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- Perturbations to the intersystem crossing of proflavin upon ...Perturbations to the intersystem crossing of proflavin upon binding to DNA and poly d(A-IU) from triplet-delayed emission spectroscopy
Biophysical Journal, Volume 54, Issue 4, 1 October 1988, Pages 627-635
W.E. Lee and W.C. Galley
AbstractThe steady-state prompt fluorescence, phosphorescence and delayed fluorescence spectra and triplet lifetimes of free proflavin and proflavin bound to native DNA and alternating poly d(A-IU) were obtained as a function of temperature in a buffer-glycerol solvent. The intensity of the proflavin E-type delayed fluorescence (DF) relative to both the phosphorescence (Ph) and the prompt fluorescence (F) was observed to increase with temperature, and plots of both ln (DF/Ph) and ln (DF/(F.tau T] as a function of 1/T were linear over a wide range of temperatures. Although the activation energies for the thermal repopulation of the proflavin excited singlet state from the triplet obtained from the slopes of these plots were essentially unchanged on binding, perturbations to the S1----T1 intersystem crossing rate constants extracted from the intercepts at infinite temperature were observed. The marked enhancement of the intersystem crossing that occurs with binding to the iodinated polynucleotide reflects an external heavy atom perturbation upon the intercalated dye which also induces a shortening in the triplet lifetime. With proflavin bound to DNA an enhancement to the S1----T1 intersystem crossing, though lesser in magnitude than for poly d(A-IU), is observed but with no change to the triplet lifetime. The well-studied fluorescence quenching of DNA-bound proflavin is a result of this increase in the intersystem crossing. It is proposed that these non-heavy atom enhancements in the intersystem crossing are due to distortions of the molecular plane of the bound proflavin molecule. In total these analyses provide a complete description of the excited state processes of the proflavin molecule and their variations with temperature.
Abstract | PDF (882 kb) - Low temperature structures of dCpG-proflavine. Conformationa...Low temperature structures of dCpG-proflavine. Conformational and hydration effects
Biophysical Journal, Volume 63, Issue 6, 1 December 1992, Pages 1572-1578
B. Schneider, S.L. Ginell and H.M. Berman
AbstractThe structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85–97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296 A. Cold temperature was refined isotropically with 2,846 reflections 8.0–0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks.
Abstract | PDF (791 kb) - Intercalation of Proflavine and a Platinum Derivative of Pro...Intercalation of Proflavine and a Platinum Derivative of Proflavine into Double-Helical Poly(A)
Biophysical Journal, Volume 77, Issue 5, 1 November 1999, Pages 2717-2724
Carlo Ciatto, Maria L. D’Amico, Giovanni Natile, Fernando Secco and Marcella Venturini
AbstractThe equilibria and kinetics of the interactions of proflavine (PR) and its platinum-containing derivative [{PtCl(tmen)}{HNCH(NHCHCH)}] (PRPt) with double-stranded poly(A) have been investigated by spectrophotometry and Joule temperature-jump relaxation at ionic strength 0.1M, 25°C, and pH 5.2. Spectrophotometric measurements indicate that base-dye interactions are prevailing. T-jump experiments with polarized light showed that effects due to field-induced alignment could be neglected. Both of the investigated systems display two relaxation effects. The kinetic features of the reaction are discussed in terms of a two-step series mechanism in which a precursor complex DS is formed in the fast step, which is then converted to a final complex in the slow step. The rate constants of the fast step are =(2.5±0.4)×10Ms, =(2.4±0.1)×10s for poly(A)-PR and =(2.3±0.1)×10Ms, =(1.6±0.2)×10s for poly(A)-PRPt. The rate constants for the slow step are =(4.5±0.5)×10s, =(1.7±0.1)×10s for poly(A)-PR and =9.7±1.2s, =10.6±0.2s for poly(A)-PRPt. Spectrophotometric measurements yield for the equilibrium constants and site size the values =(4.5±0.1)×10M, =1.3±0.5 for poly(A)-PR and =(2.9±0.1)×10M, =2.3±0.6 for poly(A)-PRPt. The values of are similar and lower than expected for diffusion-limited reactions. The values of are similar as well. It is suggested that the formation of DS involves only the proflavine residues in both systems. In contrast, the values of and in poly(A)-PRPt are much lower than in poly(A)-PR. The results suggest that in the complex DS of poly(A)-PRPt both proflavine and platinum residues are intercalated. In addition, a very slow process was detected and ascribed to the covalent binding of Pt(II) to the adenine.
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Copyright © 1996 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 71, Issue 3, 1179-1190, 1 September 1996
doi:10.1016/S0006-3495(96)79322-0
Research Article
Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate
H. Resat and M. Mezei
Abstract
The grand canonical ensemble Monte Carlo molecular simulation method is used to investigate hydration patterns in the crystal hydrate structure of the dCpG/proflavine intercalated complex. The objective of this study is to show by example that the recently advocated grand canonical ensemble simulation is a computationally efficient method for determining the positions of the hydrating water molecules in protein and nucleic acid structures. A detailed molecular simulation convergence analysis and an analogous comparison of the theoretical results with experiments clearly show that the grand ensemble simulations can be far more advantageous than the comparable canonical ensemble simulations.
