Base-pair Parameters Research Articles

The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations.

DNA-RNA hybrid duplexes play essential roles during the reverse transcription of RNA viruses and DNA replication. The opening and conformation changes of individual base pairs are critical to their biological functions. However, the microscopic mechanisms governing base pair closing and opening at the atomic level remain poorly understood. In this study, we investigated the thermodynamic and kinetic parameters of the dA-rU base pair in a DNA-RNA hybrid duplex using 4 μs all-atom molecular dynamics (MD) simulations at different temperatures. Our results showed that the thermodynamic parameters of the dA-rU base pair aligned with the predictions of the nearest-neighbor model and were close to those of the AU base pair in RNA. The temperature dependence of the average lifetimes of both the open and the closed states, as well as the transition path times, were obtained. The free-energy barrier for a single base pair opening and closing arises from an increase in enthalpy due to the disruption of the base-stacking interactions and hydrogen bonding, along with an entropy loss attributed to the accompanying restrictions, such as torsional angle constraints and solvent viscosity.

A standard reference frame and geometry for nucleosomes.

The nucleosome is often described as a histone-DNA complex containing eight histones and 145-147 base pairs of DNA. The reality is more complex. Here we evaluate approximately 500 nucleosomes from the Research Collaboratory for Structural Biology with the goal of establishing a reference frame and standard geometry for describing the internal structure of mono-nucleosomes and the stacking of nucleosomes in arrays and clusters. Our reference frame places the center of mass of the nucleosome's octameric core at the origin. The positive x-axis aligns with the symmetry axis of the nucleosome and passes through the central base pair or base pair step associated with the octamer. The z-axis is defined by fitting a regular helix (constant pitch and radius) to the nucleosome. The positive direction is determined by the choice of reading strand. Two methods for defining this helix are explored. One fits a helix to the center line of the DNA, which is itself determined according to a standard reference geometry for DNA base pairs. The other fits a helix to the centers of mass obtained from the histones. The z-axes, so defined, are slightly askew. Over 100 nucleosomes are used to define a standard reference geometry for the histones and for super helices with 145, 146 and 147 base pairs. In all structures, the cumulative sum of Rise, Twist and arclength are linear functions of base pair index with R2 values in excess of 0.999. The standard geometry supports a rigorous definition of entry-exit angle and identification of structural anomalies. Select examples demonstrate how generalizations of the inter and intra base pair parameters can be utilized to analyze the internal structure of mono-nucleosomes, their stacking in arrays and clusters, and the ab initio assembly of atomic and coarse-grained structures.

Bending of Canonical and G/T Mismatched DNAs.

Mismatched base pairs alter the flexibility and intrinsic curvature of DNA. The role of such DNA features is not fully understood in the mismatch repair pathway. MutS/DNA complexes exhibit DNA bending, PHE intercalation, and changes of base-pair parameters near the mismatch. Recently, we have shown that base-pair opening in the absence of MutS can discriminate mismatches from canonical base pairs better than DNA bending. However, DNA bending in the absence of MutS was found to be rather challenging to describe correctly. Here, we present a computational study on the DNA bending of canonical and G/T mismatched DNAs. Five types of geometric parameters covering template-based bending toward the experimental DNA structure, global, and local geometry parameters were employed in biased molecular dynamics in the absence of MutS. None of these parameters showed higher discrimination than the base-pair opening. Only roll could induce a sharply localized bending of DNA as observed in the experimental MutS/DNA structure. Further, we demonstrated that the intercalation of benzene mimicking PHE decreases the energetic cost of DNA bending without any effect on mismatch discrimination.

Base-Pairs' Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules.

By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson–Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons’ dispersion relation. The existence of synchronized collective oscillations enhancing the - orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.

Importance of base-pair opening for mismatch recognition.

Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs.

A dynamic view of DNA structure within the nucleosome: Biological implications

Most of eukaryotic cellular DNA is packed in nucleosome core particles (NCPs), in which the DNA (DNANCP) is wrapped around histones. The influence of this organization on the intrinsic local dynamics of DNA is largely unknown, in particular because capturing such information from experiments remains notoriously challenging. Given the importance of dynamical properties in DNA functions, we addressed this issue using CHARMM36 MD simulations of a nucleosome containing the NCP positioning 601 sequence and four related free dodecamers. Comparison between DNANCP and free DNA reveals a limited impact of the dense DNA-histone interface on correlated motions of dinucleotide constituents and on fluctuations of inter base pair parameters. A characteristic feature intimately associated with the DNANCP super-helical path is a set of structural periodicities that includes a marked alternation of regions enriched in backbone BI and BII conformers. This observation led to uncover a convincing correspondence between the sequence effect on BI/BII propensities in both DNANCP and free DNA, strengthening the idea that the histone preference for particular DNA sequences relies on those intrinsic structural properties.These results offer for the first time a detailed view of the DNA dynamical behavior within NCP. They show in particular that the DNANCP dynamics is substantial enough to preserve the ability to structurally adjust to external proteins, for instance remodelers. Also, fresh structural arguments highlight the relevance of relationships between DNA sequence and structural properties for NCP formation. Overall, our work offers a more rational framework to approach the functional, biological roles of NCP.

Stacking geometry between two sheared Watson-Crick basepairs: Computational chemistry and bioinformatics based prediction

BackgroundMolecular modeling of RNA double helices is possible using most probable values of basepair parameters obtained from crystal structure database. The A:A w:wC non-canonical basepair, involving Watson-Crick edges of two Adenines in cis orientation, appears quite frequently in database. Bimodal distribution of its Shear, due to two different H-bonding schemes, introduces the confusion in assigning most the probable value. Its effect is pronounced when the A:A w:wC basepair stacks on Sheared wobble G:U W:WC basepairs. MethodsWe employed molecular dynamics simulations of three possible double helices with GAG, UAG and GAU sequence motifs at their centers and quantum chemical calculation for non-canonical A:A w:wC basepair stacked on G:U W:WC basepair. ResultsWe noticed stable structures of GAG motif with specifically negative Shear of the A:A basepair but stabilities of the other motifs were not found with A:A w:wC basepairing. Hybrid DFT-D and MP2 stacking energy analyses on dinucleotide step sequences, A:A w:wC::G:U W:WC and A:A w:wC::U:G W:WC reveal that viable orientation of A:A::G:U prefers one of the H-bonding modes with negative Shear, supported by crystal structure database. The A:A::U:G dinucleotide, however, prefers structure with only positive Shear. ConclusionsThe quantum chemical calculations explain why MD simulations of GAG sequence motif only appear stable. In the cases of the GAU and UAG motifs “tug of war” situation between positive and negative Shears of A:A w:wC basepair induces conformational plasticity. General significanceWe have projected comprehensive reason behind the promiscuous nature of A:A w:wC basepair which brings occasional structural plasticity.

Effects of Mg2+ on the binding of the CREB/CRE complex: Full-atom molecular dynamics simulations**Project supported by the National Natural Science Foundation of China (Grant Nos. 11705064, 11675060, and 91730301), the Fundamental Research Funds for the Central Universities, China (Grant Nos. 2662016QD005 and 26622018JC017), and the Huazhong Agricultural University Scientific and Technological Self-Innovation Foundation Program, China (Grant No. 2015RC021).

Metal ions play critical roles in the interaction between deoxyribonucleic acid (DNA) and protein. The experimental research has demonstrated that the Mg2+ ion can affect the binding between transcription factor and DNA. In our work, by full-atom molecular dynamic simulation, the effects of the Mg2+ ion on the cyclic adenosine monophosphate (cAMP) response element binding protein (CREB)/cAMP response elements (CRE) complex are investigated. It is illustrated that the number of hydrogen bonds formed at the interface between protein and DNA is significantly increased when the Mg2+ ion is added. Hence, an obvious change in the structure of the DNA is observed. Then the DNA base groove and base pair parameters are analyzed. We find that, due to the introduction of the Mg2+ ion, the DNA base major groove becomes narrower. A potential mechanism for this observation is proposed. It is confirmed that the Mg2+ ion can enhance the stability of the DNA–protein complex.

The nearest neighbor and next nearest neighbor effects on the thermodynamic and kinetic properties of RNA base pair.

The thermodynamic and kinetic parameters of an RNA base pair with different nearest and next nearest neighbors were obtained through long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The results indicate that thermodynamic parameters of GC base pair are dependent on the nearest neighbor base pair, and the next nearest neighbor base pair has little effect, which validated the nearest-neighbor model. The closing and opening rates of the GC base pair also showed nearest neighbor dependences. At certain temperature, the closing and opening rates of the GC pair with nearest neighbor AU is larger than that with the nearest neighbor GC, and the next nearest neighbor plays little role. The free energy landscape of the GC base pair with the nearest neighbor GC is rougher than that with nearest neighbor AU.

Quaternion modeling of the helical path for analysis of the shape of the DNA molecule

The three­dimensional shape of a DNA molecule is a key property influencing its functional specificity and the nature of its molecular interactions. The characteristic shape into which a DNA molecule folds under certain conditions is a manifestation of its micromechanical and structural features, which are sequence­dependent. DNA shape­related properties can there fore be determined in a predictable manner. A number of models have been designed to describe intrinsic DNA curvature, incorporating a set of helical parameters which can be applied to operative three­dimensional reconstruction of the DNA structures. Alternatively, desired base pair parameters can be computed based on publicly available information about atomic DNA structures. Further, taking the base pairs as rigid bodies, their relative location in space can be estimated based on these parameters. Matrices are a common method to implement any rigid body transformations and are widely used in the modeling of DNA structures. Quaternions are the more straightforward and robust alternative for matrices. Unit quaternions can represent only a rotation, whereas dual quaternions combine rotation and translation into a single state. In the present guide, the algebra of unit and dual quaternions is applied for the first time to modeling of the DNA helical path, based on conformational parameters of the base pair steps. Although dual quaternions are preferable for modeling of DNA structure in detail, the use of unit quaternions is sufficient to predict the DNA trajectory and all calculations of DNA shape features. In order to analyze DNA shape and chain sta ­ tistics, and predict the micromechanical properties of DNA molecules based on coordinates of the helical path, the widely used as well as original algorithms for computing DNA curvature, radius of gyration, persistence length and phasing of DNA bends are described. Taken together, these algorithms will be useful both in the in silico analysis of relatively short DNA fragments as well as in topological mapping of whole genomes.

Biasing Simulations of DNA Base Pair Parameters with Application to Propellor Twisting in AT/AT, AA/TT, and AC/GT Steps and Their Uracil Analogs.

An accurate and efficient implementation of the six DNA base pair parameters as order parameters for enhanced sampling simulations is presented. The parameter definitions are defined by vector algebra operations on a reduced atomic set of the base pair, and correlate very well with standard definitions. Application of the model is illustrated by umbrella sampling simulations of propeller twisting within AT/AT, AA/TT, and AC/GT steps and their uracil analogs. Strong correlations are found between propeller twisting and a number of conformational parameters, including buckle, opening, BI/BII backbone configuration, and sugar puckering. The thymine methyl group is observed to notably alter the local conformational free energy landscape, with effects within and directly upstream of the thymine containing base pair.

Molecular dynamics simulation and free energy analysis of the interaction of platinum-based anti-cancer drugs with DNA

Cisplatin and oxaliplatin are two widely-used anti-cancer drugs which covalently bind to a same location in DNA strands. Platinum agents make intrastrand and interstrand cross-links with the N7 atoms of guanine nucleotides which prevent DNA from polymerization by causing a distortion in the double helix. Molecular dynamics simulations and free energy calculations were carried out to investigate the binding of two platinum-based anti-cancer drugs with DNA. We compared the binding of these drugs which differ in their carrier ligands, and hence their potential interactions with DNA. When a platinum agent binds to nucleotides, it causes a high amount of deformation in DNA structure. To find the extent of deformation, torsion angles and base pair and groove parameters of DNA were considered. These parameters were compared with normal B-DNA which was considered as the undamaged DNA. The formation of hydrogen bonds between drugs and DNA nucleotides was examined in solution. It was shown that oxaliplatin forms more hydrogen bonds than cisplatin. Our results confirm that the structure of the platinated DNA rearranges significantly and cisplatin tries to deform DNA more than oxaliplatin. The binding free energies were also investigated to understand the affinities, types and the contributions of interactions between drugs and DNA. It was concluded that oxaliplatin tendency for binding to DNA is more than cisplatin in solvent environment. The binding free energy was calculated based on the MM/PBSA and MM/GBSA methods and the results of QM/MM calculations verified them.

Analysis of the structural and thermodynamic parameters of the hydrogen bond in complementary pairs of DNA and RNA bases

Density functional methods involving the B3LYP functional and M062X, WB97XD, and B97D ones optimized for calculations of long-range interactions are used to carry out theoretical analysis of the structural and thermodynamic parameters of complementary adenine-thymine, adenine-uracil, and guanine-cytosine base pairs with hydrogen bonds. The calculated values of the structural and thermodynamic parameters are corrected according to the basis superposition error. The enthalpy factor is demonstrated to prevail over the entropy one during the formation of the guanine—cytosine complex, indicating that the equilibrium constant is of great importance. It is discussed whether the M062X, WB97XD, and B97D functionals can be applied to describe hydrogen-bonded systems.

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

DNA within the living cells experiences a diverse range of temperature, ranging from freezing condition to hot spring water. How the structure, the mechanical properties of DNA, and the solvation dynamics around DNA changes with the temperature is important to understand the functionality of DNA under those acute temperature conditions. In that notion, we have carried out molecular dynamics simulations of a DNA oligomer, containing TATA-box sequence for three different temperatures (250K, 300K and 350K). We observed that the structure of the DNA, in terms of backbone torsion angles, sugar pucker, base pair parameters, and base pair step parameters, did not show any unusual properties within the studied range of temperatures, but significant structural alteration was noticed between BI and BII forms at higher temperature. As expected, the flexibility of the DNA, in terms of the torsional rigidity and the bending rigidity is highly temperature dependent, confirming that flexibility increases with increase in temperature. Additionally, the groove widths of the studied DNA showed temperature sensitivity, specifically, the major groove width decreases and the minor groove width increases, respectively, with the increase in temperature. We observed that at higher temperature, water around both the major and the minor groove of the DNA is less structured. However, the water dynamics around the minor groove of the DNA is more restricted as compared to the water around the major groove throughout the studied range of temperatures, without any anomalous behavior.

The thermodynamics and kinetics of a nucleotide base pair.

The thermodynamic and kinetic parameters of an RNA base pair were obtained through a long-time molecular dynamics simulation of the opening-closing switch process of the base pair near its melting temperature. The thermodynamic parameters were in good agreement with the nearest-neighbor model. The opening rates showed strong temperature dependence, however, the closing rates showed only weak temperature dependence. The transition path time was weakly temperature dependent and was insensitive to the energy barrier. The diffusion constant exhibited super-Arrhenius behavior. The free energy barrier of breaking a single base stack results from the enthalpy increase, ΔH, caused by the disruption of hydrogen bonding and base-stacking interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss, ΔS, caused by the restriction of torsional angles. These results suggest that a one-dimensional free energy surface is sufficient to accurately describe the dynamics of base pair opening and closing, and the dynamics are Brownian.

The N(2)-Furfuryl-deoxyguanosine Adduct Does Not Alter the Structure of B-DNA.

N(2)-Furfuryl-deoxyguanosine (fdG) is carcinogenic DNA adduct that originates from furfuryl alcohol. It is also a stable structural mimic of the damage induced by the nitrofurazone family of antibiotics. For the structural and functional studies of this model N(2)-dG adduct, reliable and rapid access to fdG-modified DNAs are warranted. Toward this end, here we report the synthesis of fdG-modified DNAs using phosphoramidite chemistry involving only three steps. The functional integrity of the modified DNA has been verified by primer extension studies with DNA polymerases I and IV from E. coli. Introduction of fdG into a DNA duplex decreases the Tm by ∼1.6 °C/modification. Molecular dynamics simulations of a DNA duplex bearing the fdG adduct revealed that though the overall B-DNA structure is maintained, this lesion can disrupt W-C H-bonding, stacking interactions, and minor groove hydrations to some extent at the modified site, and these effects lead to slight variations in the local base pair parameters. Overall, our studies show that fdG is tolerated at the minor groove of the DNA to a better extent compared with other bulky DNA damages, and this property will make it difficult for the DNA repair pathways to detect this adduct.

Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics

The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI ↔ BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0εζOLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representation of B-DNA in solution, despite residual shortcomings. This improved representation allows new and deeper interpretation of the experimental observables, including regarding the behavior of facing phosphate groups in complementary dinucleotides, and their modulation by the sequence. It also provides the opportunity to extensively revisit and refine the coupling between backbone states and inter base pair parameters, which emerges as a common theme across all the complementary dinucleotides. In sum, the global agreement between simulations and experiment reveals new aspects of intrinsic DNA mechanics, a key component of DNA-protein recognition.

Dynamic hydrogen bonding and DNA flexibility in minor groove binders: molecular dynamics simulation of the polyamide f-ImPyIm bound to the Mlu1 (MCB) sequence 5'-ACGCGT-3' in 2:1 motif.

Molecular dynamics simulations of the DNA 10-mer 5'-CCACGCGTGG-3' alone and complexed with the formamido-imidazole-pyrrole-imidazole (f-ImPyIm) polyamide minor groove binder in a 2:1 fashion were conducted for 50 ns using the pbsc0 parameters within the AMBER 12 software package. The change in DNA structure upon binding of f-ImPyIm was evaluated via minor groove width and depth, base pair parameters of Slide, Twist, Roll, Stretch, Stagger, Opening, Propeller, and x-displacement, dihedral angle distributions of ζ, ε, α, and γ determined using the Curves+ software program, and hydrogen bond formation. The dynamic hydrogen bonding between the f-ImPyIm and its cognate DNA sequence was compared to the static image used to predict sequence recognition by polyamide minor groove binders. Many of the predicted hydrogen bonds were present in less than 50% of the simulation; however, persistent hydrogen bonds between G5/15 and the formamido group of f-ImPyIm were observed. It was determined that the DNA is wider in the Complex than without the polyamide binder; however, there is flexibility in this particular sequence, even in the presence of the f-ImPyIm as evidenced by the range of minor groove widths the DNA exhibits and the dynamics of the hydrogen bonding that binds the two f-ImPyIm ions to the minor groove. The Complex consisting of the DNA and the 2 f-ImPyIm binders shows slight fraying of the 5' end of the 10-mer at the end of the simulation, but the portion of the oligomer responsible for recognition and binding is stable throughout the simulation. Several structural changes in the Complex indicate that minor groove binders may have a more active role in inhibiting transcription than just preventing binding of important transcription factors.

POSITIONING OF Ftz–F1 DOMAIN AFFECTS ON THE ACTIVITY OF HUMAN LRH-1: MOLECULAR DYNAMICS STUDY ON HUMAN LRH-1-DNA COMPLEXES

Molecular dynamics simulations for hLRH-1 (human liver receptor homologue-1) — DNA complexes were to investigate how the Ftz-F1 domain to regulate the transcriptional activity of hLRH-1. Comparative analyses of the three MD trajectories of hLRH-1 complexes suggest that the differential transcriptional activities of the wild-type hLRH-1, double-mutant and triple-mutant are due to alterative protein-DNA interactions. Further, the changes of position of Ftz–F1 domain can only exert limited effects on structures of the DBD (DNA binding domain), while the differences in the bound DNA's bending angles and helical parameters of key base pairs in the three systems result from the altering in distributions of the electrostatic potential surface, which varies with the positioning between the Ftz–F1 and the DBD. The disruptions or weakening of key interactions on several base pairs in the core sequence are mainly due to their distinct displacements from the helical axis in the mutant forms. So the Ftz-F1 domain can regulate the activity of the hLRH-1 by influencing conformations of the bound DNA.

Structure of an RNA/DNA dodecamer corresponding to the HIV-1 polypurine tract at 1.6 Å resolution

The crystal structure of an RNA/DNA hybrid dodecamer, r(5'-uaaaagaaaagg):d(5'-CCTTTTCTTTTA), which contains three-quarters of the polypurine tract (PPT) sequence of theHIV RNA genome is reported. The hybrid structure was determined at 1.6 Å resolution and was found to have the A-form conformation. However, the presence of alternate conformations along the RNA template strand indicated increased flexibility of the PPT sequence. Two segments (atnucleotides 1-2 and 6-8) of the RNA chain have two conformations exhibiting differences in torsion and pseudorotation angles. For conformation I((1-2), (6-8)), 25% of the RNA sugars have the C2'-exo pucker and the rest have the expected C3'-endo pucker. The II(1-2) and II(6-8) conformations of the RNA strand have one sugar with the C2'-exo pucker. None of theribose rings exist in the C2'-endo form, in contrast to a previous report which postulated a C2'-endo ribose as a key structural element of the PPT. The widths of the minor groove for conformations I((1-2), (6-8)) and II((1-2), (6-8)) of the RNA strand are 9.2-10.5 and 9.4-10.7 Å, respectively. Both ranges are very close to the intervals accepted for A-form RNA duplexes. On the opposing DNA primer strand most of the sugars are C3'-endo, except for the 3'-terminal sugars, which are C2'-endo (T22) or O4'-endo (T23 and A24). The duplex includes a noncanonical u1(anti)·A24(syn) base interaction with only one hydrogen bond between the bases. This noncanonical base interaction at the 5'-end of the template distorts the values of the helical parameters of the adjacent base pair.