title: Sequence and temperature dependence of the interbase hydrogen-bond breathing modes in B-DNA polymers: comparison with low-frequency Raman peaks and their role in helix melting.
abstract: We carry out temperature-dependent lattice dynamics calculations to determine the vibrational normal modes associated with the interbase H-bond breathing motion in several B-DNA copolymers at temperatures from room temperature to the melting temperatures. We take into consideration Raman selection rules and incorporate a simple empirical model of Raman susceptibility in the interbase H bonds in our calculation and compare them to Raman measurements. Our calculations are carried out using empirical force constants that are not further refined to low-frequency spectra. Our calculations show the existence of strong interbase H-bond breathing modes at frequencies and with relative oscillator strengths close to the observed Raman peaks in the range of 60-140 cm-1 for the DNA sequences considered except for one helix. The correlation between the calculated and observed frequencies and oscillator strengths indicates that the observed Raman peaks in the frequency range are likely interbase H-bond breathing modes. We find that these modes exhibit sizable temperature as well as sequence dependence. We show the softening of these modes on approaching thermal denaturation that is also in agreement with the observed behavior in Raman and melting measurements. The sensitivity of the calculation on the empirical model of Raman susceptibility and the possible reasons for the discrepancy between a few calculated values and observations are discussed.
authors.affiliation: Department of Physics, Purdue University, West Lafayette, Indiana 47907-1306, USA.
authors.forename: Y Z
authors.initials: YZ
authors.lastname: Chen
authors.forename: E W
authors.initials: EW
authors.lastname: Prohofsky
mesh_terms: D000818:Animals; D002417:Cattle; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008433:Mathematics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011089:Polydeoxyribonucleotides / Q000737:chemistry*; D013059:Spectrum Analysis, Raman; D013950:Thymus Gland; D014732:Vibration
chemical_list: D011089:Polydeoxyribonucleotides; D004247:DNA