ArticleMacromolecules2013
Presentation of large DNA molecules for analysis as nanoconfined dumbbells.
Article in Macromolecules, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed.
- Developing an insert to protect large DNA molecules during cell lysis.BioTechniques · 2025Article
- Concentration of lambda concatemers using a 3D printed device.Electrophoresis · 2023Article
- Analysis of Bisulfite Via a Nitro Derivative of Cyanine-3 (NCy3) in the Microfluidic Channel.Journal of fluorescence · 2019Article
- Development of 3D printed mesofluidic devices to elute and concentrate DNA.Electrophoresis · 2019Article
- A simple dialysis device for large DNA molecules.BioTechniques · 2019Article
- Microscale Objects via Restructuring of Large, Double-Stranded DNA Molecules.ACS applied materials & interfaces · 2018Article
- Single-molecule DNA-mapping and whole-genome sequencing of individual cells.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Measuring the wall depletion length of nanoconfined DNA.The Journal of chemical physics · 2018Article
- Determining if DNA Stained with a Cyanine Dye Can Be Digested with Restriction Enzymes.Journal of visualized experiments : JoVE · 2018Article
- Electrostatic confinement and manipulation of DNA molecules for genome analysis.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Spatial confinement induces hairpins in nicked circular DNA.Nucleic acids research · 2017Article
- Allele-Specific Quantification of Structural Variations in Cancer Genomes.Cell systems · 2016Article
- Maligner: a fast ordered restriction map aligner.Bioinformatics (Oxford, England) · 2016Article
- Identifying DNA methylation in a nanochannel.Science and technology of advanced materials · 2016Article
- Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014).Analytical and bioanalytical chemistry · 2015Review
- Self-consistent description of electrokinetic phenomena in particle-based simulations.The Journal of chemical physics · 2015Article
- Visualizing the entire DNA from a chromosome in a single frame.Biomicrofluidics · 2015Article
- Hydrodynamics of DNA confined in nanoslits and nanochannels.The European physical journal. Special topics · 2014Article
- DNA translocation through short nanofluidic channels under asymmetric pulsed electric field.Biomicrofluidics · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multi-pronged approach that marshaled molecular confinement, ionic environment, and DNA elastic properties-but tressed by molecular simulations-we have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green's function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the "Odijk regime" does indeed start when the confinement dimensions size are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics.
Identifiers
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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.