Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching

5-Bromouracil disrupts nucleosome positioning by inducing A-form-like DNA conformation in yeast cells

5-Bromodeoxyuridine (BrdU) modulates expression of particular genes associated with cellular differentiation and senescence. Our previous studies have suggested an involvement of chromatin structure in this phenomenon. Here, we examined the effect of 5-bromouracil on nucleosome positioning in vivo using TALS plasmid in yeast cells. This plasmid can stably and precisely be assembled nucleosomes aided by the alpha2 repressor complex bound to its alpha2 operator. Insertion of AT-rich sequences into a site near the operator destabilized nucleosome positioning dependent on their length and sequences. Addition of BrdU almost completely disrupted nucleosome positioning through specific AT-tracts. The effective AT-rich sequences migrated faster on polyacrylamide gel electrophoresis, and their mobility was further accelerated by substitution of thymine with 5-bromouracil. Since this property is indicative of a rigid conformation of DNA, our results suggest that 5-bromouracil disrupts nucleosome positioning by inducing A-form-like DNA.

Effect of a water molecule on the sugar puckering of uridine, 2'-deoxyuridine, and 2'-O-methyl uridine inserted in duplexes

We used high-level quantum mechanical calculations to determine the pucker (north type or south type) of various compounds: uridine, 2'-deoxyuridine, and 2'-O-methyl uridine. Although the dihedrals of the backbone are set close to their experimental values in double-stranded nucleic acids, calculations using density functional theory show that, in vacuo or in a continuum mimicking the dielectric properties of water, the south puckering conformations of uridine is favored. This contrasts with experimental data: most ribonucleosides inserted into a duplex have the north puckering. We show here that the north puckering is favored when an explicit water molecule is introduced into the calculation. The orientations of the 2' group and of the water molecule have implications for the prevalence of the north puckering. We studied several orientations of the water molecule binding uracil O2 and the 2' group and estimated the energy barriers in the path between the north-to-south conformations. The north puckering is more favored in 2'-OH than in 2'-OCH3 compounds in the presence of the explicit water molecule.

DNA bending induced by carbocyclic sugar analogs constrained to the north conformation

DNA bending caused by introduction of carbocyclic sugars constrained to the north conformation was studied, using explicit solvent molecular dynamic (MD) simulations. The native Drew-Dickerson (DD) dodecamer and its three modifications containing north carbocyclic sugars in the 7th (T7*), 8th (T8*) or both 7th and 8th (T7T8*) nucleotide positions were examined. Introduction of the carbocyclic sugar results in A-form conformations for the alpha, beta, chi, zeta, and sugar pucker backbone parameters in the modified nucleotides. Increased steric repulsion between the sugar and its parent base in the modified oligonucleotides impacts the roll and cup dinucleotide step parameters, increasing the bending of the oligomer axis. Increased buckling of the substituted nucleotides disrupts the usual stabilizing base stacking interactions. The level of overall bending depends on the number and position of carbocyclic sugars introduced in the DNA sequence. Single sugar substitutions are unable to induce substantial bending due to the neighboring unmodified nucleotides counterbalancing the distortion. Significant bending can, however, be induced by two consecutive north sugars (T7T8*), which is in agreement with experimental results. The modified oligomers populate a wide range of bend angles, indicating that they maintain flexibility in the bent state. The present results suggest that insertion of carbocyclic sugars into DNA or RNA duplexes can be used to engineer bending of the duplexes without impacting the electrostatic or chemical properties of the phosphodiester backbone, thereby serving as excellent tools for experimental elucidation of nucleic acid structure-function relationships.

Direct evaluation of a kinetic model for RecA-mediated DNA-strand exchange: the importance of nucleic acid dynamics and entropy during homologous genetic recombination

The Escherichia coli RecA protein is the prototype of a class of proteins that play central roles in genomic repair and recombination in all organisms. The unresolved mechanistic strategy by which RecA aligns a single strand of DNA with a duplex DNA and mediates a DNA strand switch is central to understanding homologous recombination. We explored the mechanism of RecA-mediated DNA-strand exchange using oligonucleotide substrates with the intrinsic fluorophore 6-methylisoxanthopterin. Pre-steady-state spectrofluorometric analysis elucidated the earliest transient intermediates formed during recombination and delineated the mechanistic strategy by which RecA facilitates this process. The structural features of the first detectable intermediate and the energetic characteristics of its formation were consistent with interactions between a few bases of the single-stranded DNA and the minor groove of a locally melted or stretched duplex DNA. Further analysis revealed RecA to be an unusual enzyme in that entropic rather than enthalpic contributions dominate its catalytic function, and no unambiguously active role for the protein was detected in the earliest molecular events of recombination. The data best support the conclusion that the mechanistic strategy of RecA likely relies on intrinsic DNA dynamics.

Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure

We analyzed structural features of 11,038 direct atomic contacts (either electrostatic, H-bonds, hydrophobic, or other van der Waals interactions) extracted from 139 protein-DNA and 49 protein-RNA nonhomologous complexes from the Protein Data Bank (PDB). Globally, H-bonds are the most frequent interactions (approximately 50%), followed by van der Waals, hydrophobic, and electrostatic interactions. From the protein viewpoint, hydrophilic amino acids are over-represented in the interaction databases: Positively charged amino acids mainly contact nucleic acid phosphate groups but can also interact with base edges. From the nucleotide point of view, DNA and RNA behave differently: Most protein-DNA interactions involve phosphate atoms, while protein-RNA interactions involve more frequently base edge and ribose atoms. The increased participation of DNA phosphate involves H-bonds rather than salt bridges. A statistical analysis was performed to find the occurrence of amino acid-nucleotide pairs most different from chance. These pairs were analyzed individually. Finally, we studied the conformation of DNA in the interaction sites. Despite the prevalence of B-DNA in the database, our results suggest that A-DNA is favored in the interaction sites.

Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I e2 protein: the protein binding effect on DNA and the recognition mechanism

Molecular dynamics simulations of a total duration of 30 ns in explicit solvent were carried out on the BPV-1-E2 protein complexed to a high-affinity DNA target containing the two hydrogen-bonded ACCG.CGGT half-sites separated by the noncontacted ACGT sequence. The analysis of the trajectories focuses on the DNA structure and on the dynamics. The data are compared to those issued from recent simulations made on three free targets that recognize E2 with different affinities. E2 does not drastically perturb the mechanic properties of the free DNA: the structural relationships between the BI/BII backbone substates and some helical parameters are preserved in the complex despite a severe slowing down of the phosphate group motions. The structures of both free and bound half-sites are very close to each other although the conformational space explored by these regions is narrowed when they are contacted by the protein. The enhanced plasticity found in the best free target spacers, mainly manifested through the backbone motions, allows a clear overlap between several free and bound global DNA features such as the base displacement. Furthermore, this flexibility is preserved in the complex. Our results support the hypothesis that E2 takes advantage of free predistorted structures that may minimize the DNA deformation cost. In addition, we observe that E2 is far from totally stiffening the DNA, suggesting that the entropic penalty inherent in the complex formation could be limited.

Towards an understanding of DNA recognition by the methyl-CpG binding domain 1

CpG methylation determines a variety of biological functions of DNA. The methylation signal is interpreted by proteins containing a methyl-CpG binding domain (MBDs). Based on the NMR structure of MBD1 complexed with methylated DNA we analysed the recognition mode by means of molecular dynamics simulations. As the protein is monomeric and recognizes a symmetrically methylated CpG step, the recognition mode is an asymmetric one. We find that the two methyl groups do not contribute equally to the binding energy. One methyl group is associated with the major part of the binding energy and the other one nearly does not contribute at all. The contribution of the two cytosine methyl groups to binding energy is calculated to be -3.6 kcal/mol. This implies a contribution of greater than two orders of magnitude to the binding constant. The conserved amino acid Asp32 is known to be essential for DNA binding by MBD1, but so far no direct contact with DNA has been observed. We detected a direct DNA base contact to Asp32. This could be the main reason for the importance of this amino acid. MBD contacts DNA exclusively in the major groove, the minor groove is reserved for histone contacts. We found a deformation of the minor groove shape due to complexation by MBD1, which indicates an information transfer between the major and the minor groove.

Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d

Sac7d, a small, abundant, sequence-general DNA-binding protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius, causes a single-step sharp kink in DNA (∼60°) via the intercalation of both Val26 and Met29. These two amino acids were systematically changed in size to probe their effects on DNA kinking. Eight crystal structures of five Sac7d mutant–DNA complexes have been analyzed. The DNA-binding pattern of the V26A and M29A single mutants is similar to that of the wild-type, whereas the V26A/M29A protein binds DNA without side chain intercalation, resulting in a smaller overall bending (∼50°). The M29F mutant inserts the Phe29 side chain orthogonally to the C2pG3 step without stacking with base pairs, inducing a sharp kink (∼80°). In the V26F/M29F-GCGATCGC complex, Phe26 intercalates deeply into DNA bases by stacking with the G3 base, whereas Phe29 is stacked on the G15 deoxyribose, in a way similar to those used by the TATA box-binding proteins. All mutants have reduced DNA-stabilizing ability, as indicated by their lower T_m values. The DNA kink patterns caused by different combinations of hydrophobic side chains may be relevant in understanding the manner by which other minor groove-binding proteins interact with DNA.

Changes in DNA bending induced by restricting nucleotide ring pucker studied by weak alignment NMR spectroscopy

Changes in bending of the DNA helix axis caused by the introduction of conformationally locked nucleotide analogs into the center region of the palindromic Dickerson dodecamer, d(CGCGAATTCGCG)(2), have been studied by NMR measurement of residual one-bond (13)C-(1)H dipolar couplings. Thymidine analogs, in which the deoxyribose was substituted by bicyclo[3.1.0]hexane, were incorporated in the T7, T8, and T7T8 positions. These nucleotide analogs restrict the ring pucker to the C2'-exo or "north" conformation, instead of C2'-endo or "south," which dominates in regular B-form DNA. For all three oligomers, bending toward the major groove is found relative to the native molecule. The effects are additive with bending of 5 +/- 1 degrees per locked nucleotide. Measurement of the change in bending is more accurate than measurement of the bending angle itself and requires far fewer experimental data.

Simulation and modeling of nucleic acid structure, dynamics and interactions

In moving towards the simulation of larger nucleic acid assemblies over longer timescales that include more accurate representations of the environment, we are nearing the end of an era characterized by single nanosecond molecular dynamics simulation of nucleic acids. We are excited by the promise and predictability of the modeling methods, yet remain prudently cautious of sampling and force field limitations. Highlights include the accurate representation of subtle drug-DNA interactions, the detailed study of modified and unusual nucleic acid structures, insight into the influence of dynamics on the structure of DNA, and exploration of the interaction of solvent and ions with nucleic acids.