title: Effect of crowding on the conformation of interwound DNA strands from neutron scattering measurements and Monte Carlo simulations.
abstract: With a view to determining the distance between the two opposing duplexes in supercoiled DNA, we have measured small angle neutron scattering from pHSG298 plasmid (2675 base pairs) dispersed in saline solutions. Experiments were carried out under full and zero average DNA neutron scattering contrast using hydrogenated plasmid and a 1:1 mixture of hydrogenated and perdeuterated plasmid, respectively. In the condition of zero average contrast, the scattering intensity is directly proportional to the single DNA molecule scattering function (form factor), irrespective of the DNA concentration and without complications from intermolecular interference. The form factors are interpreted with Monte Carlo computer simulation. For this purpose, the many body problem of a dense DNA solution was reduced to the one of a single DNA molecule in a congested state by confinement in a cylindrical potential. It was observed that the interduplex distance decreases with increasing concentration of salt as well as plasmid. Therefore, besides ionic strength, DNA crowding is shown to be important in controlling the interwound structure and site juxtaposition of distal segments of supercoiled DNA. This first study exploiting zero average DNA contrast has been made possible by the availability of perdeuterated plasmid.
authors.affiliation: Department of Physics, National University of Singapore, Singapore.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Zhu
authors.forename: Siow Yee
authors.initials: SY
authors.lastname: Ng
authors.forename: Amar Nath
authors.initials: AN
authors.lastname: Gupta
authors.forename: Yuan Ping
authors.initials: YP
authors.lastname: Feng
authors.forename: Bow
authors.initials: B
authors.lastname: Ho
authors.forename: Alain
authors.initials: A
authors.lastname: Lapp
authors.forename: Stefan U
authors.initials: SU
authors.lastname: Egelhaaf
authors.forename: V Trevor
authors.initials: VT
authors.lastname: Forsyth
authors.forename: Michael
authors.initials: M
authors.lastname: Haertlein
authors.forename: Martine
authors.initials: M
authors.lastname: Moulin
authors.forename: Ralf
authors.initials: R
authors.lastname: Schweins
authors.forename: Johan R C
authors.initials: JR
authors.lastname: van der Maarel
mesh_terms: D001703:Biophysics / Q000379:methods; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004278:DNA, Superhelical / Q000737:chemistry*; D017666:Deuterium Oxide; D007477:Ions; D009010:Monte Carlo Method; D009502:Neutrons; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000378:metabolism; D012492:Salts / Q000737:chemistry / Q000494:pharmacology; D012542:Scattering, Radiation; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry
chemical_list: D004278:DNA, Superhelical; D007477:Ions; D012492:Salts; D012997:Solvents; D014867:Water; D004247:DNA; D017666:Deuterium Oxide