ArticleInternational journal of numerical analysis and modeling2009
THE MELTING MECHANISM OF DNA TETHERED TO A SURFACE.
Article in International journal of numerical analysis and modeling, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Acceleration of DNA melting kinetics using alternating electric fields.The Journal of chemical physics · 2018Article
- Melting dynamics of short dsDNA chains in saline solutions.SpringerPlus · 2015Article
- Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs.Journal of computer-aided molecular design · 2014Article
- Heat-transfer-based detection of SNPs in the PAH gene of PKU patients.International journal of nanomedicine · 2014Article
- Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond.Nucleic acids research · 2012Article
- Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach.Journal of physics. Condensed matter : an Institute of Physics journal · 2011Article
- A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach.Computer physics communications · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The details of melting of DNA immobilized on a chip or nanoparticle determines the sensitivity and operating characteristics of many analytical and synthetic biotechnological devices. Yet, little is known about the differences in how the DNA melting occurs between a homogeneous solution and that on a chip. We used molecular dynamics simulations to explore possible pathways for DNA melting on a chip. Simulation conditions were chosen to ensure that melting occurred in a submicrosecond timescale. The temperature was set to 400 K and the NaCl concentration was set to 0.1 M. We found less symmetry than in the solution case where for oligomeric double-stranded nucleic acids both ends melted with roughly equal probability. On a prepared silica surface we found melting is dominated by fraying from the end away from the surface. Strand separation was hindered by nonspecific surface adsorption at this temperature. At elevated temperatures the melted DNA was attracted to even uncharged organically coated surfaces demonstrating surface fouling. While hybridization is not the simple reverse of melting, this simulation has implications for the kinetics of hybridization.
Identifiers
19802357PMC2755589What OpenQuestion holds
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.