Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels

Monolithic DNApatite: An Elastic Apatite with Sub-Nanometer Scale Organo-Inorganic Structures

Hydroxyapatite (HA) exhibits outstanding biocompatibility, bioactivity, osteoconductivity, and natural anti-inflammatory properties. Pure HA, ion-doped HA, and HA-polymer composites are investigated, but critical limitations such as brittleness remain; numerous efforts are being made to address them. Herein, the novel self-crystallization of a polymeric single-stranded deoxyribonucleic acid (ssDNA) without additional phosphate ions for synthesizing deoxyribonucleic apatite (DNApatite) is presented. The synthesized DNApatite, DNA1Ca2.2(PO4)1.3OH2.1, has a repetitive dual phase of inorganic HA crystals and amorphous organic ssDNA at the sub-nm scale, forming nanorods. Its mechanical properties, including toughness and elasticity, are significantly enhanced compared with those of HA nanorod, with a Young's modulus similar to that of natural bone.

Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles

Due to the vast length scale inside the cell nucleus, multiscale models are required to understand chromatin folding, structure, and dynamics and how they regulate genomic activities such as DNA transcription, replication, and repair. We study the interactions and structure of condensed phases formed by the universal building block of chromatin, the nucleosome core particle (NCP), using bottom-up multiscale coarse-grained (CG) simulations with a model extracted from all-atom MD simulations. In the presence of the multivalent cations Mg(H2O)62+ or CoHex3+, we analyze the internal structures of the NCP aggregates and the contributions of histone tails and ions to the aggregation patterns. We then derive a "super" coarse-grained (SCG) NCP model to study the macroscopic scale phase separation of NCPs. The SCG simulations show the formation of NCP aggregates with Mg(H2O)62+ concentration-dependent densities and sizes. Variation of the CoHex3+ concentrations results in highly ordered lamellocolumnar and hexagonal columnar phases in agreement with experimental data. The results give detailed insights into nucleosome interactions and for understanding chromatin folding in the cell nucleus.

Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA

The response of double-stranded DNA to external mechanical stress plays a central role in its interactions with the protein machinery in the cell. Modern atomistic force fields have been shown to provide highly accurate predictions for the fine structural features of the duplex. In contrast, and despite their pivotal function, less attention has been devoted to the accuracy of the prediction of the elastic parameters. Several reports have addressed the flexibility of double-stranded DNA via all-atom molecular dynamics, yet the collected information is insufficient to have a clear understanding of the relative performance of the various force fields. In this work, we fill this gap by performing a systematic study in which several systems, characterized by different sequence contexts, are simulated with the most popular force fields within the AMBER family, bcs1 and OL15, as well as with CHARMM36. Analysis of our results, together with their comparison with previous work focused on bsc0, allows us to unveil the differences in the predicted rigidity between the newest force fields and suggests a roadmap to test their performance against experiments. In the case of the stretch modulus, we reconcile these differences, showing that a single mapping between sequence-dependent conformation and elasticity via the crookedness parameter captures simultaneously the results of all force fields, supporting the key role of crookedness in the mechanical response of double-stranded DNA.

Melting and Bubble Formation in a Double-Stranded DNA: Microscopic Aspects of Early Base-Pair Opening Events and the Role of Water

Despite its rigid structure, DNA is a remarkably flexible molecule. Flexibility is essential for biological functions (such as transcription and gene repair), which require large-amplitude structural changes such as bubble formation. The bubbles thus formed are required to have a certain stability of their own and survive long on the time scale of molecular motions. A molecular understanding of fluctuations leading to quasi-stable structures is not available. Through extensive atomistic molecular dynamics simulations, we identify a sequence of microscopic events that culminate in local bubble formation, which is initiated by base-pair (BP) opening, resulting from the cleavage of native BP hydrogen bonds (HBs). This is followed by the formation of mismatched BPs with non-native contacts. These metastable structures can either revert to their original forms or undergo a flipping transition to form a local bubble that can span across 3-4 BPs. A substantial distortion of the DNA backbone and a disruption of BP stacking are observed because of the structural changes induced by these local perturbations. We also explored how water helps in the entire process. A small number of water molecules undergo rearrangement to stabilize the intermediate states by forming HBs with DNA bases. Water thus acts as a lubricant that counteracts the enthalpic penalty suffered from the loss of native BP contacts. Although the process of bubble formation is reversible, the sequence of steps involved poses an entropic barrier, preventing it from easily retracing the path to the native state.

Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations

Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are commonplace in nature. To better understand how the repulsion is overcome, we used experimental and computational approaches to investigate how the orientational preferences of DNA helices depend on the concentration and valence of mobile cations. We used Förster resonance energy transfer (FRET) to probe the relative orientations of two 24-bp helices held together via a freely rotating PEG linker. At low cation concentrations, the helices preferred more "cross"-like orientations over those closer to parallel, and this preference was reduced with increasing salt concentrations. The results were in good quantitative agreement with Poisson-Boltzmann (PB) calculations for monovalent salt (Na+). However, PB underestimated the ability of mixtures of monovalent and divalent ions (Mg2+) to reduce the conformational preference. As a complementary approach, we performed all-atom molecular dynamics (MD) simulations and found better agreement with the experimental results. While MD and PB predict similar electrostatic forces, MD predicts a greater accumulation of Mg2+ in the ion atmosphere surrounding the DNA. Mg2+ occupancy is predicted to be greater in conformations close to the parallel orientation than in conformations close to the crossed orientation, enabling a greater release of Na+ ions and providing an entropic gain (one bound ion for two released). MD predicts an entropy gain larger than that of PB because of the increased Mg2+ occupancy. The entropy changes have a negligible effect at low Mg2+ concentrations because the free energies are dominated by electrostatic repulsion. However, as the Mg2+ concentration increases, charge screening is more effective and the mixing entropy produces readily detectable changes in packing preferences. Our results underline the importance of mixing entropy of counterions in nucleic acid interactions and provide a new understanding on the impact of a mixed ion atmosphere on the packing of DNA helices.

Asymmetric Periodic Boundary Conditions for All-Atom Molecular Dynamics and Coarse-Grained Simulations of Nucleic Acids

Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT), and isothermal-isobaric (NpT) ensembles. In their simplest application, a biological system of interest is placed in the middle of a solvation box, which is chosen 'sufficiently large' to minimize any numerical artifacts associated with the periodic boundary conditions. This practical approach brings limitations to the size of biological systems that can be simulated. Here, we study simulations of effectively infinitely long nucleic acids, which are solvated in the directions perpendicular to the polymer chain, while periodic boundary conditions are also applied along the polymer chain. We study the effects of these asymmetric periodic boundary conditions (APBC) on the simulated results, including the mechanical properties of biopolymers and the properties of the surrounding solvent. To get some further insights into the advantages of using the APBC, a coarse-grained worm-like chain model is first studied, illustrating how the persistence length can be extracted from the local properties of the polymer chain, which are less affected by the APBC than some global averages. This is followed by all-atom molecular dynamics simulations of DNA in ionic solutions, where we use the APBC to investigate sequence-dependent properties of DNA molecules and properties of the surrounding solvent.

The development of nucleic acids force fields: From an unchallenged past to a competitive future

Molecular dynamics simulations have strongly matured as a method to study biomolecular processes. Their validity, however, is determined by the accuracy of the underlying force fields that describe the forces between all atoms. In this article, we review the development of nucleic acids force fields. We describe the early attempts in the 1990s and emphasize their strong influence on recent force fields. State-of-the-art force fields still use the same Lennard-Jones parameters derived 25 years ago in spite of the fact that these parameters were in general not fitted for nucleic acids. In addition, electrostatic parameters also are deprecated, which may explain some of the current force field deficiencies. We compare different force fields for various systems and discuss new tests of the recently developed Tumuc1 force field. The OL-force fields and Tumuc1 are arguably the best force fields to describe the DNA double helix. However, no force field is flawless. In particular, the description of sugar-puckering remains a problem for nucleic acids force fields. Future refinements are required, so we review methods for force field refinement and give an outlook to the future of force fields.

Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding

DNA carries the genetic information required for the synthesis of RNA and proteins and plays an important role in many processes of biological development. Understanding the three-dimensional (3D) structures and dynamics of DNA is crucial for understanding their biological functions and guiding the development of novel materials. In this review, we discuss the recent advancements in computer methods for studying DNA 3D structures. This includes molecular dynamics simulations to analyze DNA dynamics, flexibility, and ion binding. We also explore various coarse-grained models used for DNA structure prediction or folding, along with fragment assembly methods for constructing DNA 3D structures. Furthermore, we also discuss the advantages and disadvantages of these methods and highlight their differences.

An associative memory Hamiltonian model for DNA and nucleosomes

A model for DNA and nucleosomes is introduced with the goal of studying chromosomes from a single base level all the way to higher-order chromatin structures. This model, dubbed the Widely Editable Chromatin Model (WEChroM), reproduces the complex mechanics of the double helix including its bending persistence length and twisting persistence length, and their respective temperature dependence. The WEChroM Hamiltonian is composed of chain connectivity, steric interactions, and associative memory terms representing all remaining interactions leading to the structure, dynamics, and mechanical characteristics of the B-DNA. Several applications of this model are discussed to demonstrate its applicability. WEChroM is used to investigate the behavior of circular DNA in the presence of positive and negative supercoiling. We show that it recapitulates the formation of plectonemes and of structural defects that relax mechanical stress. The model spontaneously manifests an asymmetric behavior with respect to positive or negative supercoiling, similar to what was previously observed in experiments. Additionally, we show that the associative memory Hamiltonian is also capable of reproducing the free energy of partial DNA unwrapping from nucleosomes. WEChroM is designed to emulate the continuously variable mechanical properties of the 10nm fiber and, by virtue of its simplicity, is ready to be scaled up to molecular systems large enough to investigate the structural ensembles of genes. WEChroM is implemented in the OpenMM simulation toolkits and is freely available for public use.

C-B-A Test of DNA Force Fields

The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the noncanonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B-C and B-A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar-phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.

Design, molecular dynamics simulation, and investigation of the mechanical behavior of DNA origami nanotubes with auxetic and honeycomb structures

Numerous applications of DNA origami nanotubes for load-bearing purposes necessitate the improvement of properties and mechanical behavior of these types of structures, as well as the use of innovative structures such as metamaterials. To this end, the present study aims to investigate the design, molecular dynamics (MD) simulation, and mechanical behavior of DNA origami nanotube structures consisting of honeycomb and re-entrant auxetic cross-sections. The results revealed both structures kept their structural stability. In addition, DNA origami based-nanotube with auxetic cross-section exhibits negative Poisson's ratio (NPR) under tensile loading. Furthermore, MD simulation results demonstrated that the values of stiffness, specific stiffness, energy absorption, and specific energy absorption in the structure with an auxetic cross-section are higher than that of a honeycomb cross-section, similar to their behavior in macro-scale structures. The finding of this study is to propose re-entrant auxetic structure as the next generation of DNA origami nanotubes. In addition, it can be utilized to aid scientists with the design and fabrication of novel auxetic DNA origami structures.Communicated by Ramaswamy H. Sarma.

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.

The binding model of adenosine-specific DNA aptamer: Umbrella sampling study

We report a novel model of the selective binding mechanism of adenosine-specific DNA aptamer. Our theoretical investigations of AMP (Adenosine monophosphate) dissociation from aptamer-AMP complexes reveals new details of aptamer molecular specificity and stabilisation factors. Umbrella sampling MD calculations using parmbsc1 force field shows that the disordered structure of the internal loop of the unbound aptamer hairpin has a characteristic packing of guanines, which prevents barrier-free penetration of ligands into the site cavity. Also, this disordered structure of the unbound aptamer has a network of hydrogen bonds stabilising the cavity near the target guanines within the binding sites during the whole binding process. We suggested that the first AMP molecule binds to the disordered structure of the site closest to the aptamer hairpin stem and spends some free energy on ordering of the internal loop. Then the second AMP molecule binds to the ordered site closest to the aptamer hairpin loop with a lower energy gain. As a result, the induced-fit binding model is the most applicable for this aptamer and does not contradict the modern experimental NMR and calorimetry data.

Activation/Inhibition of Gene Expression Caused by Alcohols: Relationship with the Viscoelastic Property of a DNA Molecule

Alcohols are used in the life sciences because they can condense and precipitate DNA. Alcohol consumption has been linked to many diseases and can alter genetic activity. In the present report, we carried out experiments to make clear how alcohols affect the efficiency of transcription-translation (TX-TL) and translation (TL) by adapting cell-free gene expression systems with plasmid DNA and RNA templates, respectively. In addition, we quantitatively analyzed intrachain fluctuations of single giant DNA molecules based on the fluctuation-dissipation theorem to gain insight into how alcohols affect the dynamical property of a DNA molecule. Ethanol (2-3%) increased gene expression levels four to five times higher than the control in the TX-TL reaction. A similar level of enhancement was observed with 2-propanol, in contrast to the inhibitory effect of 1-propanol. Similar alcohol effects were observed for the TL reaction. Intrachain fluctuation analysis through single DNA observation showed that 1-propanol markedly increased both the spring and damping constants of single DNA in contrast to the weak effects observed with ethanol, whereas 2-propanol exhibits an intermediate effect. This study indicates that the activation/inhibition effects of alcohol isomers on gene expression correlate with the changes in the viscoelastic mechanical properties of DNA molecules.

Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA

The Hoogsteen (HG) base pairing conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studies. However, the mechanism of the conformational transition is not well understood. A detailed understanding of the process of WC to HG base pair transition can provide a deeper understanding of DNA repair and recognition. In an earlier study, we explored the free energy landscape for this process using extensive computer simulation with the CHARMM36 force field. In this work, we study the impact of force field models in describing the WC to HG base pairing transition using meta-eABF enhanced sampling, quasi-harmonic entropy calculation, and nonbonded energy analysis. The secondary structures of both base pairing forms and the topology of the free energy landscapes were consistent over different force field models, although the relative free energy, entropy, and the interaction energies tend to vary. The relative stability of the WC and HG conformations is dictated by a delicate balance between the enthalpic stabilization and the reduced entropy of the structurally rigid HG structure. These findings highlight the impact that subtleties in force field models can have on accurately modeling DNA base pair dynamics and should stimulate further computational investigations into other dynamically important motions in DNA.

Computer Aided Development of Nucleic Acid Applications in Nanotechnologies

Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.

A Simulation Study of the Effect of Naturally Occurring Point Mutations on the SRY-DNA Complex

Molecular dynamics (MD) simulations were conducted in order to investigate the effect of the naturally occurring point mutations of the transcription factor (TF) sex-determining region Y (SRY) on the structure and dynamics of the SRY-DNA complex. The normal SRY, along with the two mutants I13T and G40R, comprising point mutations on the SRY chain, which have been clinically identified in patients with sex developmental disorders, were modeled as DNA complexes. Our modeling work aims at elucidating atomic-level structural determinants of the aberrant SRY-DNA complexation by means of μs-long MD. The results suggest that the observed disorders brought about by the G40R-DNA and I13T-DNA may arise predominantly from the destabilization of the complex being in accord with in vitro assays found elsewhere and from modifications of the DNA bending as revealed in this study. Comparative potential of mean force computations, over a sequence of short separation distances for the three complexes, verified a higher stability of the normal SRY-DNA. Examining the way the SRY mutations modulate the SRY-DNA complex dynamics at the microscopic level is important also toward elucidating molecular determinants of function for proteins capable of binding to DNA.

Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions

The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both dsDNA and ssDNA from the sequence. Combined with a Monte Carlo simulated annealing algorithm and CG force fields involving the sequence-dependent base-pairing/stacking interactions and an implicit electrostatic potential, the present model successfully folds 20 dsDNAs (≤52nt) and 20 ssDNAs (≤74nt) into the corresponding native-like structures just from their sequences, with an overall mean RMSD of 3.4Å from the experimental structures. For DNAs with various lengths and sequences, the present model can make reliable predictions on stability, e.g., for 27 dsDNAs with/without bulge/internal loops and 24 ssDNAs including pseudoknot, the mean deviation of predicted melting temperatures from the corresponding experimental data is only ~2.0°C. Furthermore, the model also quantificationally predicts the effects of monovalent or divalent ions on the structure stability of ssDNAs/dsDNAs.

To determine 3D structures and quantify stability of single- (ss) and double-stranded (ds) DNAs is essential to unveil the mechanisms of their functions and to further guide the production and development of novel materials. Although many DNA models have been proposed to reproduce the basic structural, mechanical, or thermodynamic properties of dsDNAs based on the secondary structure information or preset constraints, there are very few models can be used to investigate the ssDNA folding or dsDNA assembly from the sequence. Furthermore, due to the polyanionic nature of DNAs, metal ions (e.g., Na⁺ and Mg²⁺) in solutions can play an essential role in DNA folding and dynamics. Nevertheless, ab initio predictions for DNA folding in ion solutions are still an unresolved problem. In this work, we developed a novel coarse-grained model to predict 3D structures and thermodynamic stabilities for both ssDNAs and dsDNAs in monovalent/divalent ion solutions from their sequences. As compared with the extensive experimental data and available existing models, we showed that the present model can successfully fold simple DNAs into their native-like structures, and can also accurately reproduce the effects of sequence and monovalent/divalent ions on structure stability for ssDNAs including pseudoknot and dsDNAs with/without bulge/internal loops.

A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions

The nucleosome core particle (NCP) is a large complex of 145-147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome-nucleosome attraction in the presence of multivalent cations (Mg(H₂O)₆²⁺ or Co(NH₃)₆³⁺) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP-NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers.

Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach

We propose an approach to help interpret polymer force-extension curves that exhibit plateau regimes. When coupled to a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force-extension curves. The applicability of the approach to the force-extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.

Bicyclo-DNA mimics with enhanced protein binding affinities: insights from molecular dynamics simulations

DNA-protein interactions occur at all levels of DNA expression and replication and are crucial determinants for the survival of a cell. Several modified nucleotides have been utilized to manipulate these interactions and have implications in drug discovery. In the present article, we evaluated the binding of bicyclo-nucleotides (generated by forming a methylene bridge between C1' and C5' in sugar, leading to a bicyclo system with C2' axis of symmetry at the nucleotide level) to proteins. We utilized four ssDNA-protein complexes with experimentally known binding free energies and investigated the binding of modified nucleotides to proteins via all-atom explicit solvent molecular dynamics (MD) simulations (200 ns), and compared the binding with control ssDNA-protein systems. The modified ssDNA displayed enhanced binding to proteins as compared to the control ssDNA, as seen by means of MD simulations followed by MM-PBSA calculations. Further, the Delphi-based electrostatic estimation revealed that the high binding of modified ssDNA to protein might be related to the enhanced electrostatic complementarity displayed by the modified ssDNA molecules in all the four systems considered for the study. The improved binding achieved with modified nucleotides can be utilized to design and develop anticancer/antisense molecules capable of targeting proteins or ssRNAs.Communicated by Ramaswamy H. Sarma.

Recent Efforts and Milestones for Simulating Nucleic Acid FRET Experiments through Computational Methods

Computational methods can greatly aid nucleic acid fluorescence experiments by either offering fully detailed atomic insights into the conformations and interactions present in the studied system or by providing accurate simulations of the fundamental parameters. Fluorescence-based optical biosensors show great potential for clinical diagnosis of life-altering diseases with a very high specificity. Many of the designs for such rely on the concept of Förster resonance energy transfer (FRET). Currently, the methods used experimentally make use of theoretical assumptions which fundamentally affect the results. Having a detailed atomistic overview or significant simulated parameters could improve the understanding of the calculations and provide much more accurate outcomes. However, there are many challenges that need to be addressed before standardized computational protocols can be employed. This review is meant to highlight the progress made for computational methods used to simulate FRET experiments for nucleic acid probes. Recent advances have been made in computational tools, such as force field parametrizations and improved protocols. Complementary simulations to experimental data are also comprised in the this review.

Impact of DNA Adduct Size, Number, and Relative Position on the Toxicity of Aromatic Amines: A Molecular Dynamics Case Study of ANdG- and APdG-Containing DNA Duplexes

Human exposure to aromatic amines (AAs) can result in carcinogenic DNA adducts. To complement previous work geared toward understanding the mutagenicity of AA-derived adducts, which has almost exclusively studied (monoadducted) DNA containing a single lesion, the present work provides the first in-depth comparison of the structure of monoadducted and diadducted DNA duplexes. Specifically, molecular dynamics (MD) simulations were initially performed on DNA containing the nonmutagenic single-ringed N-(deoxyguanosin-8-yl)-aniline (^ANdG) or the mutagenic four-ringed N-(deoxyguanosin-8-yl)-1-aminopyrene (^APdG) lesion at G₁, G₂, or G₃ in the AA deletion hotspot (5'-G₁G₂CG₃CC) in the anti or syn glycosidic orientation (B/S duplex conformation). Subsequently, diadducted strands were assessed that span each combination of damaged sites (G₁G₂ (nearest neighbors), G₂G₃ (next-nearest neighbors), and G₁G₃ (two intervening nucleotides)) and anti/syn lesion glycosidic orientations. Despite other N-linked C8-dG adducts exhibiting sequence dependence conformational heterogeneity, a single ^ANdG or ^APdG lesion induces helical conformational homogeneity that is exclusively controlled by aryl moiety size. However, the preferred damaged DNA conformation can change upon the addition of a second adduct depending on lesion separation, with neighboring lesions stabilizing a nonmutagenic conformation and next-nearest damaged sites stabilizing a promutagenic conformation regardless of adduct size. As a result, diadducted DNA is found to adopt conformations that are unfavored for the corresponding monoadducted system, pointing to differential replication and repair outcomes for diadducted DNA compared to those for monoadducted DNA. Thus, although the toxicity of monoadducted DNA is most significantly dictated by lesion size, the toxicity can increase or decrease upon a second damaging event depending on lesion size and relative position. Overall, our work adds the number of lesions and their spatial separation to the growing list of factors that determine the structure and biological outcomes of adducted DNA.

Beyond the double helix: DNA structural diversity and the PDB

The determination of the double helical structure of DNA in 1953 remains the landmark event in the development of modern biological and biomedical science. This structure has also been the starting point for the determination of some 2000 DNA crystal structures in the subsequent 68 years. Their structural diversity has extended to the demonstration of sequence-dependent local structure in duplex DNA, to DNA bending in short and long sequences and in the DNA wound round the nucleosome, and to left-handed duplex DNAs. Beyond the double helix itself, in circumstances where DNA sequences are or can be induced to unwind from being duplex, a wide variety of topologies and forms can exist. Quadruplex structures, based on four-stranded cores of stacked G-quartets, are prevalent though not randomly distributed in the human and other genomes and can play roles in transcription, translation, and replication. Yet more complex folds can result in DNAs with extended tertiary structures and enzymatic/catalytic activity. The Protein Data Bank is the depository of all these structures, and the resource where structures can be critically examined and validated, as well as compared one with another to facilitate analysis of conformational and base morphology features. This review will briefly survey the major structural classes of DNAs and illustrate their significance, together with some examples of how the use of the Protein Data Bank by for example, data mining, has illuminated DNA structural concepts.

Bottom-Up Coarse-Grained Modeling of DNA

Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, "melting," and DNA condensation.

Interactions of a DNA G-quadruplex with TMAO and urea: a molecular dynamics study on co-solute compensation mechanisms

We study the individual and combined influence of TMAO and urea on a basket-type DNA G-quadruplex by means of atomistic molecular dynamics (MD) simulations. In combination with the Kirkwood-Buff theory of solutions, we propose a simple mechanism to elucidate the impact of TMAO and urea on the G-quadruplex. Our results reveal the importance of the molecular accumulation around the DNA in terms of stabilizing or destabilizing effects. The results for mixtures show only a weak interaction between both co-solutes, which highlights the additivity of contributions. Despite the fact, that TMAO can to some extent compensate the adverse impact of urea on the G-quadruplex structure, the destabilizing influence is not completely eliminated. This observation opens the door for further research on selective stabilization of DNA G-quadruplexes by modulating the concentrations of TMAO and urea in solution.

Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer

Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter Slide has to change first, and the molecule should take the E-form. After that, the Roll parameter changes. In the present work, we simulated the kinetics of the B-A transition in the Drew-Dickerson dodecamer, a known B-philic DNA oligomer. We used the "sugar" coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A- and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence "Slide first, Roll later" in kinetics, and the E-DNA is not a necessary step for the transition between the B- and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein.

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.

Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics

Nucleic acids play critical roles in carrying genetic information, participating in catalysis, and preserving chromosomal structure. Despite over a century of study, efforts to understand the dynamics and structure-function relationships of DNA and RNA at the atomic level are still ongoing. Molecular dynamics (MD) simulations augment experiments by providing atomistic resolution and quantitative relationships between structure and conformational energy. Steady advancements in computer hardware, software, and atomistic force fields (FFs) over 40 years have facilitated new discoveries. Here, we review nucleic acid FF development with emphasis on recent refinements that have improved descriptions of important nucleic acid properties. We then discuss several key examples of successes and challenges in modeling nucleic acid structure and dynamics using the latest FFs.

Molecular dynamics simulations of DNA-DNA and DNA-protein interactions

The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA-protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured enough to characterize the interaction free energy with quantitative precision. Here, we describe recent progress toward increasing the realism of such simulations by refining the accuracy of the molecular dynamics force field, and we highlight recent application of the method to systems of outstanding biological interest.

Discovery and design of soft polymeric bio-inspired materials with multiscale simulations and artificial intelligence

Establishing the “Materials 4.0” paradigm requires intimate knowledge of the virtual space in materials design.