Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action

Phenanthriplatin (PtPPH) is a monovalent platinum(II)-based complex with a large cytotoxicity against cancer cells. Although the aqua-activated drug has been assumed to be the precursor for DNA damage, it is still under debate whether the way in which that metallodrug attacks to DNA is dominated by a direct binding to a guanine base or rather by an intercalated intermediate product. Aiming to capture the mechanism of action of PtPPH, the present contribution used theoretical tools to systematically assess the sequence of all possible mechanisms on drug activation and reactivity, for example, hydrolysis, intercalation, and covalent damage to DNA. Ab initio quantum mechanical (QM) methods, hybrid QM/QM′ schemes, and independent gradient model approaches are implemented in an unbiased protocol. The performed simulations show that the cascade of reactions is articulated in three well-defined stages: (i) an early and fast intercalation of the complex between the DNA bases, (ii) a subsequent hydrolysis reaction that leads to the aqua-activated form, and (iii) a final formation of the covalent bond between PtPPH and DNA at a guanine site. The permanent damage to DNA is consequently driven by that latter bond to DNA but with a simultaneous π–π intercalation of the phenanthridine into nucleobases. The impact of the DNA sequence and the lateral backbone was also discussed to provide a more complete picture of the forces that anchor the drug into the double helix.

Can Cyanuric Acid and 2,4,6-Triaminopyrimidine Containing Ribonucleosides be Components of Prebiotic RNA? Insights from QM Calculations and MD Simulations

As a step toward assessing their fitness as pre-RNA nucleobases, we employ DFT and MD simulations to analyze the noncovalent interactions of cyanuric acid (CA) and 2,4,6-triaminopyrimidine (TAP), and the structural properties of the associated ribonucleosides (rNs) and oligonucleotides. Our calculations reveal that the TAP : CA pair has a comparable hydrogen-bond strength to the canonical A : U pair. This strengthens the candidature of CA and TAP as prebiotic nucleobases. Further, the stacking between two canonical nucleobases is stronger than those between TAP or CA and a canonical base, as well as those between two TAP and/or CA, which indicates that enhanced stacking may have served as a driving force for the evolution from prebiotic to canonical nucleobases. Similarities in the DFT-derived anti/syn rotational barriers and MD-derived (anti) glycosidic conformation of the CA and TAP rNs and canonical rNs further substantiate their candidature as pre-RNA components. Greater deglycosylation barriers (as obtained by DFT calculations) for TAP rNs compared to canonical rNs suggest TAP rNs indicate higher resistance to environmental factors, while lower barriers indicate that CA rNs were likely more suitable for less-challenging locations. Finally, the tight packing in narrow CA:TAP-containing helices suggests that the prebiotic polymers were shielded from water, which would aid their evolution into self-replicating systems. Our calculations thus support proposals that CA and TAP can act as nucleobases of pre-RNA.

Energy interactions in amyloid-like fibrils from NNQQNY

We use large-scale MP2 calculations to analyze the interactions appearing in amyloid fibers, which are difficult to determine experimentally. To this end, dimers and trimers of the hexapeptide NNQQNY from the yeast prion-like protein Sup35 were considered as model systems. We studied the energy interactions present in the three levels of organization in which the formation of amyloid fibrils is structured. The structural changes in the hydrogen bonds were studied too. It was found that the most energetic process is the formation of the β-sheet, which is equally due to both hydrogen bonds and van der Waals interactions. The aromatic rings help stabilize these aggregates through stacking of the aromatic rings of tyrosine, the stability produced by the aromatics residues increasing with their aromaticity. The formation of the basic unit of the assembled proto-fiber, the steric zipper, is less energetic and is associated to both dispersion forces and hydrogen bonds. The interactions between pair of β-sheets across the peptide-to-peptide contact through the tyrosine rings are cooperative and due to dispersion effects. Moreover, the strength of this interaction can rationalize the variation of mobility of the aromatic ring in the tyrosine units found in solid NMR experiments.

Detection of an en masse and reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation

The role that DNA conformation plays in the biochemistry of cells has been the subject of intensive research since DNA polymorphism was discovered. B-DNA has long been considered the native form of DNA in cells although alternative conformations of DNA are thought to occur transiently and along short tracts. Here, we report the first direct observation of a fully reversible en masse conformational transition between B- and A-DNA within live bacterial cells using Fourier transform infrared (FTIR) spectroscopy. This biospectroscopic technique allows for non-invasive and reagent-free examination of the holistic biochemistry of samples. For this reason, we have been able to observe the previously unknown conformational transition in all four species of bacteria investigated. Detection of this transition is evidence of a previously unexplored biological significance for A-DNA and highlights the need for new research into the role that A-DNA plays as a cellular defence mechanism and in stabilizing the DNA conformation. Such studies are pivotal in understanding the role of A-DNA in the evolutionary pathway of nucleic acids. Furthermore, this discovery demonstrates the exquisite capabilities of FTIR spectroscopy and opens the door for further investigations of cell biochemistry with this under-used technique.

Coupling between hydrogen atoms transfer and stacking interaction in adenine-thymine/guanine-cytosine complexes: a theoretical study

Four different complexes of two base pairs, an adenine-thymine and a guanine-cytosine one, have been studied in order to understand the modifications induced by the staking interaction between the two base pairs on the hydrogen atoms transfers between the bases in either base pair. The inclusion of these two kinds of interactions allows us to clarify if some properties, as the mechanism of hydrogen transfer, is exclusively a local effect of a base pair or can be modified by a more long-range interaction between the base pairs. The results on these four complexes are compared with those of the monomeric systems, the A-T and G-C base pair, and with those of the A-T and G-C dimers. The specificity of each complex and of each hydrogen bond has been analyzed.

Theoretical investigation of the coupling between hydrogen-atom transfer and stacking interaction in adenine-thymine dimers

Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.

yDNA versus yyDNA pyrimidines: computational analysis of the effects of unidirectional ring expansion on the preferred sugar-base orientation, hydrogen-bonding interactions and stacking abilities

The properties of natural, y- and yy-pyrimidines are compared using computational (B3LYP, MP2) methods. Ring expansion upon incorporation of benzene or naphthalene into the natural pyrimidines affects the preferred orientation of the base about the glycosidic bond in the corresponding nucleoside to a similar extent. Specifically, although the natural pyrimidines preferentially adopt the anti orientation with respect to the 2'-deoxyribose moiety, the expanded analogues will likely display (anti/syn) conformational heterogeneity, which may lead to alternate hydrogen-bonding modes in double-stranded duplexes. Nevertheless, the A:T Watson-Crick hydrogen-bond strengths do not significantly change upon base expansion, while the G:C interaction energy is slightly strengthened upon incorporation of either expanded pyrimidine. The largest effect of base expansion occurs in the stacking energies. Specifically, the maximum (most negative) stacking energies in isolated dimers formed by aligning the nucleobase centers of mass can be increased up to 45% by inclusion of a single y-pyrimidine and up to 55% by consideration of a yy-pyrimidine. Similar increases in the stacking interactions are found when a simplified duplex model composed of two stacked (hydrogen-bonded) base pairs is considered, where both the intrastrand and interstrand stacking interactions can be increased and the effects are more pronounced for the yy-pyrimidines. Moreover, the total stability (sum of all hydrogen-bonding and stacking interactions) is greater for duplexes containing expanded yy-pyrimidines compared to y-pyrimidines, which is mainly due to enhanced stacking interactions. Thus, our calculations suggest that multiple unidirectional increases in the size of the nucleobase spacer can continuously enhance the stability of expanded duplexes.

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics

Sequence-dependent local variations of helical parameters, structure, and flexibility are crucial for molecular recognition processes involving B-DNA. A-tracts, i.e., stretches of several consecutive adenines in one strand that are in phase with the DNA helical repeat, mediate significant DNA bending. During the past few decades, there have been intense efforts to understand the sequence dependence of helical parameters in DNA. Molecular dynamics (MD) simulations can provide valuable insights into the molecular mechanism behind the relationship between sequence and structure. However, although recent improvements in empirical force fields have helped to capture many sequence-dependent B-DNA properties, several problems remain, such as underestimation of the helical twist and suspected underestimation of the propeller twist in A-tracts. Here, we employ reference quantum mechanical (QM) calculations, explicit solvent MD, and bioinformatics to analyze the underestimation of propeller twisting of A-tracts in simulations. Although we did not identify a straightforward explanation, we discovered two imbalances in the empirical force fields. The first was overestimation of stacking interactions accompanied by underestimation of base-pairing energy, which we attribute to anisotropic polarizabilities that are not reflected by the isotropic force fields. This may lead to overstacking with potentially important consequences for MD simulations of nucleic acids. The second observed imbalance was steric clash between A(N1) and T(N3) nitrogens of AT base pairs in force-field descriptions, resulting in overestimation of the AT pair stretch in MD simulations. We also substantially extend the available set of benchmark estimated CCSD(T)/CBS data for B-DNA base stacking and provide a code that allows the generation of diverse base-stacking geometries suitable for QM computations with predefined intra- and interbase pair parameters.

Intramolecular base stacking of dinucleoside monophosphate anions in aqueous solution

Time-dependent motions of 32 deoxyribodinucleoside and ribodinucleoside monophosphate anions in aqueous solution at 310 K were monitored during 40 ns using classical molecular dynamics (MD). In all studied molecules, spontaneous stacking/unstacking transitions occurred on a time-scale of 10 ns. To facilitate the structural analysis of the sampled configurations we defined a reaction coordinate for the nucleobase stacking that considers both the angle between the planes of the two nucleobases and the distance between their mass-centers. Additionally, we proposed a physically meaningful transient point on this coordinate that separates the stacked and unstacked states. We applied this definition to calculate free energies for stacking of all pairwise combinations of adenine, thymine (uracil), cytosine and guanine moieties embedded in studied dinucleosides monophosphate anions. The stacking equilibrium constants decreased in the order 5'-AG-3' > GA ~ GG ~ AA > GT ~ TG ~ AT ~ GC ~ AC > CG ~ TA > CA ~ TC ~ TT ~ CT ~ CC. The stacked conformations of AG occurred 10 times more frequently than its unstacked conformations. On the other hand, the last five base combinations showed a greater preference for the unstacked than the stacked state. The presence of an additional 2'-OH group in the RNA-based dinucleoside monophosphates increased the fraction of stacked complexes but decreased the compactness of the stacked state. The calculated MD trajectories were also used to reveal prevailing mutual orientation of the nucleobase dipoles in the stacked state.

A computational proposal for the experimentally observed discriminatory behavior of hypoxanthine, a weak universal nucleobase

A computational model composed of six nucleobases was used to investigate why hypoxanthine does not yield duplexes of equal stability when paired opposite each of the natural DNA nucleobases. The magnitudes of all nearest-neighbor interactions in a DNA helix were calculated, including hydrogen-bonding, intra- and interstrand stacking interactions, as well as 1-3 intrastrand stacking interactions. Although the stacking interactions in DNA relevant arrangements are significant and account for at least one third of the total stabilization energy in our nucleobase complexes, the trends in the magnitude of the stacking interactions cannot explain the relative experimental melting temperatures previously reported in the literature. Furthermore, although the total hydrogen-bonding interactions explain why hypoxanthine preferentially pairs with cytosine, the experimental trend for the remaining nucleobases (A, T, G) is not explained. In fact, the calculated pairing preference of hypoxanthine matches that determined experimentally only when the sum of all types of nearest-neighbor interactions is considered. This finding highlights a strong correlation between the relative magnitude of the total nucleobase-nucleobase interactions and measured melting temperatures for DNA strands containing hypoxanthine despite the potential role of other factors (including hydration, temperature, sugar-phosphate backbone). By considering a large range of sequence combinations, we reveal that the binding preference of hypoxanthine is strongly dependent on the nucleobase sequence, which may explain the varied ability of hypoxanthine to universally bind to the natural bases. As a result, we propose that future work should closely examine the interplay between the dominant nucleobase-nucleobase interactions and the overall strand stability to fully understand how sequence context affects the universal binding properties of modified bases and to aid the design of new molecules with ambiguous pairing properties.

Feasibility study of hydrogen-bonded nucleic acid base pairs in gas and water phases — A theoretical study

To investigate the base pair binding probabilities for nucleic acid bases, numerous models were studied for contacts between adenine, thymine, guanine, cytosine, and uracil using density functional theory (DFT) in combination with the 6–311G* basis set. We obtained an assessment for the energy given by our calculations in gas and aqueous phases, which showed that it should be incorporated into hydrogen bonding and propeller rotational energies. The 42 complexes of base pairs (5 regular and 37 irregular base pairs) were proposed and their hydrogen-bonding (H-bonding) properties were verified. The hydrogen bonds in some irregular base pairs, including CC, UU, and TT (series 1), were stronger than in regular GC and AT base pairs. Also, the strength of the hydrogen bonds in the proposed base pairs, including CU, GG, GU, and TU (series 2), were similar to regular base pairs from an energetic point of view. The propeller rotations revealed a higher rotational barrier energy (6–7.5 kcal/mol; 1 cal = 4.184 J) for irregular base pairs (series 1 and 2) than regular GC and AT ones (1–3 kcal/mol). Nevertheless, the trend in these affinities of the complex contact probabilities and their biological properties were confirmed by our calculations.

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Non-additivity of base-base interactions in all ten possible model dinucleotide steps were analyzed on MP2/aug-cc-pvDZ quantum chemistry level. Conformations of four nucleobases exactly matched to ones occurring in B-DNA crystals. In most of thw 162 analyzed tetramers both three- and four-body contributions are negligible except for d(GpG) steps. However, in these dinucleotides both contributions are always of opposite signs and in all cases the sum of all non-additive part of intermolecular interactions do not exceed 2.6 kcal mol(-1). This stands for less than 5% of the overall binding energy of dinucleotide steps. Also replacements of guanine with 8-oxoguanine in d(GpG) systems introduces non-additivity of the same magnitude as for canonical dinucleotides. It is observed linear relationships between values of total binding energy obtained in the tetramer basis set and estimated energy exclusively in dimers basis sets with assumption of pairwise additivities. For all analyzed dinucleotides steps there are also linear correlations between amount of non-additive contributions and magnitude of pairs interactions. Based on differences in electrostatic contribution to the total binding energy of four nucleobases and polarity of dinucleotide steps three distinct classes of dinucleotide steps were identified.

Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?

High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal x mol(-1), which is almost 50% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA and A-RNA is the GC/GC [corrected] step that is well separated from the second most stable step CG/CG. [corrected] Also the least stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal x mol(-1) per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of DeltaG degrees(37) free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs.

DNA duplex stability: the role of preorganized electrostatics

The insertion of a DNA base moiety at the end of a DNA duplex to form a Watson-Crick or wobble pair during DNA annealing or replication is a step of fundamental biological importance. Therefore, we investigated the energetics of a formation of the terminal G x C, G x T, and G x A base pairs in DNA containing a 5'-dangling G adjacent to the base insertion point using differential scanning calorimetry and computer simulations. The energies calculated along classical molecular dynamics trajectories in aqueous solution were analyzed in the framework of linear-response approximation (LRA) to obtain relative free energies for the base insertion and their electrostatic, van der Waals, and preorganization components. Using the generic set of LRA parameters, the calculated free energies disfavored the mispair formation by 2.5 (G x C --> G x T) and 1.7 (G x C --> G x A) kcal/mol, in reasonable agreement with the experimental free energy differences of 1.8 and 1.4 kcal/mol, respectively. The calculated preorganization components of these free energies of 0.6 (G x C --> G x T) and -0.1 (G x C --> G x A) kcal/mol show that electrostatic preorganization, which is an important source of DNA replication fidelity, plays a lesser role in the mispair destabilization in the absence of DNA polymerase.

The post-SCF quantum chemistry characteristics of inter- and intra-strand stacking interactions in d(CpG) and d(GpC) steps found in B-DNA, A-DNA and Z-DNA crystals

The energies of intra- and inter-strand stacking interactions in model d(GpC) and d(CpG) two-base-pair steps were estimated by MP2/aug-cc-pVDZ single point calculations corrected for basis superposition errors. The stacked two-nucleobase pairs were constructed using experimental values of base pair and base step parameters taken from Nucleic Acid Database (http://ndbserver.rutgers.edu/). Three distinct polymorphic forms were analysed, namely A-, B- and Z-DNA. The applied methodology enables statistical analysis of structural and energetic diversities. The structural relationships between polymorphic forms are quite complex and depend on the sequence of pairs. The variability of parameters such as shift and tilt is almost the same irrespective of the polymorphic form and sequence of steps analysed. In contrast, shift and twist distributions easily discriminate all three polymorphic forms of DNA. Interestingly, despite significant structural diversities, the energies of the most frequent energy ranges are comparable irrespective of the polymorphic form and base sequence. There was observed compensation of inter- and intra-strand interactions, especially for d(GpC) and d(CpG) steps found in A- and B-DNA. Thus, among many other roles, these pairs act as a kind of energetic buffer, balancing the double helix.

A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine

The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.

Synthesis of 2'-O-methyl-RNAs incorporating a 3-deazaguanine, and UV melting and computational studies on its hybridization properties

2′-O-Methyl-RNAs incorporating 3-deazaguanine (c³G) were synthesized by use of N,N-diphenylcarbamoyl and N,N-dimethylaminomethylene as its base protecting groups to suppress sheared-type 5′-GA-3′/5′-GA-3′ tandem mismatched base pairing which requires the N³ atom. These modified RNAs hybridized more weakly with the complementary and single mismatch-containing RNAs than the unmodified RNAs. The T_m experiments were performed to clarify the effects of replacement of the fifth G with c³G on stabilization of 2′-O-methyl-(5′-CGGCGAGGAG-3′)/5′-CUCCGAGCCG-3′ and 2′-O-methyl-(5′-CGGGGACGAG-3′)/5′-CUCGGACCCG-3′duplexes, which form sheared-type and face-to-face type 5′-GA-3′/5′-GA-3′ tandem mismatched base pairs, respectively. Consequently, this replacement led to more pronounced destabilization of the former duplex that needs the N³ atom for the sheared-type base pair than the latter that does not need it for the face-to-face type base pair. A similar tendency was observed for 2′-O-methyl-RNA/DNA duplexes. These results suggest that the N³ atom of G plays an important role in stabilization of the canonical G/C base pair as well as the base discrimination and its loss suppressed formation of the undesired sheared-type mismatched base pair. Computational studies based on ab initio calculations suggest that the weaker hydrogen bonding ability and larger dipole moment of c³G can be the origin of the lower T_m.

Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps

Base-stacking energies in ten unique B-DNA base-pair steps and some other arrangements were evaluated by the second-order Møller-Plesset (MP2) method, complete basis set (CBS) extrapolation, and correction for triple (T) electron-correlation contributions. The CBS(T) calculations were compared with decade-old MP2/6-31G*(0.25) reference data and AMBER force field. The new calculations show modest increases in stacking stabilization compared to the MP2/6-31G*(0.25) data and surprisingly large sequence-dependent variation of stacking energies. The absolute force-field values are in better agreement with the new reference data, while relative discrepancies between quantum-chemical (QM) and force-field values increase modestly. Nevertheless, the force field provides good qualitative description of stacking, and there is no need to introduce additional pair-additive electrostatic terms, such as distributed multipoles or out-of-plane charges. There is a rather surprising difference of about 0.1 A between the vertical separation of base pairs predicted by quantum chemistry and derived from crystal structures. Evaluations of different local arrangements of the 5'-CG-3' step indicate a sensitivity of the relative stacking energies to the level of calculation. Thus, describing quantitative relations between local DNA geometrical variations and stacking may be more complicated than usually assumed. The reference calculations are complemented by continuum-solvent assessment of solvent-screening effects.

Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations

The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single-crystal X-ray techniques. The structure was refined to completion using refmac5.1.24, resulting in a residual R-factor of 20.0% (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to 1.75 A, resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs, respectively, clearly cataloging the structure to class I. As the bulky NH2 group on guanine was believed to prevent binding of the drug in the minor groove, the detailed nature of several of the amidinium and guanidinium end contacts were further investigated by ab initio quantum chemical methods.

DNA basepair step deformability inferred from molecular dynamics simulations

The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers: d(GCCTATAAACGCCTATAA) and d(CTAGGTGGATGACTCATT). From an analysis of the structural fluctuations, the harmonic potential energy functions for all 10 unique steps with respect to the six step parameters have been evaluated. In the case of roll, three distinct groups of steps have been identified: the flexible pyrimidine-purine (YR) steps, intermediate purine-purine (RR), and stiff purine-pyrimidine (RY). The YR steps appear to be the most flexible in tilt and partially in twist. Increasing stiffness from YR through RR to RY was observed for rise, whereas shift and slide lack simple trends. A proposed measure of the relative importance of couplings identifies the slide-rise, twist-roll, and twist-slide couplings to play a major role. The force constants obtained are of similar magnitudes to those based on a crystallographic ensemble. However, the current data have a less complicated and less pronounced sequence dependence. A correlation analysis reveals concerted motions of neighboring steps and thus exposes limitations in the dinucleotide model. The comparison of DNA deformability from this and other studies with recent quantum-chemical stacking energy calculations suggests poor correlation between the stacking and flexibility.

DNA sequence-dependent deformability?insights from computer simulations

The article reviews some recent developments in studying DNA sequence-dependent deformability, with emphasis on computer modeling. After a brief outline of available experimental techniques, we proceed to computational methods and focus on atomic-resolution molecular dynamics (MD) simulations. A sequence-dependent local (base-pair step) force field inferred from MD is compared with force fields obtained by other techniques. Various methods for establishing global (flexible-rod) DNA elastic constants are reviewed, including an approach based on atomic resolution MD. The problem of defining the global deformation variables, as well as the question of anisotropy and nonlocal effects, are discussed. As an example, both local and global deformability calculations from atomic-resolution MD of EcoRI dodecamer are presented.

Stabilisation of the transition state of phosphodiester bond cleavage within linear single-stranded oligoribonucleotides

The effect of base sequence on the stability of the transition state (TS) of phosphodiester bond cleavage within linear single-stranded oligoribonucleotides has been studied in order to better understand why the reactivity of some phosphodiester bonds is enhanced compared to an unconstrained linkage. Molecular dynamics simulations of 3.0 ns were carried out for 14 oligonucleotides that contain in the place of the scissile phosphodiester bond a phosphorane structure mimicking the TS of the bond cleavage. The hydrolytic stability of the same oligonucleotides had previously been reported. Both the non-bridging oxyanions and the leaving 5[prime or minute]-oxygen of the pentacoordinated phosphorane moiety were observed to form hydrogen bonds with solvent water molecules in a similar way with all the compounds studied. In addition, water mediated hydrogen bonds between the phosphorane non-bridging oxyanions and the bases of the 3[prime or minute]-flanking sequence were detected with some of the compounds, but not with the most labile ones. Hence, it seems that the enhanced cleavage of some internucleosidic linkages does not result from the TS stabilisation by hydrogen bonding. With heterooligomers, the stacking of bases next to the cleavage site was observed to be enhanced on going from the initial state to the TS, whereas within uracil homooligomer, having initially negligible stacking, no change in the magnitude of stacking was seen. Accordingly, while strong stacking in the initial state is known to retard the phosphodiester bond cleavage, it may in the TS accelerate the reaction. Therefore, enhanced stacking on going from the initial state to transition state appears to be a factor that markedly contributes to the hydrolytic stability of phosphodiester bonds within oligonucleotides and may, at least partly, explain accelerated cleavage compared to fully unconstrained bonds, such as those in polyuridylic acid.

Unique tertiary and neighbor interactions determine conservation patterns of Cis Watson-Crick A/G base-pairs

X-ray, phylogenetic and quantum chemical analysis of molecular interactions and conservation patterns of cis Watson-Crick (W.C.) A/G base-pairs in 16S rRNA, 23S rRNA and other molecules was carried out. In these base-pairs, the A and G nucleotides interact with their W.C. edges with glycosidic bonds oriented cis relative to each other. The base-pair is stabilised by two hydrogen bonds, the C1'-C1' distance is enlarged and the G(N2) amino group is left unpaired. Quantum chemical calculations show that, in the absence of other interactions, the unpaired amino group is substantially non-planar due to its partial sp(3) pyramidalization, while the whole base-pair is internally propeller twisted and very flexible. The unique molecular properties of the cis W.C. A/G base-pairs make them distinct from other base-pairs. They occur mostly at the ends of canonical helices, where they serve as interfaces between the helix and other motifs. The cis W.C. A/G base-pairs play crucial roles in natural RNA structures with salient sequence conservation patterns. The key contribution to conservation is provided by the unpaired G(N2) amino group that is involved in a wide range of tertiary and neighbor contacts in the crystal structures. Many of them are oriented out of the plane of the guanine base and utilize the partial sp(3) pyramidalization of the G(N2). There is a lack of A/G to G/A covariation, which, except for the G(N2) position, would be entirely isosteric. On the contrary, there is a rather frequent occurrence of G/A to G/U covariation, as the G/U wobble base-pair has an unpaired amino group in the same position as the cis W.C. G/A base-pair. The cis W.C. A/G base-pairs are not conserved when there is no tertiary or neighbor interaction. Obtaining the proper picture of the interactions and phylogenetic patterns of the cis W.C. A/G base-pairs requires a detailed analysis of the relation between the molecular structures and the energetics of interactions at a level of single H-bonds and contacts.

The base sequence dependent flexibility of linear single-stranded oligoribonucleotides correlates with the reactivity of the phosphodiester bond

The effect of base sequence on the structure and flexibility of linear single-stranded RNA molecules and the influence of the base sequence on phosphodiester bond reactivity have been studied. Molecular dynamics simulations of 2.1 ns were carried out for nine chimeric oligonucleotides containing only one unsubstituted ribo unit, all the rest of sugars being 2'-O-methylated. The base sequence has recently been reported to make a big contribution to the reactivity of these compounds. A detailed examination of the interaction energies between the base moieties shows that base stacking is strongly context-dependent and cooperative. The strength of stacking at the site susceptible to chain cleavage by intramolecular transesterification was observed to be dependent on both the flanking bases of the cleavage site and those further apart in the molecule. The interaction energies between the bases in the vicinity of the scissile linkage were found to correlate well with the experimental phosphodiester bond cleavage rates: the stronger the bases close to the cleavage site are stacked, the slower the cleavage rate is.

Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies

Ab initio quantum-chemical calculations with inclusion of electron correlation significantly contributed to our understanding of molecular interactions of DNA and RNA bases. Some of the most important findings are introduced in the present overview: structures and energies of hydrogen bonded base pairs, nature of base stacking, interactions between metal cations and nucleobases, nonplanarity of isolated nucleobases and other monomer properties, tautomeric equilibria of nucleobases, out-of-plane hydrogen bonds and amino acceptor interactions. The role of selected molecular interactions in nucleic acids is discussed and representative examples where these interactions occur are given. Also, accuracy of density functional theory, semiempirical methods, distributed multipole analysis and empirical potentials is commented on. Special attention is given to our very recent reference calculations on base stacking and H-bonding. Finally, we briefly comment on the relationship between advanced ab initio quantum-chemical methods and large-scale explicit solvent molecular dynamics simulations of nucleic acids.

Temperature-dependence of UV laser one-electron oxidative guanine modifications as a probe of local stacking fluctuations and conformational transitions

By monitoring R(pip)/R(Fpg), i.e. the relative sensitivity to hot piperidine and to formamidopyrimidine DNA glycosylase (Fpg protein) of the guanine lesions induced in DNA exposed to UV laser irradiation, we have previously observed that the formation of the two major types of one-electron oxidative guanine modifications, oxazolone and 7,8-dihydro-8-oxoguanine (8-oxodG), depends on DNA conformational features. While oxazolone is largely predominant at each site of single-stranded DNA (R(pip)>R(Fpg)), 8-oxodG is the major lesion at most of the sites of double-stranded DNA (R(pip)<R(Fpg)). In the present study, we investigated the temperature dependence of R(pip) and R(Fpg) at individual sites of a DNA sequence during the transition between the double-stranded and the melted random coiled states. The striking result is that the transition curves of the ratio R(pip)/R(Fpg) display a shape similar to the helix-coil melting profile of the DNA fragment determined from UV absorbance measurements with, at individual sites, subtle differences in the slope of the curves and in the temperature at the mid-point of the transitions. At a few guanine residues of the DNA duplex, R(pip)>R(Fpg) at 20 degrees C and the ratio R(pip)/R(Fpg) does not vary significantly during the melting process. Interestingly, these guanine residues display a high sensitivity to dimethyl sulfoxide methylation while the opposite cytosine residues are unsensitive, suggesting that the prevalence of R(pip) over R(Fpg) is related not to base-pairing disruption but rather to the local helical alteration of the B-DNA stacking geometry. This leads us to propose that the slight variations in the ratios R(pip)/R(Fpg) observed, at individual sites, at temperatures below the helix-coil transition reflect local small-scale breathing motions, unstacking single dinucleotide steps prior to opening. Our results thus support the view that the temperature dependence of the ratio of R(pip)/R(Fpg) at sites of B-DNA provides a sensitive probe of the DNA internal local thermal stability and are discussed in relation with the mechanisms proposed for the intramolecular rearrangement of the guanyl radical.

Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG

The crystal structure of the DNA dodecamer duplex CATGGGCCCATG lies on a structural continuum along the transition between A- and B-DNA. The dodecamer possesses the normal vector plot and inclination values typical of B-DNA, but has the crystal packing, helical twist, groove width, sugar pucker, slide and x-displacement values typical of A-DNA. The structure shows highly ordered water structures, such as a double spine of water molecules against each side of the major groove, stabilizing the GC base pairs in an A-like conformation. The different hydration of GC and AT base pairs provides a physical basis for solvent-dependent facilitation of the A<-->B helix transition by GC base pairs. Crystal structures of CATGGGCCCATG and other A/B-DNA intermediates support a 'slide first, roll later' mechanism for the B-->A helix transition. In the distribution of helical parameters in protein-DNA crystal structures, GpG base steps show A-like properties, reflecting their innate predisposition for the A conformation.

The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA

Sequences of four or more AT base pairs without a 5'-TA-3' step, so-called A-tracts, influence the global properties of DNA by causing curvature of the helix axis if phased with the helical repeat and also influence nucleosome packaging. Hence it is interesting to understand this phenomenon on the molecular level, and numerous studies have been devoted to investigations of dynamical and structural features of A-tract DNA. It was early observed that anomalously slow base pair-opening kinetics were a striking physical property unique to DNA A-tracts (Leroy, J. L., Charretier, E., Kochoyan, M., and Gueron, M. (1988) Biochemistry 27, 8894-8898). Furthermore, a strong correlation between DNA curvature and anomalously slow base pair-opening dynamics was found. In the present work it is shown, using imino proton exchange measurements by NMR spectroscopy that the main contribution to the dampening of the base pair-opening fluctuations in A-tracts comes from the C5 methylation of the thymine base. Because the methyl group has been shown to have a very limited effect on the DNA curvature as well as the structure of the DNA helix, the thymine C5 methyl group stabilizes the helix directly. Empirical potential energy calculations show that methylation of the tract improves the stacking energy of a base pair with its neighbors in the tract by 3-4 kcal/mol.

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

Unrestrained 5-20-ns explicit-solvent molecular dynamics simulations using the Cornell et al. force field have been carried out for d[GCG(N)11GCG]2 (N, purine base) considering guanine*cytosine (G*C), adenine*thymine (A*T), inosine*5-methyl-cytosine (I*mC), and 2-amino-adenine*thymine (D*T) basepairs. The simulations unambiguously show that the structure and elasticity of N-tracts is primarily determined by the presence of the amino group in the minor groove. Simulated A-, I-, and AI-tracts show almost identical structures, with high propeller twist and minor groove narrowing. G- and D-tracts have small propeller twisting and are partly shifted toward the A-form. The elastic properties also differ between the two groups. The sequence-dependent electrostatic component of base stacking seems to play a minor role. Our conclusions are entirely consistent with available experimental data. Nevertheless, the propeller twist and helical twist in the simulated A-tract appear to be underestimated compared to crystallographic studies. To obtain further insight into the possible force field deficiencies, additional multiple simulations have been made for d(A)10, systematically comparing four major force fields currently used in DNA simulations and utilizing B and A-DNA forms as the starting structure. This comparison shows that the conclusions of the present work are not influenced by the force field choice.

An FTIR and CD study of the structural effects of G-tract length and sequence context on DNA conformation in solution

Fourier transform infrared (FTIR) and CD spectroscopy have been used to investigate the structural effects of G-tract length and flanking sequence on the conformation of DNA G-tracts in aqueous solution. Particularly, a possible predisposition for A-form features has been probed, since this may be important for protein-DNA interactions. Five different G-tract-containing DNA duplexes have been studied: d[CATGGCCATG](2), d[CATGGGCCCATG](2), d[CATGGGGCCCCATG](2,) d[AGGGGCCCCT](2), and d[TGGGGCCCCA](2). In addition, a DNA duplex lacking a G-tract center was probed (d[CATATGCATATG](2)). The CD and FTIR results show that the G-tract-containing sequences are all in a dominating B-DNA conformation in solution. However, certain spectral variations reflect structural effects of sequence context and G-tract length. CD spectra and FTIR results in the 1800-1500 cm(-1) region show that the base-stacking pattern is greatly affected by the sequence context. The FTIR backbone 1250-1000 cm(-1) region shows the antisymmetric non-bridging phosphate vibration around 1225 cm(-1) in all sequences, demonstrating the overall B-conformation of the backbone. The FTIR sugar 900-800 cm(-1) region shows variable contributions of two bands around 865 cm(-1) and 840 cm(-1), reflecting the N and S-type of sugar pucker. The relative intensities of the 865 cm(-1) and 840 cm(-1) bands have been proposed in the literature to quantitatively yield the contribution of N and S-type of sugar pucker, respectively. This correlation is supported by the present study. Furthermore, the contributions of N-type sugar in the DNA sequences studied indicate structural propensities that agree with trends in reported crystal structures of the same sequences: (1) d[CATGGCCATG](2), for which FTIR shows the lowest contribution of N-type sugar puckering in solution, crystallizes in a B-like conformation; (2) d[AGGGGCCCCT](2), with the highest degree of N-type sugar puckering of all the sequences studied, crystallizes in an A-like conformation; (3) d[CATGGGCCCATG](2), with an N-type contribution intermediate between that of d[CATGGCCATG](2) and d[AGGGGCCCCT](2), crystallizes in an A/B intermediate conformation.

Solution structure of the dodecamer d-(CATGGGCC-CATG)2 is B-DNA. Experimental and molecular dynamics study

The DNA duplex d-(CATGGGCCCATG)2 has been studied in solution by FTIR, NMR and CD. The experimental approaches have been complemented by series of large-scale unrestrained molecular dynamics simulation with explicit inclusion of solvent and counterions. Typical proton-proton distances extracted from the NMR spectra and the CD spectra are completely in agreement with slightly modified B-DNA. By molecular dynamics simulation, starting from A-type sugar pucker, a spontaneous repuckering to B-type sugar pucker was observed. Both experimental and theoretical approaches suggest for the dodecamer d-(CATGGGCCCATG)2 under solution conditions puckering of all 2'-deoxyribose residues in the south conformation (mostly C2'-endo) and can exclude significant population of sugars in the north conformation (C3'-endo). NMR, FTIR and CD data are in agreement with a B-form of the dodecamer in solution. Furthermore, the duplex shows a cooperative B-A transition in solution induced by addition of trifluorethanol. This contrasts a recently published crystal structure of the same oligonucleotide found as an intermediate between B- and A-DNA where 23 out of 24 sugar residues were reported to adopt the north (N-type) conformation (C3'-endo) like in A-DNA (Ng, H. L., Kopka, M. L. and Dickerson, R. E., Proc. Natl. Acad. Sci. U S A 97, 2035-2039 (2000)). The simulated structures resemble standard B-DNA. They nevertheless show a moderate shift towards A-type stacking similar to that seen in the crystal, despite the striking difference in sugar puckers between the MD and X-ray structures. This is in agreement with preceding MD reports noticing special stacking features of G-tracts exhibiting a tendency towards the A-type stacking supported by the CD spectra also reflecting the G-tract stacking. MD simulations reveal several noticeable local conformational variations, such as redistribution of helical twist and base pair roll between the central GpC steps and the adjacent G-tract segments, as well as a substantial helical twist variability in the CpA(TpG) steps combined with a large positive base pair roll. These local variations are rather different from those seen in the crystal.