ArticleBiophysical journal2009
The length and viscosity dependence of end-to-end collision rates in single-stranded DNA.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 34 citations in OpenAlex.
- Evidence of a Three-State Mechanism in DNA Hairpin Folding.Journal of the American Chemical Society · 2025Article
- Nanosecond chain dynamics of single-stranded nucleic acids.Nature communications · 2024Article
- Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics.The journal of physical chemistry. B · 2014Article
- Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA.Biophysical journal · 2013Article
- Non-Markovian polymer reaction kinetics.Nature chemistry · 2012Article
- Universality in the timescales of internal loop formation in unfolded proteins and single-stranded oligonucleotides.Biophysical journal · 2010Article
- A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs.Journal of the American Chemical Society · 2010Article
- The rate of intramolecular loop formation in DNA and polypeptides: the absence of the diffusion-controlled limit and fractional power-law viscosity dependence.The journal of physical chemistry. B · 2009Article
- Engineering New Aptamer Geometries for Electrochemical Aptamer-Based Sensors.Proceedings of SPIE--the International Society for Optical Engineering · 2009Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Intramolecular dynamics play an essential role in the folding and function of biomolecules and, increasingly, in the operation of many biomimetic technologies. Thus motivated we have employed both experiment and simulation to characterize the end-to-end collision dynamics of unstructured, single-stranded DNAs ranging from 6 to 26 bases. We find that, because of the size and flexibility of the optical reporters employed experimentally, end-to-end collision dynamics exhibit little length dependence at length scales <11 bases. For longer constructs, however, the end-to-end collision rate exhibits a power-law relationship to polymer length with an exponent of -3.49 +/- 0.13. This represents a significantly stronger length dependence than observed experimentally for unstructured polypeptides or predicted by polymer scaling arguments. Simulations indicate, however, that the larger exponent stems from electrostatic effects that become important over the rather short length scale of these highly charged polymers. Finally, we have found that the end-to-end collision rate also depends linearly on solvent viscosity, with an experimentally significant, nonzero intercept (the extrapolated rate at zero viscosity) that is independent of chain length--n observation that sheds new light on the origins of the "internal friction" observed in the dynamics of many polymer 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.