Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations.

Kaitlin Bullard, Deborah Okyere, Shelbi J Foster, Asmaa A Sadoon, Jiali Li, Jingyi Chen, Yong Wang

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Article in Biosensors, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

7 authors.

Kaitlin BullardDepartment of Physics, University of Arkansas, Fayetteville, AR 72701, USA.

Deborah OkyereMaterials Science and Engineering Program, University of Arkansas, Fayetteville, AR 72701, USA.

Shelbi J FosterDepartment of Physics, University of Arkansas, Fayetteville, AR 72701, USA.

Asmaa A SadoonDepartment of Physics, University of Arkansas, Fayetteville, AR 72701, USA.

Jiali LiDepartment of Physics, University of Arkansas, Fayetteville, AR 72701, USA.

Jingyi ChenMaterials Science and Engineering Program, University of Arkansas, Fayetteville, AR 72701, USA.ORCID 0000-0003-0012-9640

Yong WangDepartment of Physics, University of Arkansas, Fayetteville, AR 72701, USA.ORCID 0000-0002-8601-8302

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Bent DNA amplifying sensors were recently developed to amplify and quantify the interactions of DNA with various salts and molecules. However, a thorough quantitative understanding of their mechanism is missing. Here, using all-atom molecular dynamics (MD) simulations, we investigate the behavior and dynamics of sharply bent DNA molecules in the absence and presence of Mg

Indexed as

Biosensing TechniquesDNAMolecular Dynamics SimulationFluorescence Resonance Energy TransferMagnesiumNucleic Acid ConformationDNAMagnesiumDNA bowsFRETmelting curveNAMDVMD

Identifiers

PMID40422011

DOI10.3390/bios15050272

PMCPMC12109749

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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.