Polymer properties of polythymine as revealed by translational diffusion

Doose S, Barsch H, Sauer M (2007)
Biophysical Journal 93(4): 1224-1234.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ;
Abstract / Bemerkung
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 L-p, we found that L-p approximate to l(m), 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 L-p of various labeled and nonlabeled polythymine derivatives. We found excellent agreement for the length dependence of simulated S and experimental R-h 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.; 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; 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.
Erscheinungsjahr
Zeitschriftentitel
Biophysical Journal
Band
93
Ausgabe
4
Seite(n)
1224-1234
ISSN
PUB-ID

Zitieren

Doose S, Barsch H, Sauer M. Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal. 2007;93(4):1224-1234.
Doose, S., Barsch, H., & Sauer, M. (2007). Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal, 93(4), 1224-1234. doi:10.1529/biophysj.107.107342
Doose, S., Barsch, H., and Sauer, M. (2007). Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal 93, 1224-1234.
Doose, S., Barsch, H., & Sauer, M., 2007. Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal, 93(4), p 1224-1234.
S. Doose, H. Barsch, and M. Sauer, “Polymer properties of polythymine as revealed by translational diffusion”, Biophysical Journal, vol. 93, 2007, pp. 1224-1234.
Doose, S., Barsch, H., Sauer, M.: Polymer properties of polythymine as revealed by translational diffusion. Biophysical Journal. 93, 1224-1234 (2007).
Doose, Sören, Barsch, Hannes, and Sauer, Markus. “Polymer properties of polythymine as revealed by translational diffusion”. Biophysical Journal 93.4 (2007): 1224-1234.

28 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

An implicit divalent counterion force field for RNA molecular dynamics.
Henke PS, Mak CH., J Chem Phys 144(10), 2016
PMID: 26979708
Prostate-specific RNA aptamer: promising nucleic acid antibody-like cancer detection.
Marangoni K, Neves AF, Rocha RM, Faria PR, Alves PT, Souza AG, Fujimura PT, Santos FA, Araújo TG, Ward LS, Goulart LR., Sci Rep 5(), 2015
PMID: 26174796
A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology.
Ander M, Subramaniam S, Fahmy K, Stewart AF, Schäffer E., PLoS Biol 13(8), 2015
PMID: 26271032
DNA-Directed Fluorescence Switching of Silver Clusters.
Ganguly M, Bradsher C, Goodwin P, Petty JT., J Phys Chem C Nanomater Interfaces 119(49), 2015
PMID: 30220954
Transfer of low-molecular weight single-stranded DNA through the membrane of a high-flux dialyzer.
Tao X, Hoenich N, Handelman SK, Levin NW, Kotanko P, Handelman GJ., Int J Artif Organs 37(7), 2014
PMID: 25044384
Flexibility of single-stranded DNA measured by single-molecule FRET.
Kang J, Jung J, Kim SK., Biophys Chem 195(), 2014
PMID: 25194278
Near-infrared silver cluster optically signaling oligonucleotide hybridization and assembling two DNA hosts.
Petty JT, Nicholson DA, Sergev OO, Graham SK., Anal Chem 86(18), 2014
PMID: 25157472
A complementary palette of NanoCluster Beacons.
Obliosca JM, Babin MC, Liu C, Liu YL, Chen YA, Batson RA, Ganguly M, Petty JT, Yeh HC., ACS Nano 8(10), 2014
PMID: 25299363
Silver clusters as both chromophoric reporters and DNA ligands.
Petty JT, Giri B, Miller IC, Nicholson DA, Sergev OO, Banks TM, Story SP., Anal Chem 85(4), 2013
PMID: 23330780
Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model.
Meisburger SP, Sutton JL, Chen H, Pabit SA, Kirmizialtin S, Elber R, Pollack L., Biopolymers 99(12), 2013
PMID: 23606337
Optical sensing by transforming chromophoric silver clusters in DNA nanoreactors.
Petty JT, Story SP, Juarez S, Votto SS, Herbst AG, Degtyareva NN, Sengupta B., Anal Chem 84(1), 2012
PMID: 22098274
Ionic strength-dependent persistence lengths of single-stranded RNA and DNA.
Chen H, Meisburger SP, Pabit SA, Sutton JL, Webb WW, Pollack L., Proc Natl Acad Sci U S A 109(3), 2012
PMID: 22203973
Single-molecule views of protein movement on single-stranded DNA.
Ha T, Kozlov AG, Lohman TM., Annu Rev Biophys 41(), 2012
PMID: 22404684
Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions.
Bollmann S, Löllmann M, Sauer M, Doose S., Phys Chem Chem Phys 13(28), 2011
PMID: 21687885
DNA sensing by amplifying the number of near-infrared emitting, oligonucleotide-encapsulated silver clusters.
Petty JT, Sengupta B, Story SP, Degtyareva NN., Anal Chem 83(15), 2011
PMID: 21702495
Hydrodynamic properties of human adhesion/growth-regulatory galectins studied by fluorescence correlation spectroscopy.
Göhler A, André S, Kaltner H, Sauer M, Gabius HJ, Doose S., Biophys J 98(12), 2010
PMID: 20550917
The length and viscosity dependence of end-to-end collision rates in single-stranded DNA.
Uzawa T, Cheng RR, Cash KJ, Makarov DE, Plaxco KW., Biophys J 97(1), 2009
PMID: 19580758
Loop dependence of the stability and dynamics of nucleic acid hairpins.
Kuznetsov SV, Ren CC, Woodson SA, Ansari A., Nucleic Acids Res 36(4), 2008
PMID: 18096625
Stretching and unzipping nucleic acid hairpins using a synthetic nanopore.
Zhao Q, Comer J, Dimitrov V, Yemenicioglu S, Aksimentiev A, Timp G., Nucleic Acids Res 36(5), 2008
PMID: 18208842
Base-Directed Formation of Fluorescent Silver Clusters.
Sengupta B, Ritchie C, Buckman J, Johnsen K, Goodwin P, Petty J., J Phys Chem C Nanomater Interfaces 112(48), 2008
PMID: 30319723
Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy.
Manohar S, Mantz AR, Bancroft KE, Hui CY, Jagota A, Vezenov DV., Nano Lett 8(12), 2008
PMID: 19368004

67 References

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, 1969

AUTHOR UNKNOWN, 1949

AUTHOR UNKNOWN, 1979

AUTHOR UNKNOWN, 1996

AUTHOR UNKNOWN, 1988
Ten years of tension: single-molecule DNA mechanics.
Bustamante C, Bryant Z, Smith SB., Nature 421(6921), 2003
PMID: 12540915

AUTHOR UNKNOWN, 1988
Flexibility of RNA.
Hagerman PJ., Annu Rev Biophys Biomol Struct 26(), 1997
PMID: 9241416
Direct observation of motion of single F-actin filaments in the presence of myosin.
Yanagida T, Nakase M, Nishiyama K, Oosawa F., Nature 307(5946), 1984
PMID: 6537825
Tracer studies on f-actin fluctuations.
Le Goff L, Hallatschek O, Frey E, Amblard F., Phys. Rev. Lett. 89(25), 2002
PMID: 12484923
Thermal fluctuations of grafted microtubules provide evidence of a length-dependent persistence length.
Pampaloni F, Lattanzi G, Jonas A, Surrey T, Frey E, Florin EL., Proc. Natl. Acad. Sci. U.S.A. 103(27), 2006
PMID: 16801537
Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape.
Gittes F, Mickey B, Nettleton J, Howard J., J. Cell Biol. 120(4), 1993
PMID: 8432732
Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy.
Murphy MC, Rasnik I, Cheng W, Lohman TM, Ha T., Biophys. J. 86(4), 2004
PMID: 15041689
A semiflexible polymer model applied to loop formation in DNA hairpins.
Kuznetsov SV, Shen Y, Benight AS, Ansari A., Biophys. J. 81(5), 2001
PMID: 11606297

AUTHOR UNKNOWN, 2002

AUTHOR UNKNOWN, 2001

AUTHOR UNKNOWN, 1977

AUTHOR UNKNOWN, 1977
The electrostatic persistence length of polymers beyond the OSF limit.
Everaers R, Milchev A, Yamakov V., Eur Phys J E Soft Matter 8(1), 2002
PMID: 15010979

AUTHOR UNKNOWN, 1993

AUTHOR UNKNOWN, 1995
Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins.
Laurence TA, Kong X, Jager M, Weiss S., Proc. Natl. Acad. Sci. U.S.A. 102(48), 2005
PMID: 16287971
Radial distribution function of rod-like polyelectrolytes.
Zandi R, Rudnick J, Golestanian R., Eur Phys J E Soft Matter 9(1), 2002
PMID: 15010928
DNA transport by a micromachined Brownian ratchet device.
Bader JS, Hammond RW, Henck SA, Deem MW, McDermott GA, Bustillo JM, Simpson JW, Mulhern GT, Rothberg JM., Proc. Natl. Acad. Sci. U.S.A. 96(23), 1999
PMID: 10557291
Probing single DNA mobility with fluorescence correlation microscopy.
Tatarkova SA, Berk DA., Phys Rev E Stat Nonlin Soft Matter Phys 71(4 Pt 1), 2005
PMID: 15903707
Reassessing random-coil statistics in unfolded proteins.
Fitzkee NC, Rose GD., Proc. Natl. Acad. Sci. U.S.A. 101(34), 2004
PMID: 15314216
Random-coil behavior and the dimensions of chemically unfolded proteins.
Kohn JE, Millett IS, Jacob J, Zagrovic B, Dillon TM, Cingel N, Dothager RS, Seifert S, Thiyagarajan P, Sosnick TR, Hasan MZ, Pande VS, Ruczinski I, Doniach S, Plaxco KW., Proc. Natl. Acad. Sci. U.S.A. 101(34), 2004
PMID: 15314214

AUTHOR UNKNOWN, 1996

AUTHOR UNKNOWN, 1971

AUTHOR UNKNOWN, 1990
Size-dependent DNA mobility in cytoplasm and nucleus.
Lukacs GL, Haggie P, Seksek O, Lechardeur D, Freedman N, Verkman AS., J. Biol. Chem. 275(3), 2000
PMID: 10636854
The dimensions of DNA in solution.
Mandelkern M, Elias JG, Eden D, Crothers DM., J. Mol. Biol. 152(1), 1981
PMID: 7338906

AUTHOR UNKNOWN, 1984

AUTHOR UNKNOWN, 1990
Structure and dynamics of M13mp19 circular single-strand DNA: effects of ionic strength.
Wilson DH, Price HL, Henderson J, Hanlon S, Benight AS., Biopolymers 29(2), 1990
PMID: 2331504

AUTHOR UNKNOWN, 2001
Stretching single stranded DNA, a model polyelectrolyte.
Dessinges MN, Maier B, Zhang Y, Peliti M, Bensimon D, Croquette V., Phys. Rev. Lett. 89(24), 2002
PMID: 12484983
Replication by a single DNA polymerase of a stretched single-stranded DNA.
Maier B, Bensimon D, Croquette V., Proc. Natl. Acad. Sci. U.S.A. 97(22), 2000
PMID: 11050232
Hairpin formation and elongation of biomolecules.
Montanari A, Mezard M., Phys. Rev. Lett. 86(10), 2001
PMID: 11289884
Dynamics of unfolded polypeptide chains in crowded environment studied by fluorescence correlation spectroscopy.
Neuweiler H, Lollmann M, Doose S, Sauer M., J. Mol. Biol. 365(3), 2006
PMID: 17084857
Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding.
Krieger F, Fierz B, Bieri O, Drewello M, Kiefhaber T., J. Mol. Biol. 332(1), 2003
PMID: 12946363

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 2001

AUTHOR UNKNOWN, 2003
The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy.
Kim J, Doose S, Neuweiler H, Sauer M., Nucleic Acids Res. 34(9), 2006
PMID: 16687657

AUTHOR UNKNOWN, 1995

AUTHOR UNKNOWN, 2004
VMD: visual molecular dynamics.
Humphrey W, Dalke A, Schulten K., J Mol Graph 14(1), 1996
PMID: 8744570

AUTHOR UNKNOWN, 2000

AUTHOR UNKNOWN, 2002

AUTHOR UNKNOWN, 2007

AUTHOR UNKNOWN, 1953

AUTHOR UNKNOWN, 1998
Single-molecule studies of DNA mechanics.
Bustamante C, Smith SB, Liphardt J, Smith D., Curr. Opin. Struct. Biol. 10(3), 2000
PMID: 10851197
The poly(rU) coil: a minimum-energy model that matches experimental observations.
Hingerty BE, Broyde SB, Olson WK., Biopolymers 21(6), 1982
PMID: 6178444

AUTHOR UNKNOWN, 1965
Unified description of electrophoresis and diffusion for DNA and other polyions.
Stellwagen E, Lu Y, Stellwagen NC., Biochemistry 42(40), 2003
PMID: 14529285

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 17513377
PubMed | Europe PMC

Suchen in

Google Scholar