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Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Improving biosensor analysis
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Theory and applications of the generalized born solvation model in macromolecular simulations
inferredcites →https://doi.org/10.1002/anie.201802890openalex-snapshot
On the Stability of DNA Origami Nanostructures in Low‐Magnesium Buffers
inferredcites →https://doi.org/10.1002/bip.360340506openalex-snapshot
Solution structure and dynamics of DNA topoisomers: Dynamic light scattering studies and Monte Carlo simulations
inferredcites →https://doi.org/10.1002/jcc.20084openalex-snapshot
UCSF Chimera—A visualization system for exploratory research and analysis
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Single‐Molecule Reconstruction of Oligonucleotide Secondary Structure by Atomic Force Microscopy
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Computer Visualization of Three-Dimensional Image Data Using IMOD
inferredcites →https://doi.org/10.1007/978-1-4939-3631-1_5openalex-snapshot
Imaging DNA Structure by Atomic Force Microscopy
inferredcites →https://doi.org/10.1007/s001090050112openalex-snapshot
Triplex DNA: fundamentals, advances, and potential applications for gene therapy
inferredcites →https://doi.org/10.1007/s12274-014-0681-yopenalex-snapshot
Tuning the translational freedom of DNA for high speed AFM
inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot
VMD: Visual molecular dynamics
inferredcites →https://doi.org/10.1016/j.bpj.2008.11.013openalex-snapshot
Theoretical Analysis of Disruptions in DNA Minicircles
inferredcites →https://doi.org/10.1016/j.bpj.2016.12.034openalex-snapshot
Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA
inferredcites →https://doi.org/10.1016/j.bpj.2019.11.1312openalex-snapshot
Coarse-Grained Modeling of DNA Plectoneme Formation in the Presence of Base-Pair Mismatches
inferredcites →https://doi.org/10.1016/j.cell.2010.08.001openalex-snapshot
Cellular Strategies for Regulating DNA Supercoiling: A Single-Molecule Perspective
inferredcites →https://doi.org/10.1016/j.str.2006.08.004openalex-snapshot
Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles
inferredcites →https://doi.org/10.1016/s0006-3495(80)85139-3openalex-snapshot
X-ray scattering from randomly oriented superhelices. Circular superhelical DNA
inferredcites →https://doi.org/10.1016/s1097-2765(01)00392-6openalex-snapshot
Recognition of Specific DNA Sequences
inferredcites →https://doi.org/10.1016/s1568-7864(02)00222-7openalex-snapshot
DNA bending by the human damage recognition complex XPC–HR23B
inferredcites →https://doi.org/10.1017/s0033583512000054openalex-snapshot
Bullied no more: when and how DNA shoves proteins around
inferredcites →https://doi.org/10.1021/acs.jctc.5b00035openalex-snapshot
Comparison of Molecular Contours for Measuring Writhe in Atomistic Supercoiled DNA
inferredcites →https://doi.org/10.1021/acsnano.8b06994openalex-snapshot
Free Energy Landscape and Dynamics of Supercoiled DNA by High-Speed Atomic Force Microscopy
inferredcites →https://doi.org/10.1021/ct300275sopenalex-snapshot
Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA
inferredcites →https://doi.org/10.1021/ct300418hopenalex-snapshot
MMPBSA.py : An Efficient Program for End-State Free Energy Calculations
inferredcites →https://doi.org/10.1021/ct400154jopenalex-snapshot
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters
inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
inferredcites →https://doi.org/10.1021/ja981121qopenalex-snapshot
Molecular Dynamics Simulations in Aqueous Solution of Triple Helices Containing d(G·C·C) Trios
inferredcites →https://doi.org/10.1021/nl301857popenalex-snapshot
Atomic Force Microscopy with Nanoscale Cantilevers Resolves Different Structural Conformations of the DNA Double Helix
inferredcites →https://doi.org/10.1021/nn400071nopenalex-snapshot
Beyond the Helix Pitch: Direct Visualization of Native DNA in Aqueous Solution
inferredcites →https://doi.org/10.1038/gt.2010.123openalex-snapshot
Transfection of shRNA-encoding Minivector DNA of a few hundred base pairs to regulate gene expression in lymphoma cells
inferredcites →https://doi.org/10.1038/ncomms9440openalex-snapshot
Structural diversity of supercoiled DNA
inferredcites →https://doi.org/10.1038/nmeth.3658openalex-snapshot
Parmbsc1: a refined force field for DNA simulations
inferredcites →https://doi.org/10.1038/s41467-018-03369-8openalex-snapshot
Circular DNA elements of chromosomal origin are common in healthy human somatic tissue
inferredcites →https://doi.org/10.1038/s41565-018-0149-4openalex-snapshot
High-speed photothermal off-resonance atomic force microscopy reveals assembly routes of centriolar scaffold protein SAS-6
inferredcites →https://doi.org/10.1038/s41586-019-1763-5openalex-snapshot
Circular ecDNA promotes accessible chromatin and high oncogene expression
inferredcites →https://doi.org/10.1038/s41594-019-0188-zopenalex-snapshot
DNA stretching induces Cas9 off-target activity
inferredcites →https://doi.org/10.1038/sj.embor.7400898openalex-snapshot
A common topology for bacterial and eukaryotic transcription initiation?
inferredcites →https://doi.org/10.1038/srep07655openalex-snapshot
Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
inferredcites →https://doi.org/10.1039/a800429copenalex-snapshot
X-Ray and molecular dynamics studies of concanavalin-A glucoside and mannoside complexes Relating structure to thermodynamics of binding
inferredcites →https://doi.org/10.1063/1.466363openalex-snapshot
Computer simulations of NaCl association in polarizable water
inferredcites →https://doi.org/10.1073/pnas.1113532109openalex-snapshot
Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA
inferredcites →https://doi.org/10.1073/pnas.1414156112openalex-snapshot
Detecting cancers through tumor-activatable minicircles that lead to a detectable blood biomarker
inferredcites →https://doi.org/10.1073/pnas.261477898openalex-snapshot
DNA supercoiling allows enhancer action over a large distance
inferredcites →https://doi.org/10.1073/pnas.80.11.3284openalex-snapshot
Structural and dynamic differences between supercoiled and linear DNA from proton NMR.
inferredcites →https://doi.org/10.1073/pnas.85.17.6292openalex-snapshot
Intramolecular DNA triplexes in supercoiled plasmids.
inferredcites →https://doi.org/10.1073/pnas.94.2.496openalex-snapshot
Visualization of supercoiled DNA with atomic force microscopy in situ
inferredcites →https://doi.org/10.1080/07391102.1999.10508297openalex-snapshot
A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat
inferredcites →https://doi.org/10.1088/0953-8984/18/14/s01openalex-snapshot
Exploring writhe in supercoiled minicircle DNA
inferredcites →https://doi.org/10.1093/nar/gkl504openalex-snapshot
High-throughput assays for DNA gyrase and other topoisomerases
inferredcites →https://doi.org/10.1093/nar/gkm1125openalex-snapshot
Kinking the double helix by bending deformation
inferredcites →https://doi.org/10.1093/nar/gkp137openalex-snapshot
Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
inferredcites →https://doi.org/10.1093/nar/gkp234openalex-snapshot
Local and global effects of strong DNA bending induced during molecular dynamics simulations
inferredcites →https://doi.org/10.1093/nar/gkq1312openalex-snapshot
Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA
inferredcites →https://doi.org/10.1093/nar/gkr666openalex-snapshot
Cooperative kinking at distant sites in mechanically stressed DNA
inferredcites →https://doi.org/10.1093/nar/gkw007openalex-snapshot
Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes
inferredcites →https://doi.org/10.1093/nar/gkw815openalex-snapshot
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation
inferredcites →https://doi.org/10.1093/nar/gky266openalex-snapshot
Visualizing structure-mediated interactions in supercoiled DNA molecules
inferredcites →https://doi.org/10.1093/nar/gkz155openalex-snapshot
Small extrachromosomal circular DNAs, microDNA, produce short regulatory RNAs that suppress gene expression independent of canonical promoters
inferredcites →https://doi.org/10.1093/nar/gkz586openalex-snapshot
Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes
inferredcites →https://doi.org/10.1093/nar/gkz797openalex-snapshot
Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase
inferredcites →https://doi.org/10.1101/2020.09.23.309609openalex-snapshot
TopoStats – a program for automated tracing of biomolecules from AFM images
inferredcites →https://doi.org/10.1101/cshperspect.a014233openalex-snapshot
Cellular MYCro Economics: Balancing MYC Function with MYC Expression
inferredcites →https://doi.org/10.1103/physrevlett.109.228101openalex-snapshot
Length Scale Dependence of DNA Mechanical Properties
inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot
Matplotlib: A 2D Graphics Environment
inferredcites →https://doi.org/10.1109/mcse.2010.145openalex-snapshot
Automatic Lip-Contour Extraction and Mouth-Structure Segmentation in Images
inferredcites →https://doi.org/10.1128/microbiolspec.plas-0036-2014openalex-snapshot
Topological Behavior of Plasmid DNA
inferredcites →https://doi.org/10.1146/annurev.bi.64.070195.000433openalex-snapshot
TRIPLEX DNA STRUCTURES
inferredcites →https://doi.org/10.1146/annurev.genet.36.032902.111815openalex-snapshot
DNA Topology-Mediated Control of Global Gene Expression in Escherichia coli
inferredcites →https://doi.org/10.1371/journal.pcbi.1002484openalex-snapshot
Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA
inferredcites →https://doi.org/10.15131/shef.data.13103327openalex-snapshot
Software: TopoStats - an automated tracing program for AFM images
inferredcites →https://doi.org/10.1529/biophysj.106.097782openalex-snapshot
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
inferredcites →https://doi.org/10.1529/biophysj.108.132829openalex-snapshot
Unmasking Imaging Forces on Soft Biological Samples in Liquids When Using Dynamic Atomic Force Microscopy: A Case Study on Viral Capsids
inferredcites →https://doi.org/10.1534/g3.117.300141openalex-snapshot
Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens
inferredcites →https://doi.org/10.17504/protocols.io.bncemateopenalex-snapshot
Atomic Force Microscopy of DNA and DNA-Protein Interactions v1
inferredcites →https://doi.org/10.2478/s11534-011-0096-2openalex-snapshot
Gwyddion: an open-source software for SPM data analysis
inferredcites →https://doi.org/10.3390/genes10020169openalex-snapshot
The Effect of DNA Topology on Observed Rates of R-Loop Formation and DNA Strand Cleavage by CRISPR Cas12a
inferredcites →https://doi.org/10.5281/zenodo.4105979openalex-snapshot
agnesnoy/SerraLINE: SerraLINE v1.0
inferredcites →https://doi.org/10.6084/m9.figshare.13116890openalex-snapshot
Atomic force microscopy and atomistic molecular dynamics simulation data to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution.
inferredcites →https://doi.org/10.7554/elife.36557openalex-snapshot
DNA sequence encodes the position of DNA supercoils
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1017/s0033583521000068openalex-snapshot
A molecular view of DNA flexibility
inferred← citeshttps://doi.org/10.1021/jacsau.5c00800openalex-snapshot
HU Searches and Binds Specific DNA via a Multistep Process Combining Weak Electrostatic Binding, Protein Reorientation, and DNA Flexibility
inferred← citeshttps://doi.org/10.1038/s41594-021-00678-3openalex-snapshot
Three-dimensional genome organization via triplex-forming RNAs
inferred← citeshttps://doi.org/10.1101/2020.04.17.047076openalex-snapshot
Integration host factor bends and bridges DNA in a multiplicity of binding modes with varying specificity
inferred← citeshttps://doi.org/10.1101/2020.09.23.309609openalex-snapshot
TopoStats – a program for automated tracing of biomolecules from AFM images
inferred← citeshttps://doi.org/10.1126/sciadv.abf3641openalex-snapshot
Single-molecule measurements reveal that PARP1 condenses DNA by loop stabilization
inferred← citeshttps://doi.org/10.17504/protocols.io.bncemateopenalex-snapshot
Atomic Force Microscopy of DNA and DNA-Protein Interactions v1
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