ArticleNucleic acids research2020
ssDNA diffuses along replication protein A via a reptation mechanism.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 36 citations in OpenAlex.
- DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins.Nature communications · 2025Article
- Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA.Nucleic acids research · 2025Article
- Redox regulation: mechanisms, biology and therapeutic targets in diseases.Signal transduction and targeted therapy · 2025Review
- Sodium Ion-Induced Structural Transition on the Surface of a DNA-Interacting Protein.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation.Nucleic acids research · 2024Article
- Hunting the Cell CycleLife (Basel, Switzerland) · 2024Article
- A pH-Dependent Coarse-Grained Model for Disordered Proteins: Histidine Interactions Modulate Conformational Ensembles.The journal of physical chemistry letters · 2024Article
- Rapid Long-distance Migration of RPA on Single Stranded DNA Occurs Through Intersegmental Transfer Utilizing Multivalent Interactions.Journal of molecular biology · 2024Article
- Chemical Inhibition of RPA by HAMNO Alters Cell Cycle Dynamics by Impeding DNA Replication and G2-to-M Transition but Has Little Effect on the Radiation-Induced DNA Damage Response.International journal of molecular sciences · 2023Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- "Helicase" Activity promoted through dynamic interactions between a ssDNA translocase and a diffusing SSB protein.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Phase separation properties of RPA combine high-affinity ssDNA binding with dynamic condensate functions at telomeres.Nature structural & molecular biology · 2023Article
- Interdomain dynamics in human Replication Protein A regulates kinetics and thermodynamics of its binding to ssDNA.PloS one · 2023Article
- Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA.Nucleic acids research · 2022Article
- Nuclear localization of human MEIOB requires its NLS in the OB domain and interaction with SPATA22.Acta biochimica et biophysica Sinica · 2022Article
- Replication Protein A Utilizes Differential Engagement of Its DNA-Binding Domains to Bind Biologically Relevant ssDNAs in Diverse Binding Modes.Biochemistry · 2022Article
- Review
- What Are the Molecular Requirements for Protein Sliding along DNA?The journal of physical chemistry. B · 2021Article
- Modeling Effects of Surface Properties and Probe Density for Nanoscale Biosensor Design: A Case Study of DNA Hybridization near Surfaces.The journal of physical chemistry. B · 2021Article
- Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair.Critical reviews in biochemistry and molecular biology · 2020Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA along 60 nt ssDNA using a coarse-grained model in which the ssDNA-RPA interface was modeled by both aromatic and electrostatic interactions. Our study provides direct evidence of bulge formation during the diffusion of ssDNA along RPA. Bulges can form at a few sites along the interface and store 1-7 nt of ssDNA whose release, upon bulge dissolution, leads to propagation of ssDNA diffusion. These findings thus support the reptation mechanism, which involves bulge formation linked to the aromatic interactions, whose short range nature reduces cooperativity in ssDNA diffusion. Greater cooperativity and a larger diffusion coefficient for ssDNA diffusion along RPA are observed for RPA variants with weaker aromatic interactions and for interfaces homogenously stabilized by electrostatic interactions. ssDNA propagation in the latter instance is characterized by lower probabilities of bulge formation; thus, it may fit the sliding-without-bulge model better than the reptation model. Thus, the reptation mechanism allows ssDNA mobility despite the extensive and high affinity interface of RPA with ssDNA. The short-range aromatic interactions support bulge formation while the long-range electrostatic interactions support the release of the stored excess ssDNA in the bulge and thus the overall diffusion.
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