ArticleComputer physics communications2010
A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach.
Article in Computer physics communications, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Surface-Enhanced Raman Spectroscopy for Viral Diagnostics: Principles, Strategies, Clinical Challenges, and Future Directions.Chemical reviews · 2026Review
- Addressing the Challenges of Solid-State Nanopores: Strategies for Performance Enhancement.International journal of molecular sciences · 2026Review
- Single-Molecule DNA Tweezers Enable Programmable Control of Enzyme Activity via Arbitrary Molecular Cues.Angewandte Chemie (International ed. in English) · 2025Article
- Conformationally Locked Peptide-DNA Nanostructures for CRISPR-Amplified Activity-Based Sensing.Angewandte Chemie (International ed. in English) · 2025Article
- Leveraging Protein-Ligand and DNA Interactions to Control Hydrogel Mechanics.Journal of the American Chemical Society · 2025Article
- Nano-Phase Separation and Analyte Binding in Aptasensors Investigated by Nano-IR Spectroscopy.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Spatio-temporal organization of theEcoSal Plus · 2024Review
- Force-transducing molecular ensembles at growing microtubule tips control mitotic spindle size.Nature communications · 2024Article
- Rapid Systematic Screening of Bispecific Antibody Surrogate Geometries for T-Cell Engagement Using DNA Nanotechnology.Journal of the American Chemical Society · 2024Article
- Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain.Nature communications · 2024Article
- Surface-Enhanced Raman Spectroscopy (SERS)-Based Sensors for Deoxyribonucleic Acid (DNA) Detection.Molecules (Basel, Switzerland) · 2024Review
- Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain.bioRxiv : the preprint server for biology · 2024Article
- Enhancing Endosomal Escape and Gene Regulation Activity for Spherical Nucleic Acids.Small (Weinheim an der Bergstrasse, Germany) · 2024Article
- Programmable all-DNA hydrogels based on rolling circle and multiprimed chain amplification products.APL bioengineering · 2023Article
- A CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection.Theranostics · 2022Article
- Flex Printed Circuit Board Implemented Graphene-Based DNA Sensor for Detection of SARS-CoV-2.IEEE sensors journal · 2021Article
- Resistive amplitude fingerprints during translocation of linear molecules through charged solid-state nanopores.The Journal of chemical physics · 2020Article
- Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1.Cell systems · 2019Article
- Anomalous Elastic Properties of Attraction-Dominated DNA Self-Assembled 2D Films and the Resultant Dynamic Biodetection Signals of Microbeam Sensors.Nanomaterials (Basel, Switzerland) · 2019Article
- Phage-like packing structures with mean field sequence dependence.Journal of computational chemistry · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6-8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte-Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all atom simulations. Our average tilt results are also in agreement with all atom simulations for the case of dense systems.
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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.