ArticleBiophysical journal2007
Polymer properties of polythymine as revealed by translational diffusion.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 75 citations in OpenAlex.
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- Photonic Crystal Surface Mode Real-Time Imaging of RAD51 DNA Repair Protein Interaction with the ssDNA Substrate.Biosensors · 2024Article
- Interrupted DNA and Slow Silver Cluster Luminescence.The journal of physical chemistry. C, Nanomaterials and interfaces · 2023Article
- Can Hindered Transport Models for Rigid Spheres Predict the Rejection of Single Stranded DNA from Porous Membranes?Membranes · 2022Article
- Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles.Nature methods · 2022Article
- Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.The journal of physical chemistry letters · 2022Article
- Nanopores in Atomically Thin 2D Nanosheets Limit Aqueous Single-Stranded DNA Transport.Physical review letters · 2021Article
- Sugar-Pucker Force-Induced Transition in Single-Stranded DNA.International journal of molecular sciences · 2021Article
- Conformational Changes of Immobilized Polythymine due to External Stressors Studied with Temperature-Controlled Electrochemical Microdevices.Langmuir : the ACS journal of surfaces and colloids · 2021Article
- Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV.Beilstein journal of organic chemistry · 2021Article
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.Journal of chemical theory and computation · 2018Article
- Persistence Length and Cooperativity Estimation of Single Stranded DNA using FCS Combined with HYDRO Program.Journal of fluorescence · 2017Article
- A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology.PLoS biology · 2015Article
- Prostate-specific RNA aptamer: promising nucleic acid antibody-like cancer detection.Scientific reports · 2015Article
- Terminal lipophilization of a unique DNA dodecamer by various nucleolipid headgroups: Their incorporation into artificial lipid bilayers and hydrodynamic properties.Beilstein journal of organic chemistry · 2015Article
- DNA-Directed Fluorescence Switching of Silver Clusters.The journal of physical chemistry. C, Nanomaterials and interfaces · 2015Article
- A complementary palette of NanoCluster Beacons.ACS nano · 2014Article
- Near-infrared silver cluster optically signaling oligonucleotide hybridization and assembling two DNA hosts.Analytical chemistry · 2014Article
- Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model.Biopolymers · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biopolymers, such as single-stranded DNA (ssDNA), are often described as semiflexible polymers or wormlike chains. We investigated the length dependence of diffusional properties of homogeneous ssDNA (polythymine) with up to 100 nucleotides using fluorescence correlation spectroscopy. We found that the hydrodynamic radius Rh scales according to a power law, with an exponent between 0.5 and 0.7 depending on ionic strength I. With Rh being proportional to the square root of the persistence length Lp, we found that Lp approximately Im, with m=-0.22+/-0.01 for polythymine with 100 residues. For comparison, we performed molecular dynamics (MD) simulations with a force field that accounts for short-range interactions in vacuum, and determined the characteristic polymer properties end-to-end distance R, radius of gyration S, and persistence length Lp of various labeled and nonlabeled polythymine derivatives. We found excellent agreement for the length dependence of simulated S and experimental Rh measured at 100 mM NaCl, revealing that electrostatic interactions are completely shielded in aqueous solution at such ionic strength. MD simulations further showed that polythymine with >approximately 30 residues can be described as a semiflexible polymer with negligible influence of the fluorescent label; and that static flexibility is limited by geometrical and steric constraints as expressed by an intrinsic persistence length of approximately 1.7 nm. These results provide a benchmark for theories and MD simulations describing the influence of electrostatic interactions on polyelectrolyte properties, and thus help to develop a complete and accurate description of ssDNA.
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