Water-nucleobase "stacking": H-pi and lone pair-pi interactions in the atomic resolution crystal structure of an RNA pseudoknot

The hydrogen bond acceptor capability of aromatic rings has been demonstrated both by experimental and theoretical studies, and D-H...pi interactions (H-pi interaction), where D is mainly N, O, and C, are ubiquitous in structures of macromolecules. By comparison, the interaction of a lone pair of water directly with the face of a pi-system (l.p.-pi interaction) seems counterintuitive and to date has only been studied theoretically. In the crystal structure of an RNA pseudoknot at atomic resolution, all nucleobases not involved in either intra- or intermolecular base-base stacking interactions exhibit stacking with water molecules either of the H-pi or the l.p.-pi type. The geometry observed for the l.p.-pi type water-nucleobase stacking is consistent with that predicted in recent ab initio studies.     

Stacking interactions and the twist of DNA

The importance of stacking interactions for the Twist and stability of DNA is investigated using the fully ab initio van der Waals density functional (vdW-DF). Our results highlight the role that binary interactions between adjacent sets of base pairs play in defining the sequence-dependent Twists observed in high-resolution experiments. Furthermore, they demonstrate that additional stability gained by the presence of thymine is due to methyl interactions with neighboring bases, thus adding to our understanding of the mechanisms that contribute to the relative stability of DNA and RNA. Our mapping of the energy required to twist each of the 10 unique base pair steps should provide valuable information for future studies of nucleic acid stability and dynamics. The method introduced will enable the nonempirical theoretical study of significantly larger pieces of DNA or DNA/amino acid complexes than previously possible.     

How well can new-generation density functional methods describe stacking interactions in biological systems?

We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.     

Molecular ordering of a cyano compound at a displacive transition temperature: a statistical analysis based on quantum mechanics and computer simulations

A statistical analysis has been carried out to determine the configurational preference of a pair of 4-cyanophenyl 4- n -pentylbenzoate (CPPB) molecules with respect to translatory and orientational motions. The CNDO/2 method has been employed to evaluate the net atomic charge and atomic dipole components at each atomic centre of the molecule. Configurational energy has been computed using the Rayleigh-Schodinger perturbation method. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration at the phase transition temperature using the Maxwell-Boltzmann formula. An attempt has been made to identify the most probable configuration at the phase transition temperature. Further, the flexibility of various configurations has been studied in terms of variation of probability due to small departures from the most probable configuration. On the basis of stacking, in-plane and terminal interaction energy calculations, all possible geometrical arrangements of the molecular pair have been considered. The results are discussed in the light of experimental as well as theoretical observations. The nature of the mesophase has been correlated with the parameter introduced in this paper.     

Molecular organization of 4-cyano-4′-nonylbiphenyl in a dielectric medium: A statistical analysis

The molecular organization of 4-cyano-4′-nonylbiphenyl (CNBP) in a dielectric medium has been explored using a statistical model based on quantum mechanics and computer simulation. The complete neglect differential overlap (CNDO/2) method has been employed to evaluate the net atomic charge and atomic dipole components at each atomic centre of the molecule. The modified Rayleigh-Schrodinger perturbation theory along with multicentered multipole expansion method has been employed to evaluate the long-range intermolecular interactions, while the 6-exp potential function has been assumed for short-range interactions. The total interaction energies obtained through these computations were used as input to calculate the probability of occurrence of each configuration in a dielectric medium, benzene, at room temperature (300 K) using the MB formula. The various possible geometrical arrangements between a molecular pair during the different modes of interactions have been considered. This provides theoretical support to the experimental observations.     

Molecular ordering of a cyano compound at a displacive transition temperature: a statistical analysis based on quantum mechanics and computer simulations

A statistical analysis has been carried out to determine the configurational preference of a pair of 4-cyanophenyl 4-n-pentylbenzoate (CPPB) molecules with respect to translatory and orientational motions. The CNDO/2 method has been employed to evaluate the net atomic charge and atomic dipole components at each atomic centre of the molecule. Configurational energy has been computed using the Rayleigh—Schodinger perturbation method. The total interaction energy values obtained through these computations were used to calculate the probability of each configuration at the phase transition temperature using the Maxwell—Boltzmann formula. An attempt has been made to identify the most probable configuration at the phase transition temperature. Further, the flexibility of various configurations has been studied in terms of variation of probability due to small departures from the most probable configuration. On the basis of stacking, in-plane and terminal interaction energy calculations, all possible geometrical arrangements of the molecular pair have been considered. The results are discussed in the light of experimental as well as theoretical observations. The nature of the mesophase has been correlated with the parameter introduced in this paper.     

Spectroscopic Study of the Interaction between New Fluorescent Dyes with Nucleic Acids

Considerableefforthasbeencofltinuingtofocusonthedevelopmentofnewfluorescentdyestorecognizenucleicacids'-'.Althoughdansylisawell-knownsensitivehydrophobicprobewhichhasbeenwidelyutilizedasafluorescentprobeforthestudyofproteins,yetlittleefforthasbeenfocusedontheexploringdansylamidederivativeswhichmayhavespecificeffectsonnucleicacids.Sincethebindingaffinityofsuchfluorophorestopolynucleotideswasgreatlyaffectedbytheirsidechainsubstitutions,inthisworkseveralnewdansylderivativeswithspecificbindingtonu…     

Substituent effects on aromatic stacking interactions

Synthetic supramolecular zipper complexes have been used to quantify substituent effects on the free energies of aromatic stacking interactions. The conformational properties of the complexes have been characterised using NMR spectroscopy in CDCl(3), and by comparison with the solid state structures of model compounds. The structural similarity of the complexes makes it possible to apply the double mutant cycle method to evaluate the magnitudes of 24 different aromatic stacking interactions. The major trends in the interaction energy can be rationalised using a simple model based on electrostatic interactions between the pi-faces of the two aromatic rings. However, electrostatic interactions between the substituents of one ring and the pi-face of the other make an additional contribution, due to the slight offset in the stacking geometry. This property makes aromatic stacking interactions particularly sensitive to changes in orientation as well as the nature and location of substituents.     

Understanding the recognition mechanism of protein-RNA complexes using energy based approach

Protein-RNA interactions perform diverse functions within the cell. Understanding the recognition mechanism of protein-RNA complexes is a challenging task in molecular and computational biology. In this work, we have developed an energy based approach for identifying the binding sites and important residues for binding in protein-RNA complexes. The new approach considers the repulsive interactions as well as the effect of distance between the atoms in protein and RNA in terms of interaction energy, which are not considered in traditional distance based methods to identify the binding sites. We found that the positively charged, polar and aromatic residues are important for binding. These residues influence to form electrostatic, hydrogen bonding and stacking interactions. Our observation has been verified with the experimental binding specificity of protein-RNA complexes and found good agreement with experiments. Further, the propensities of residues/nucleotides in the binding sites of proteins/RNA and their atomic contributions have been derived. Based on these results we have proposed a novel mechanism for the recognition of protein-RNA complexes: the charged and polar residues in proteins initiate recognition with RNA by making electrostatic and hydrogen bonding interactions between them; the aromatic side chains tend to form aromatic-aromatic interactions and the hydrophobic residues aid to stabilize the complex.     

Sequence-dependent effects in A-DNA double helices

To date, more than ten different A-DNA structures have been analyzed at near atomic resolution by X-ray methods. This structural information enables us for the first time, to begin to discover the rules which govern the conformation of the double helix in the A form.A detailed analysis of the various helical conformations show that local structural changes are induced by base-pair stacking interactions. Variations in stacking geometry are sequence dependent. For pyrimidine-purine sites, the stacking mode is determined by the nature of the base-pair doublet only, whereas for purine-pyrimidine and homopolymer sites the identity of neighboring base pairs is important as well.     

On the stability of single- and double-stranded DNA helices: The application of the PPT-MCF method on large fragments of DNA

The pseudo-polarization tensor mutually consistent field (PPT -MCF ) method recently introduced [1] has been applied to study the stacking interactions between the nucleotide bases in large periodic B-DNA fragments. The effects on the global and local binding properties caused by replacing one base in the periodic sequence by another base are investigated. The increase in the stability for comparable fragments owing to this base substitution is further enforced in the case of periodic alternating helices. The most important results are that the stacking interaction between two bases is slowly converging with the interbase distance and that the average contribution per base to the binding energy is repulsive. Furthermore, the energetical properties of double helix models in B- and Z-DNA configurations, respectively, consisting of up to five base pairs have been compared. It turns out that the G C G C sequence in Z-DNA is significantly more stable than either in periodic or periodic alternating B-DNA. In these cases the average energy contribution of a single Watson–Crick-type base pair is predicted also to be positive. From the calculations it follows that the double helix is not stabilized owing to the hydrogen bonding between the bases belonging to both strands, in contradiction to most other investigations.     

Analysis of stacking overlap in nucleic acid structures: algorithm and application

RNA contains different secondary structural motifs like pseudo-helices, hairpin loops, internal loops, etc. in addition to anti-parallel double helices and random coils. The secondary structures are mainly stabilized by base-pairing and stacking interactions between the planar aromatic bases. The hydrogen bonding strength and geometries of base pairs are characterized by six intra-base pair parameters. Similarly, stacking can be represented by six local doublet parameters. These dinucleotide step parameters can describe the quality of stacking between Watson–Crick base pairs very effectively. However, it is quite difficult to understand the stacking pattern for dinucleotides consisting of non canonical base pairs from these parameters. Stacking interaction is a manifestation of the interaction between two aromatic bases or base pairs and thus can be estimated best by the overlap area between the planar aromatic moieties. We have calculated base pair overlap between two consecutive base pairs as the buried van der Waals surface between them. In general, overlap values show normal distribution for the Watson–Crick base pairs in most double helices within a range from 45 to 50 Å² irrespective of base sequence. The dinucleotide steps with non-canonical base pairs also are seen to have high overlap value, although their twist and few other parameters are rather unusual. We have analyzed hairpin loops of different length, bulges within double helical structures and pseudo-continuous helices using our algorithm. The overlap area analyses indicate good stacking between few looped out bases especially in GNRA tetraloop, which was difficult to quantitatively characterise from analysis of the base pair or dinucleotide step parameters. This parameter is also seen to be capable to distinguish pseudo-continuous helices from kinked helix junctions.     

A Theoretical Analysis of the Potential Role of π–π Stacking Interactions in the Photoprotolytic Cycle of Firefly Luciferin

Firefly oxyluciferin is a photoacid that presents a pH‐sensitive fluorescence, which results from pH‐dependent changes on the conformation of self‐aggregated π–π stacking complexes. Luciferin is a derivative of oxyluciferin with very similar fluorescence and photoacidic properties. This similarity indicates that luciferin is also expected to be able to form π–π stacking complexes, but no pH‐sensitive fluorescence is found for this compound. Here, a theoretical approach is used to rationalize this finding. We have found that luciferin only forms π–π stacking complexes in the ground state at acidic pH. At basic pH and in the excited state, luciferin is present as a dianion. This species is not able to self‐aggregate, owing to repulsive electrostatic interactions. Thus, this emissive species is not subject to π–π stacking interactions; this explains its pH‐insensitive fluorescence.     

Understanding the Fundamental Role of π/π, σ/σ, and σ/π Dispersion Interactions in Shaping Carbon‐Based Materials

Noncovalent interactions involving aromatic rings, such as π‐stacking and CH/π interactions, are central to many areas of modern chemistry. However, recent studies proved that aromaticity is not required for stacking interactions, since similar interaction energies were computed for several aromatic and aliphatic dimers. Herein, the nature and origin of π/π, σ/σ, and σ/π dispersion interactions has been investigated by using dispersion‐corrected density functional theory, energy decomposition analysis, and the recently developed noncovalent interaction (NCI) method. Our analysis shows that π/π and σ/σ stacking interactions are equally important for the benzene and cyclohexane dimers, explaining why both compounds have similar boiling points. Also, similar dispersion forces are found in the benzene???methane and cyclohexane???methane complexes. However, for systems larger than naphthalene, there are enhanced stacking interactions in the aromatic dimers adopting a parallel‐displaced configuration compared to the analogous saturated systems. Although dispersion plays a decisive role in stabilizing all the complexes, the origin of the π/π, σ/σ, and σ/π interactions is different. The NCI method reveals that the dispersion interactions between the hydrogen atoms are responsible for the surprisingly strong aliphatic interactions. Moreover, whereas σ/σ and σ/π interactions are local, the π/π stacking are inherently delocalized, which give rise to a non‐additive effect. These new types of dispersion interactions between saturated groups can be exploited in the rational design of novel carbon materials.     

Combined effect of stacking and solvation on the spontaneous mutation in DNA

In DNA, base pairs are involved in two reciprocal interactions: interbase hydrogen bonds and stacking. Furthermore, base pairs also undergo the effects of the external entities present in the biological environment, such as water molecules and cations. In this contribution, the double spontaneous mutation has been studied with hybrid theoretical tools in a DNA-embedded guanine-cytosine model accounting for the impact of the first hydration shell. According to our findings, the combination of the neighboring base pairs and surrounding water molecules plays a crucial role in the double proton transfer. Indeed, as a consequence of these interactions, the double proton transfer (DPT) mechanism is altered: on the one hand, stacking and hydration strongly affect the geometry of base pairs, and, on the other hand, vicinal water molecules may play an active role in the tautomeric equilibrium by catalyzing the proton transfer reaction.     

Highly polar carbohydrates stack onto DNA duplexes via CH/π interactions

Carbohydrate-nucleic acid contacts are known to be a fundamental part of some drug-DNA recognition processes. Most of these interactions occur through the minor groove of DNA, such as in the calicheamicin or anthracycline families, or through both minor and major groove binders such as in the pluramycins. Here, we demonstrate that carbohydrate-DNA interactions are also possible through sugar capping of a DNA double helix. Highly polar mono- and disaccharides are capable of CH/π stacking onto the terminal DNA base pair of a duplex as shown by NMR spectroscopy. The energetics of the carbohydrate-DNA interactions vary depending on the stereochemistry, polarity, and contact surface of the sugar involved and also on the terminal base pair. These results reveal carbohydrate-DNA base stacking as a potential recognition motif to be used in drug design, supramolecular chemistry, or biobased nanomaterials.     

A time-dependent quantum dynamics investigation of the guanine-cytosine system: a six-dimensional model

The dynamics of the guanine-cytosine base pair has been studied in the time-dependent quantum approach. A six-dimensional model involving the nonlinear three hydrogen bridges has been utilized. The modifications induced in the hydrogen transfer from a base to the other by the explicit inclusion of the out-of-plane hydrogen atom position in the three bridges have been evidenced and the consequences on stacking interaction and base pair opening are considered. The relevance of these aspects in biological properties has been suggested.     

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.