Contribution of opening and bending dynamics to specific recognition of DNA damage.

Guanine-uracil (G.U) wobble base-pairs are a detrimental lesion in DNA. Previous investigations have shown that such wobble base-pairs are more prone to base-opening than the normal G.C base-pairs. To investigate the sequence-dependence of base-pair opening we have performed 5ns molecular dynamics simulations on G.U wobble base-pairs in two different sequence contexts, TGT/AUA and CGC/GUG. Furthermore, we have investigated the effect of replacing the guanine base in each sequence with a fluorescent guanine analogue, 6-methylisoxanthopterin (6MI). Our results indicate that each sequence opens spontaneously towards the major groove in the course of the simulations. The TGT/AUA sequence has a greater proportion of structures in the open state than the CGC/GUG sequence. Incorporation of 6MI yields wobble base-pairs that open more readily than their guanine counterparts. In order of increasing open population, the sequences are ordered as CGC<TGT<CMC<TMT, where M represents 6MI. Both members of the base-pair open towards the major groove in a symmetrically coupled motion. Opening results in breakage of the H3(U)-O6(G/6MI) hydrogen bond, and distortion of the H1(G/6MI)-O2(U) hydrogen bond. Structural consequences of the opening include the formation of the H21(G/6MI)-O2(U) hydrogen bond and a change in local solvation in the grooves and particularly near N3-H3 of uracil. Additionally, DNA flexibility is reduced in the open state for bending towards the major groove generating two nearly discrete states: closed unbent and open bent. The observed differences in the local structural and dynamical properties of the G.U base-pair may play an important role in the activity of DNA repair enzymes that initiate base excision by distorting the DNA and flipping the target base from inside the DNA helix.

[1]  H. Krokan,et al.  Properties of a recombinant human uracil-DNA glycosylase from the UNG gene and evidence that UNG encodes the major uracil-DNA glycosylase. , 1995, Biochemistry.

[2]  R. Lavery,et al.  Modelling base pair opening: the role of helical twist☆ , 1997 .

[3]  G. Varani,et al.  The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. , 2000, EMBO reports.

[4]  Mihaly Mezei.  Modified Proximity Criteria for the Analysis of the Solvation of a Polyfunctional Solute , 1988 .

[5]  W. Hunter,et al.  The structure of guanosine-thymidine mismatches in B-DNA at 2.5-A resolution. , 1993, The Journal of biological chemistry.

[6]  T Schlick,et al.  Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships. , 2001, Journal of molecular biology.

[7]  P. Tauc,et al.  DNA binding induces dissociation of the multimeric form of HIV-1 integrase: A time-resolved fluorescence anisotropy study , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[8]  D. Crothers,et al.  Nucleic Acids: Structures, Properties, and Functions , 2000 .

[9]  R Lavery,et al.  The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. , 1988, Journal of biomolecular structure & dynamics.

[10]  J. Šponer,et al.  Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs , 1996 .

[11]  J. Knutson,et al.  Fluorescence properties of pteridine nucleoside analogs as monomers and incorporated into oligonucleotides. , 1997, Analytical biochemistry.

[12]  R. Osman,et al.  Role of DNA flexibility in sequence-dependent activity of uracil DNA glycosylase. , 2002, Biochemistry.

[13]  A. Sarvazyan,et al.  Influence of base composition, base sequence, and duplex structure on DNA hydration: apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25 degrees C. , 1994, Biochemistry.

[14]  B. L. de Groot,et al.  Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds. , 2001, Journal of molecular biology.

[15]  J Langowski,et al.  Sequence-dependent elastic properties of DNA. , 2000, Journal of molecular biology.

[16]  J. Ramstein,et al.  Energetic coupling between DNA bending and base pair opening. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[17]  S. Bennett,et al.  Uracil-excision DNA repair. , 1994, Progress in nucleic acid research and molecular biology.

[18]  S. L. Lam,et al.  Low Temperature Solution Structures and Base Pair Stacking of Double Helical d(CGTACG)2 , 2002, Journal of biomolecular structure & dynamics.

[19]  Alexander S. Chin,et al.  pH-Dependent Spectroscopy and Electronic Structure of the Guanine Analogue 6,8-Dimethylisoxanthopterin † , 2003 .

[20]  J. Goodisman.  Statistical mechanics for chemists , 1997 .

[21]  M. Sundaralingam,et al.  Crystal structure of an RNA duplex r(G GCGC CC)2 with non-adjacent G*U base pairs. , 1999, Nucleic acids research.

[22]  D. Patel,et al.  Wobble dG X dT pairing in right-handed DNA: solution conformation of the d(C-G-T-G-A-A-T-T-C-G-C-G) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra. , 1986, Biochemistry.

[23]  Theoretical considerations on the "spine of hydration" in the minor groove of d(CGCGAATTCGCG).d(GCGCTTAAGCGC): Monte Carlo computer simulation. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[24]  D. Beveridge,et al.  STRUCTURAL ANALYSIS OF MOLECULAR SOLUTIONS BASED ON QUASI-COMPONENT DISTRIBUTION FUNCTIONS. APPLICATION TO (H2CO)AQ AT 25°C , 1980 .

[25]  M. Sundaralingam,et al.  Hydrogen and hydration of DNA and RNA oligonucleotides. , 2002, Biophysical chemistry.

[26]  R. Lavery,et al.  Energetic and conformational aspects of A:T base-pair opening within the DNA double helix. , 2001, Chemphyschem : a European journal of chemical physics and physical chemistry.

[27]  J. SantaLucia,et al.  Improved nearest-neighbor parameters for predicting DNA duplex stability. , 1996, Biochemistry.

[28]  F. Balis,et al.  Real-time fluorescence assay for O6-alkylguanine-DNA alkyltransferase. , 2000, Analytical biochemistry.

[29]  W. McClain,et al.  The relationship of thermodynamic stability at a G x U recognition site to tRNA aminoacylation specificity. , 1999, RNA.

[30]  P. Kollman,et al.  A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. , 1999, Journal of biomolecular structure & dynamics.

[31]  R. Osman,et al.  Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine. , 2001, Biochemistry.

[32]  U. Dornberger,et al.  High Base Pair Opening Rates in Tracts of GC Base Pairs* , 1999, The Journal of Biological Chemistry.

[33]  M. Saparbaev,et al.  3,N4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[34]  J. Cole,et al.  HU Binding to DNA: Evidence for Multiple Complex Formation and DNA Bending† , 2001 .

[35]  J. Moe,et al.  Kinetics and energetics of base-pair opening in 5'-d(CGCGAATTCGCG)-3' and a substituted dodecamer containing G.T mismatches. , 1992, Biochemistry.

[36]  R. Osman,et al.  Role of base flipping in specific recognition of damaged DNA by repair enzymes. , 2002, Journal of molecular biology.

[37]  Richard Lavery,et al.  Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations. , 2002, Journal of the American Chemical Society.