ReviewBiopolymers2009
Optical tweezers experiments resolve distinct modes of DNA-protein binding.
Review in Biopolymers, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 60 citations in OpenAlex.
- Specific Nucleic Acid Chaperone Activity of HIV-1 Nucleocapsid Protein Deduced from Hairpin Unfolding.Methods in molecular biology (Clifton, N.J.) · 2026Article
- TMPyP binding evokes a complex, tunable nanomechanical response in DNA.Nucleic acids research · 2024Article
- Left versus right: Exploring the effects of chiral threading intercalators using optical tweezers.Biophysical journal · 2022Article
- Significant Differences in RNA Structure Destabilization by HIV-1 GagDp6 and NCp7 Proteins.Viruses · 2020Article
- Pixantrone anticancer drug as a DNA ligand: Depicting the mechanism of action at single molecule level.The European physical journal. E, Soft matter · 2019Article
- Dimerization regulates both deaminase-dependent and deaminase-independent HIV-1 restriction by APOBEC3G.Nature communications · 2017Article
- Single-molecule mechanochemical characterization of E. coli pol III core catalytic activity.Protein science : a publication of the Protein Society · 2017Article
- Single-molecule studies of high-mobility group B architectural DNA bending proteins.Biophysical reviews · 2017Review
- Mechanistic differences between HIV-1 and SIV nucleocapsid proteins and cross-species HIV-1 genomic RNA recognition.Retrovirology · 2016Article
- DNA intercalation optimized by two-step molecular lock mechanism.Scientific reports · 2016Article
- Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy.Nucleic acids research · 2016Article
- A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps.Nucleic acids research · 2015Article
- Distinct nucleic acid interaction properties of HIV-1 nucleocapsid protein precursor NCp15 explain reduced viral infectivity.Nucleic acids research · 2014Article
- Differential contribution of basic residues to HIV-1 nucleocapsid protein's nucleic acid chaperone function and retroviral replication.Nucleic acids research · 2014Article
- Two-phase stretching of molecular chains.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility.Nucleic acids research · 2013Article
- A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.Nucleic acids research · 2012Article
- Paired mutations abolish and restore the balanced annealing and melting activities of ORF1p that are required for LINE-1 retrotransposition.Nucleic acids research · 2011Article
- Torsional sensing of small-molecule binding using magnetic tweezers.Nucleic acids research · 2010Article
- Biophysical characterization of DNA binding from single molecule force measurements.Physics of life reviews · 2010Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Optical tweezers are ideally suited to perform force microscopy experiments that isolate a single biomolecule, which then provides multiple binding sites for ligands. The captured complex may be subjected to a spectrum of forces, inhibiting or facilitating ligand activity. In the following experiments, we utilize optical tweezers to characterize and quantify DNA binding of various ligands. High mobility group type B (HMGB) proteins, which bind to double-stranded DNA, are shown to serve the dual purpose of stabilizing and enhancing the flexibility of double stranded DNA. Unusual intercalating ligands are observed to thread into and lengthen the double-stranded structure. Proteins binding to both double- and single-stranded DNA, such as the alpha polymerase subunit of E. coli Pol III, are characterized, and the subdomains containing the distinct sites responsible for binding are isolated. Finally, DNA binding of bacteriophage T4 and T7 single-stranded DNA (ssDNA) binding proteins is measured for a range of salt concentrations, illustrating a binding model for proteins that slide along double-stranded DNA, ultimately binding tightly to ssDNA. These recently developed methods quantify both the binding activity of the ligand as well as the mode of binding.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.