title: Probing the structure of long DNA molecules in solution using synchrotron radiation linear dichroism.
abstract: Linear dichroism (LD), a spectroscopic method for aligned samples, has been used with a synchrotron radiation source to reveal insights into the structure and stability of DNA with increasing salt concentrations (thus stabilizing the base pairing) and increasing temperature while remaining below the melting point (thus destabilizing the base pairing). Measurements have been made from 350 nm to 182 nm, and the spectral changes observed quantified using a Bayesian Markov chain Monte Carlo (MCMC) algorithm, which uses statistical methods to fit to experimental data. Based on literature H-D exchange experiments, we surmise that the cause of the spectral variations is the induction of transient single stranding of tracts in the DNA polymer, particularly those with significant content of the weaker AT base pairs. More detailed analysis of the LD data will require better nucleotide transition polarization assignments.
authors.affiliation: ZBSA, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany.
authors.forename: Martyn
authors.initials: M
authors.lastname: Rittman
authors.forename: Søren V
authors.initials: SV
authors.lastname: Hoffmann
authors.forename: Emma
authors.initials: E
authors.lastname: Gilroy
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Hicks
authors.forename: Bärbel
authors.initials: B
authors.lastname: Finkenstadt
authors.forename: Alison
authors.initials: A
authors.lastname: Rodger
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D001499:Bayes Theorem; D004247:DNA / Q000737:chemistry*; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D012492:Salts; D012996:Solutions; D013057:Spectrum Analysis; D017356:Synchrotrons; D013696:Temperature; D013816:Thermodynamics
chemical_list: D012492:Salts; D012996:Solutions; D004247:DNA