2021/CP/D1CP03408A
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CENP-B-mediated DNA loops regulate activity and stability of human centromeres
Chardon, F. et al.
2022
Molecular Cell
https://www.cell.com/molecular-cell/fulltext/S1097-2765(22)00206-4
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Co-condensation of proteins with single- and double-stranded DNA
Renger, R. et al.
2022
PNAS
https://www.pnas.org/doi/10.1073/pnas.2107871119
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HIV-1 Nucleocapsid Protein Binds Double-Stranded DNA in Multiple Modes to Regulate Compaction and Capsid Uncoating
Gien, H. et al.
2022
Viruses
https://www.mdpi.com/1999-4915/14/2/235
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Identification of the target and mode of action for the prokaryotic nucleotide excision repair inhibitor ATBC
Bernacchia, L. et al.
2022
Biosci Rep
https://portlandpress.com/bioscirep/article/42/6/BSR20220403/231296/Identification-of-the-target-and-mode-of-action
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Sequence-dependent surface condensation of a pioneer transcription factor on DNA
Morin, J. A. et al.
2022
Nature Physics
https://www.nature.com/articles/s41567-021-01462-2
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The convergence of head-on DNA unwinding forks induces helicase oligomerization and activity transition
Bi, L. et al.
2022
PNAS
https://www.pnas.org/doi/10.1073/pnas.2116462119
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Resolving the subtle details of human DNA alkyltransferase lesion search and repair mechanism by single-molecule studies
Kono, S. et al.
2022
PNAS
https://www.pnas.org/doi/10.1073/pnas.2116218119
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Rtt105 regulates RPA function by configurationally stapling the flexible domains
Kuppa, S. et al.
2022
Nature Communications
https://www.nature.com/articles/s41467-022-32860-6
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Stochastically multimerized ParB orchestrates DNA assembly as unveiled by single-molecule analysis
Guo, L. et al.
2022
Nucleic Acids Research
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac651/6651868
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Nucleosome-directed replication origin licensing independent of a consensus DNA sequence
Li, S. et al.
2022
Nature Communications
https://www.nature.com/articles/s41467-022-32657-7
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Origin recognition complex harbors an intrinsic nucleosome remodeling activity
Li, S. et al.
2022
PNAS
https://www.pnas.org/doi/epdf/10.1073/pnas.2211568119
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ATP Binding Facilitates Target Search of SWR1 Chromatin Remodeler by Promoting One-Dimensional Diffusion on DNA
Carcamo, C. C. et al.
2022
eLife
https://elifesciences.org/articles/77352
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Single-molecule analysis of DNA-binding proteins from nuclear extracts (SMADNE)
Schaich, M. et al.
2023
NAR
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad095/7058193
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Search and processing of Holliday junctions within long DNA by junction-resolving enzymes
Kaczmarczyk, A. et al.
2022
Nature Communications
https://www.nature.com/articles/s41467-022-33503-6
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Smc5/6’s multifaceted DNA binding capacities stabilize branched DNA structures
Chang, J. T-H. et al.
2022
Nature Communications
https://www.nature.com/articles/s41467-022-34928-9
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Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination
Wang, L. et. al.
2023
Molecular Cell
https://www.sciencedirect.com/science/article/abs/pii/S109727652300120X?via%3Dihub
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POLQ seals post-replicative ssDNA gaps to maintain genome stability in BRCA-deficient cancer cells
Belan, O. et al.
2022
Molecular Cell
https://www.sciencedirect.com/science/article/pii/S109727652201070X?via%3Dihub
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PICH acts as a force dependent nucleosome remodeler
Spakman, D. et al.
2022
Nature Communications
https://www.nature.com/articles/s41467-022-35040-8
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Unlicensed origin DNA melting by MCV and SV40 polyomavirus LT proteins is independent of ATP-dependent helicase activity
Wan, L. et al.
2023
PNAS
https://pnas.org/doi/10.1073/pnas.2308010120
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Cooperative interaction between AAG and UV-DDB in the removal of modified bases
Jang, S. et al.
2022
NAR
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac1145/6895195
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Single-Molecule Force Spectroscopy of Deoxyribonucleic Acid and Deoxyribonucleic Acid Polymerase Activity Impacted by Alkylating Agents
Cai, T. et al.
2023
J. Phys. Chem. Lett.
https://doi.org/10.1021/acs.jpclett.3c00740
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Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes
McCauley, M. et al.
2022
Cell Reports
https://www.cell.com/cell-reports/fulltext/S2211-1247(22)01754-5
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Stabilization of DNA fork junctions by Smc5/6 complexes revealed by single-molecule imaging
Tanasie, N-L. et al.
2022
Cell Reports
https://www.cell.com/cell-reports/fulltext/S2211-1247(22)01661-8#%20
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Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation
Montero, D. R. et al.
2023
Nature Communications
https://www.nature.com/articles/s41467-023-37093-9
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Establishment of dsDNA-dsDNA interactions by the condensin complex
Tang, M. et al.
2023
Molecular Cell
https://doi.org/10.1016/j.molcel.2023.09.019
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“Helicase” activity promoted through dynamic interactions between a ssDNA translocase and a diffusing SSB protein
Mersch, K. N. et al.
2023
PNAS
https://www.pnas.org/doi/10.1073/pnas.2216777120
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Structure and function of the RAD51BCD-XRCC2 tumour suppressor complex
Greenhough, L. A. et al.
2023
Nature Communications
https://www.nature.com/articles/s41586-023-06179-1
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Visualization of direct and diffusion-assisted RAD51 nucleation by full-length human BRCA2 protein
Belan, O. et al.
2023
Molecular Cell
https://doi.org/10.1016/j.molcel.2023.06.031
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RNase H1 facilitates recombinase recruitment by degrading DNA–RNA hybrids during meiosis
Liu, C. et al.
2023
Nucleic Acids Research
https://doi.org/10.1093/nar/gkad524
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Negative DNA supercoiling induces genome-wide Cas9 off-target activity
Newton, M. D. et al.
2023
Molecular Cell
https://doi.org/10.1016/j.molcel.2023.09.008
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Assembly mechanism of the inflammasome sensor AIM2 revealed by single molecule analysis
Sharma, M. et al.
2023
Nature Communications
https://www.nature.com/articles/s41467-023-43691-4
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E. coli RecB Nuclease Domain Regulates RecBCD Helicase Activity but not Single Stranded DNA Translocase Activity
Fazio, N. et al.
2024
Journal of Molecular Biology
https://doi.org/10.1016/j.jmb.2023.168381
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Joint Efforts of Replicative Helicase and SSB Ensure Inherent Replicative Tolerance of G-Quadruplex
Guo, L. et al.
2023
Advanced Science
https://onlinelibrary.wiley.com/doi/10.1002/advs.202307696
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A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint
Sánchez, H. et al.
2023
Nature Communications
https://www.nature.com/articles/s41467-023-42524-8
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The Histone Chaperones SET/TAF‐1β and NPM1 Exhibit Conserved Functionality in Nucleosome Remodeling and Histone Eviction in a Cytochrome c ‐Dependent Manner
Buzón, P. et al.
2023
Advanced Science
https://doi.org/10.1002/advs.202301859
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DNA binding and bridging by human CtIP in the healthy and diseased states
Lokanathan Balaji, S. et al.
2024
Nucleic Acids Research
https://doi.org/10.1093/nar/gkae538
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Single-molecule analysis of purified proteins and nuclear extracts: Insights from 8-oxoguanine glycosylase 1
Schaich, M.A. et al.
2024
DNA Repair
https://www.sciencedirect.com/science/article/abs/pii/S1568786424000016
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De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features
Montero, D. R. et al.,
2023
Biophysical Journal
https://doi.org/10.1016/j.bpj.2023.11.008
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Developing novel antimicrobials by combining cancer chemotherapeutics with bacterial DNA repair inhibitors
Bernacchia, L. et al.
2023
Plos Pathogens
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011875
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PARP1-DNA co-condensation drives DNA repair site assembly to prevent disjunction of broken DNA ends
Chappidi, N. et al.
2024
Cell
https://www.cell.com/cell/fulltext/S0092-8674(24)00052-7#%20
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Rapid Long-distance Migration of RPA on Single Stranded DNA Occurs Through Intersegmental Transfer Utilizing Multivalent Interactions
Pangeni, S. et al.
2024
Journal of Molecular Biology
https://www.sciencedirect.com/science/article/pii/S0022283624000639
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Differential dynamics specify MeCP2 function at nucleosomes and methylated DNA
Chua, G. et al.
2024
Nature Structural & Molecular Biology
https://doi.org/10.1038/s41594-024-01373-9
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Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers
Kim, J. M. et al.
2024
eLife
https://elifesciences.org/reviewed-preprints/91433
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A Biophysics Toolbox for Reliable Data Acquisition and Processing in Integrated Force–Confocal Fluorescence Microscopy
Liu, Z. et al.
2024
ACS Photonics
https://doi.org/10.1021/acsphotonics.3c01739
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TMPyP binding evokes a complex, tunable nanomechanical response in DNA
Kretzer, B. et al.
2024
Nucleic Acids Research
https://doi.org/10.1093/nar/gkae560
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ISWI catalyzes nucleosome sliding in condensed nucleosome arrays
Vizjak, P. et al.
2024
Nature Structural & Molecular Biology
https://doi.org/10.1038/s41594-024-01290-x
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FANCD2–FANCI surveys DNA and recognizes double- to single-stranded junctions
Alcón, P. et al.
2024
Nature Communications
https://doi.org/10.1038/s41586-024-07770-w
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RPA transforms RNase H1 to a bidirectional exoribonuclease for processive RNA–DNA hybrid cleavage
Li, Y. et al.
2024
Nature Communications
https://doi.org/10.1038/s41467-024-51984-5
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How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors
Goluguri, R. et al.
2024
Nucleic Acids Research
https://doi.org/10.1093/nar/gkae790
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Thymine DNA glycosylase combines sliding, hopping, and nucleosome interactions to efficiently search for 5-formylcytosine
Schnable, B. et al.
2024
Nature Communications
https://doi.org/10.1038/s41467-024-53497-7
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The human Shu complex promotes RAD51 activity by modulating RPA dynamics on ssDNA
Hengel, S. et al.
2024
Nature Communications
https://doi.org/10.1038/s41467-024-51595-0
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Probing the mechanism of nick searching by LIG1 at the single-molecule level
Chatterjee, S. et al.
2024
Nucleic Acids Research
https://doi.org/10.1093/nar/gkae865
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Protamine-Mediated Tangles Produce Extreme Deoxyribonucleic Acid Compaction
Ahlawat, V. et al.
2024
JACS
https://doi.org/10.1021/jacs.4c12468
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