Nucleic Acid Base Pairs Research Articles

Tautomerism in nucleic acid bases and base pairs: a brief overview

AbstractThis article provides a brief overview of current status of studies on nucleic acid bases and base pairs tautomeric properties in the different environments. Applications of high‐level theoretical calculations have been found to be extremely useful in interpreting and enlightening complex experimental results. Actually, theory and experiments are complementary to each other and therefore it is not surprising that application of theoretical calculations were necessary to assign relatively higher energy tautomers of guanine in the gas phase. Inability to observe the stable tautomers in the laser‐desorbed guanine in the jet‐cooled beam demands more experiments and rigorous analysis. The usefulness of theoretical methods in the assignment of tautomeric forms of other bases and base pairs has also been discussed. Furthermore, we would like to state that recent surge in the high‐level computation of system such as nucleic acid bases and base pairs is only possible due to the advancement in state‐of‐the‐art computer hardware and computational algorithms. Afterward, it is not unexpected to assume that future investigations would utilize high‐level quantum chemistry calculation more rigorously in explaining complex experimental data as well as in revealing new phenomena not studied by experiments. WIREs Comput Mol Sci 2013, 3:637–649. doi: 10.1002/wcms.1145This article is categorized under: Structure and Mechanism > Molecular Structures Structure and Mechanism > Computational Biochemistry and Biophysics

N–H Stretching Excitations in Adenosine-Thymidine Base Pairs in Solution: Pair Geometries, Infrared Line Shapes, and Ultrafast Vibrational Dynamics

We explore the N-H stretching vibrations of adenosine-thymidine base pairs in chloroform solution with linear and nonlinear infrared spectroscopy. Based on estimates from NMR measurements and ab initio calculations, we conclude that adenosine and thymidine form hydrogen bonded base pairs in Watson-Crick, reverse Watson-Crick, Hoogsteen, and reverse Hoogsteen configurations with similar probability. Steady-state concentration and temperature dependent linear FT-IR studies, including H/D exchange experiments, reveal that these hydrogen-bonded base pairs have complex N-H/N-D stretching spectra with a multitude of spectral components. Nonlinear 2D-IR spectroscopic results, together with IR-pump-IR-probe measurements, as also corroborated by ab initio calculations, reveal that the number of N-H stretching transitions is larger than the total number of N-H stretching modes. This is explained by couplings to other modes, such as an underdamped low-frequency hydrogen-bond mode, and a Fermi resonance with NH(2) bending overtone levels of the adenosine amino-group. Our results demonstrate that modeling based on local N-H stretching vibrations only is not sufficient and call for further refinement of the description of the N-H stretching manifolds of nucleic acid base pairs of adenosine and thymidine, incorporating a multitude of couplings with fingerprint and low-frequency modes.

Nucleic Acid Chaperone Activity Transforms the Energy Landscape of HIV-1 TAR RNA

Retroviral nucleocapsid (NC) proteins are nucleic acid chaperones that play a key role in the viral life cycle, including reverse transcription, where NC destabilizes the transactivation response RNA (TAR RNA) hairpin. To quantify the interaction of HIV-1 NC and TAR RNA, we use optical tweezers to exert tension upon the free ends of an individual TAR hairpin, forcing the hairpin open and then allowing it to close. We combine force-ramp experiments with a new analytical technique that quantitatively characterizes the energy landscape of equilibrium and non-equilibrium TAR hairpin unfolding and folding. We use the pulling rate dependence of the unfolding force to determine the distance to the transition state for this complex. This measurement reveals that to cause complete TAR unfolding, it is sufficient to unzip 10 bp of the 24 bp TAR hairpin stem in the absence of NC but only 5 bp of 24 in the presence of NC. Extrapolation of the measured TAR opening rate to zero pulling rate yields nearly 1000-fold faster opening with NC, equivalent to a decrease in the TAR opening barrier of 4.2 +/- 0.2 kcal/mol. Furthermore, equilibrium and complementary non-equilibrium TAR unfolding measurements using Crooks fluctuation theorem show that NC lowers the overall free energy of hairpin opening by 8.5 +/- 0.3 kcal/mol. These results demonstrate that NC destabilizes every nucleic acid base pair by strongly facilitating nucleic acid opening. This work was funded in part by Federal Funds from NCI, NIH under contract HHSN261200800001E (RJG).

Designer nucleic acids to probe and program the cell

Recent advances in nucleic acid sequencing, structural, and computational technologies have resulted in dramatic progress in our understanding of nucleic acid structure and function in the cell. This knowledge, together with the predictable base-pairing of nucleic acids and powerful synthesis and expression capabilities now offers the unique ability to program nucleic acids to form precise 3D architectures with diverse applications in synthetic and cell biology. The unique modularity of structural motifs that include aptamers, DNAzymes, and ribozymes, together with their well-defined construction rules, enables the synthesis of functional higher-order nucleic acid complexes from these subcomponents. As we illustrate here, these highly programmable, smart complexes are increasingly enabling researchers to probe and program the cell in a sophisticated manner that moves well beyond the use of nucleic acids for conventional genetic manipulation alone.

Digital and Analog Chemical Evolution

Living matter is the most elaborate, elegant, and complex hierarchical material known and is consequently the natural target for an ever-expanding scientific and technological effort to unlock and deconvolute its marvelous forms and functions. Our current understanding suggests that biological materials are derived from a bottom-up process, a spontaneous emergence of molecular networks in the course of chemical evolution. Polymer cooperation, so beautifully manifested in the ribosome, appeared in these dynamic networks, and the special physicochemical properties of the nucleic and amino acid polymers made possible the critical threshold for the emergence of extant cellular life. These properties include the precise and geometrically discrete hydrogen bonding patterns that dominate the complementary interactions of nucleic acid base-pairing that guide replication and ensure replication fidelity. In contrast, complex and highly context-dependent sets of intra- and intermolecular interactions guide protein folding. These diverse interactions allow the more analog environmental chemical potential fluctuations to dictate conformational template-directed propagation. When these two different strategies converged in the remarkable synergistic ribonucleoprotein that is the ribosome, this resulting molecular digital-to-analog converter achieved the capacity for both persistent information storage and adaptive responses to an ever-changing environment. The ancestral chemical networks that preceded the Central Dogma of Earth's biology must reflect the dynamic chemical evolutionary landscapes that allowed for selection, propagation, and diversification and ultimately the demarcation and specialization of function that modern biopolymers manifest. Not only should modern biopolymers contain molecular fossils of this earlier age, but it should be possible to use this information to reinvent these dynamic functional networks. In this Account, we review the first dynamic network created by modification of a nucleic acid backbone and show how it has exploited the digital-like base pairing for reversible polymer construction and information transfer. We further review how these lessons have been extended to the complex folding landscapes of templated peptide assembly. These insights have allowed for the construction of molecular hybrids of each biopolymer class and made possible the reimagining of chemical evolution. Such elaboration of biopolymer chimeras has already led to applications in therapeutics and diagnostics, to the construction of novel nanostructured materials, and toward orthogonal biochemical pathways that expand the evolution of existing biochemical systems. The ability to look beyond the primordial emergence of the ribosome may allow us to better define the origins of chemical evolution, to extend its horizons beyond the biology of today and ask whether evolution is an inherent property of matter unbounded by physical limitations imposed by our planet's diverse environments.

Hydrogen bond effect on the structure and vibrational spectra of complementary pairs of nucleic acid bases. III. Guanine-cytosine

Vibrational spectra of the isolated complementary guanine-cytosine pair are calculated at the B3LYP/6-311++G(d,p) level. The hydrogen bond effect on the structure, frequency positions, and intensities of normal vibrations of the pair are analyzed in comparison with the spectra of isolated guanine and cytosine molecules. Characteristic spectral features of the formation of the complementary guanine-cytosine base pair are revealed.

Molecular Structure and Interactions of Nucleic Acid Components in Nanoparticles: Ab Initio Calculations

Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 Å). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150–200 atoms with enough large basis sets (for example, 6-31G*). The aim of this work is to reveal the peculiarities of molecular and electronic structures, as well as the energy features of nanoparticles of nucleic acid components. We had carried out ab initio calculations of the molecular structure and interactions in the stacking dimer, trimer, and tetramer of nucleic base pairs and in the stacking (TpG)(ApC) dimer and (TpGpC) (ApCpG) trimer of nucleotides, which are small DNA fragments. The performed calculations of molecular structures of dimers and trimers of nucleotide pairs showed that the interplanar distance in the structures studied is equal to 3.2 Å on average, and the helical angle in a trimer is approximately equal to 30º. The distance between phosphor atoms in neighboring chains is 13.1 Å. For dimers and trimers under study, we calculated the horizontal interaction energies. The analysis of interplanar distances and angles between nucleic bases and their pairs in the calculated short oligomers of nucleic acid base pairs (stacking dimer, trimer, and tetramer) has been carried out. Studies of interactions in the calculated short oligomers showed a considerable role of the cross interaction in the stabilization of the structures. The contribution of cross interactions to the horizontal interactions grows with the length of an oligomer. Nanoparticle components get electric charges in nanoparticles. Longwave low-intensity bands can appear in the electron spectra of nanoparticles.

Electron Attachment to the Guanine–Cytosine Nucleic Acid Base Pair and the Effects of Monohydration and Proton Transfer

The guanine-cytosine (GC) radical anion and its interaction with a single water molecule is studied using ab initio and density functional methods. Z-averaged second-order perturbation theory (ZAPT2) was applied to GC radical anion for the first time. Predicted spin densities show that the radical character is localized on cytosine. The Watson-Crick monohydrated GC anion is compared to neutral GC·H2O, as well as to the proton-transferred analogue on the basis of structural and energetic properties. In all three systems, local minima are identified that correspond to water positioned in the major and minor grooves of macromolecular DNA. On the anionic surface, two novel structures have water positioned above or below the GC plane. On the neutral and anionic surfaces, the global minimum can be described as water interacting with the minor groove. These structures are predicted to have hydration energies of 9.7 and 11.8 kcal mol(-1), respectively. Upon interbase proton-transfer (PT), the anionic global minimum has water positioned in the major groove, and the hydration energy increases to 13.4 kcal mol(-1). PT GC·H2O(•-) has distonic character; the radical character resides on cytosine, while the negative charge is localized on guanine. The effects of proton transfer are further investigated through the computed adiabatic electron affinities (AEA) of GC and monohydrated GC, and the vertical detachment energies (VDE) of the corresponding anions. Monohydration increases the AEAs and VDEs by only 0.1 eV, while proton-transfer increases the VDEs substantially (0.8 eV). The molecular charge distribution of monohydrated guanine-cytosine radical anion depends heavily on interbase proton transfer.

Structural characterization of electron-induced proton transfer in the formic acid dimer anion, (HCOOH)2−, with vibrational and photoelectron spectroscopies

The (HCOOH)(2) anion, formed by electron attachment to the formic acid dimer (FA(2)), is an archetypal system for exploring the mechanics of the electron-induced proton transfer motif that is purported to occur when neutral nucleic acid base-pairs accommodate an excess electron [K. Aflatooni, G. A. Gallup, and P. D. Burrow, J. Phys. Chem. A 102, 6205 (1998); J. H. Hendricks, S. A. Lyapustina, H. L. de Clercq, J. T. Snodgrass, and K. H. Bowen, J. Chem Phys. 104, 7788 (1996); C. Desfrancois, H. Abdoul-Carime, and J. P. Schermann, ibid. 104, 7792 (1996)]. The FA(2) anion and several of its H∕D isotopologues were isolated in the gas phase and characterized using Ar-tagged vibrational predissociation and electron autodetachment spectroscopies. The photoelectron spectrum of the FA(2) anion was also recorded using velocity-map imaging. The resulting spectroscopic information verifies the equilibrium FA(2)(-) geometry predicted by theory which features a symmetrical, double H-bonded bridge effectively linking together constituents that most closely resemble the formate ion and a dihydroxymethyl radical. The spectroscopic signatures of this ion were analyzed with the aid of calculated anharmonic vibrational band patterns.

Targeting DNA G-Quadruplex Structures with Peptide Nucleic Acids

Regulation of genetic functions based on targeting DNA or RNA sequences with complementary oligonucleotides is especially attractive in the post-genome era. Oligonucleotides can be rationally designed to bind their targets based on simple nucleic acid base pairing rules. However, the use of natural DNA and RNA oligonucleotides as targeting probes can cause numerous off-target effects. In addition, natural nucleic acids are prone to degradation in vivo by various nucleases. To address these problems, nucleic acid mimics such as peptide nucleic acids (PNA) have been developed. They are more stable, show less off-target effects, and, in general, have better binding affinity to their targets. However, their high affinity to DNA can reduce their sequence-specificity. The formation of alternative DNA secondary structures, such as the G-quadruplex, provides an extra level of specificity as targets for PNA oligomers. PNA probes can target the loops of G-quadruplex, invade the core by forming PNA-DNA guanine-tetrads, or bind to the open bases on the complementary cytosine-rich strand. Not only could the development of such G-quadruplex-specific probes allow regulation of gene expression, but it will also provide a means to clarify the biological roles G-quadruplex structures may possess.

Calculation of the Energy of a Bio-Polymer as a Function of End-To-End Extension

When considering the folding of a biopolymer (DNA, RNA or protein) it is natural to express the energy of the system as a function of conformation. However, in single molecule manipulation experiments the system is most naturally characterized in terms of the end-to-end distance of the polymer, and the energy landscape itself can be measured as a function of the end-to-end distance. The relationship between energy as a function of conformation and energy as a function of end-to-end distance is extremely complex. We introduce a physical model which allows the energy landscape as a function of end-to-end distance to be calculated from knowledge of the energy as a function of conformation of the polymer. Using optical trap based experiments we show that the measured energy landscape of a DNA stem-loop structure agrees with the landscape calculated from our model with extremely high precision. We believe the combination of our model with high resolution optical trap techniques will facilitate direct measurement of the hybridization energy of nucleic acid base pairs and sequencing of double stranded RNA and DNA.

Genomic sequencing in clinical trials

Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to find its way into clinical trials both nationally and worldwide. We highlight the currently available types of genomic sequencing platforms, outline the advantages and disadvantages of each, and compare first- and next-generation techniques with respect to capabilities, quality, and cost. We describe the current geographical distributions and types of disease conditions in which these technologies are used, and how next-generation sequencing is strategically being incorporated into new and existing studies. Lastly, recent major breakthroughs and the ongoing challenges of using genomic sequencing in clinical research are discussed.

Hydrogen-bonding studies of amino acid side-chains with DNA base pairs

The interactions of the amino acid side-chains arginine (ARG), aspartic acid (ASP), asparagine (ASN), lysine (LYS) and serine (SER) with nucleic acid base pairs have been investigated using theoretical methods. The interaction energy of the short intermolecular N–H ··· N, N–H ··· O, O–H ··· O, O–H ··· N, C–H ··· O and C–H ··· N hydrogen bonds present in both isolated base pairs and complexes and its role in providing stability to the complexes have been explored. The homonuclear interactions are found to be stronger than the heteronuclear interactions. An improper hydrogen bond has been observed for some of the N–H ··· O and N–H ··· N hydrogen-bond interactions with the contraction of the N–H bond varying from 0.001 to 0.0260 Å and the corresponding blue shift of the stretching frequency by 4–291 cm−1. Localized molecular orbital energy decomposition analysis (LMOEDA) reveals that the major contributions to the energetics are from the long-range polarization (PL) interaction, and the short-range attractive (ES, EX) and repulsive (REP) interactions. The Bader's atoms in molecules (AIM) theory shows good correlation for the electron density and its Laplacian at the bond critical points (BCP) with the N–H ··· N and N–H ··· O hydrogen-bond lengths in the complexes, and gives a proper explanation for the stability of the structure. The charge-transfer from the proton acceptor to the antibonding orbital of the X–H bond in the complexes was studied using natural bond orbital (NBO) analysis.

Revisiting the Effects of Sequence and Structure on the Hydrogen Bonding and π-Stacking Interactions in Nucleic Acids

Calculated electron densities from PBE0/6-31+G(d,p) were analyzed with respect to the hydrogen bonding within a nucleic acid base pair and the π-stacking between sets of base pairs. From published X-ray crystallographic data, base pairs were isolated from a total of 11 DNA and RNA duplexes, and their experimental geometry was maintained throughout the analyses. Focusing solely on Watson-Crick base pairs, from the values of the electron density between interacting nuclei (at the bond critical points), we provide quantitative data on individual weak interactions. For hydrogen bonding, in addition to quantifying the scissoring effect in GC base pairs, the origin of the controversy around the relative stability of AT and AU base pairs is identified and resolved. Thus, it is illustrated how the conclusion as to their relative stability rests on the specific choice of oligonucleotides compared. For π-stacking, sequence effects for tandem AT base pairs are captured, quantified, and explained, and the greater sensitivity of GC, over AT, sequences to the rise parameter is established. The results presented here show that, from experimental geometries and their electron densities, previously determined effects of the sequence and structure of a duplex on the stabilizing interactions can be captured, quantified, and traced back to the geometry of the base pairs.

Unraveling the Correlated Dynamics of the Double Hydrogen Bonds of Nucleic Acid Base Pairs in Solution

Quantum mechanics/molecular mechanics hybrid simulations (CPMD/GROMOS) of nonlinear infrared spectra are performed for a modified adenine-uracil base pair in CDCl(3) solution. Employing a mapping between hydrogen bond distances and fundamental as well as overtone transition frequencies on the basis of on-the-fly snapshot potential energy curves, energy gap correlation functions are established. These correlation functions are utilized to determine pump-probe and two-dimensional photon echo spectra. Analysis of the latter yields off-diagonal peaks signifying correlated fluctuations of the N-H···N and N-H···O hydrogen bonds.

HIV-1 NC Protein Modifies Opening and Closing Kinetics of TAR RNA Hairpin

Retroviral nucleocapsid (NC) proteins are nucleic acid chaperones that play a key role in the viral life cycle, including reverse transcription, where NC destabilizes the transactivation response RNA (TAR RNA) hairpin. To quantify the interaction of HIV-1 NC and TAR RNA, we used optical tweezers to exert tension upon the free ends of the individual TAR hairpin, forcing the hairpin open and then allowing it to close. In the absence of NC, the TAR hairpin opens and closes at forces that depend upon the hairpin stability, as well as the rate of pulling and relaxation. Surprisingly, once saturated with NC, the opening forces increase, suggesting an apparent stabilization of the structure. However, the higher opening rate in the presence of NC is only observed at high pulling rates, while extrapolation of the measured TAR opening rate vs pulling rate to infinitely slow pulling yields ∼1000-fold faster opening with NC. This ability of NC to facilitate opening of the TAR hairpin is equivalent to ∼4 kcal/mol decrease in the TAR opening barrier. The stronger pulling rate dependence of TAR opening in the presence of NC indicates that fewer TAR base pairs unzip prior to complete hairpin stem destabilization. Specifically, of the 24 TAR hairpin stem base pairs it is sufficient to unzip 12 bp in the absence of but only 6 bp in the presence of NC to cause complete TAR unfolding. This result quantitatively characterizes the ability of NC to moderately destabilize every nucleic acid base pair.

On the role of mercury in the non-covalent stabilisation of consecutive U–HgII–U metal-mediated nucleic acid base pairs: metallophilic attraction enters the world of nucleic acids

Metal atoms with a closed-shell electronic structure and positive charge as for example the Au(I), Pt(II), Ag(I), Tl(I) or Hg(II) atoms do not in some compounds repel each other due to the so-called metallophilic attraction (P. Pyykkö, Chem. Rev., 1997, 97, 597-636). Here we highlight the role of the Hg(II)Hg(II) metallophilic attraction between the consecutive metal-mediated mismatched base pairs of nucleic acids. Usually, the base stacking dominates the non-covalent interactions between steps of native nucleic acids. In the presence of metal-mediated base pairs these non-covalent interactions are enriched by the metal-base interactions and the metallophilic attraction. The two interactions arising due to the metal linkage of the mismatches were found in this study to have a stabilizing effect on nucleic acid structure. The calculated data are consistent with recent experimental observations. The stabilization due to the metallophilic attraction seems to be a generally important concept for the nucleic acids containing heavy metals with short contacts.

A model study on the stacking interaction of phenanthroline ligand with nucleic acid base pairs: An ab initio, MP2 and DFT studies

The stacking of phenanthroline(phen) ligand within base pair sequences is one of the important factors for the stabilization of metalphen complex within DNA. The stacking ability of this ligand has been assessed to deduce the base pair selectivity as well as to identify the favored region of intercalation. Different level of theories have been used to predict the favorable regions for stacking interaction of phen ligand with base pair, but the results of MP2/6-31+G(d,p) is found to be reasonably good for monitoring such interactions.

Effect of hydrogen bonding on the structure and vibrational spectra of the complementary pairs of nucleic acid bases. II. adenine-thymine

The vibrational spectra of an isolated complementary adenine-thymine pair are calculated in the B3LYP/6-311++G(d,p) approximation and analyzed. The effect of hydrogen bonds on the structure is shown along with the position of frequencies and intensities of normal vibrations of the pair in comparison with the spectra of isolated thymine and adenine molecules. A comparative analysis of the hydrogen bonding effect on the IR and Raman spectra of thymine and adenine is performed

INTERACTION OF EMODIN WITH DNA BASES: A DENSITY FUNCTIONAL THEORY

In this study, we present work on the physicochemical interaction between the anticancer drug molecule Emodin (ED) and DNA. Comprehending the physicochemical properties of this drug besides the mechanism by which it interacts with DNA should eventually permit the rational design of novel anticancer or antiviral drugs. The final purpose is the clarification of this novel class of drugs as potential pharmaceutical agents. The properties of the isolated intercalator ED and its stacking interactions with adenine⋯thymine (AT) and guanine⋯cytosine (GC) (nucleic acid base pairs) in face-to-face and face-to-back models were studied by means of the density functional tightbinding (DFTB) method. This method was an approximate version of the density functional theory (DFT) method and it includes London dispersion energy. The molecular modeling of the complex formed between ED and DNA indicated that this complex was capable of contributing to the formation of a constant intercalation site. The results exhibit that ED changes affect DNA structure with reference to bond lengths, bond angles, torsion angles, and charges.