Coarse-grained DNA Model Research Articles

CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.

We present CGeNArate, a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are back-mapped to the atomistic resolution level with extreme accuracy by means of Machine Learning Approaches. The method is sequence-dependent and reproduces very well not only local, but also global physical properties of DNA. The efficiency of the method allows us to recover with a reduced computational effort high-quality atomic-resolution ensembles of segments containing many kilobases of DNA, entering into the gene range or even the entire DNA of certain cellular organelles.

Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs cgDNA.

Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs all-atom models using stiffness matrices in Fourier space (q-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version, cgDNA+. Our analysis shows that while cgDNA+ closely follows the q-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables, which are rather strong in the q → 0 (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects that manifest themselves at longer length scales. In particular, cgDNA performs poorly on twist stiffness, with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist are strongly length scale dependent: DNA is torsionally soft at a few base pair distances but becomes more rigid at distances of a few dozen base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated.

Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective.

DNA-modified gold nanoparticles (AuNPs) play a pivotal role in bio-nanotechnology, driving advancements in bio-sensing, bio-imaging, and drug delivery. Synthetic protocols have focused on maximizing the receptor density on particles by fine-tuning chemical conditions, particularly for DNA. Despite their significance, the understanding of hybridization kinetics on functionalized AuNPs is lacking, particularly how this kinetics depends on DNA density and to what extent it varies from particle-to-particle. This study explores the molecular mechanisms of DNA hybridization on densely coated AuNPs by employing a combination of single-molecule microscopy and coarse-grained molecular dynamics simulations providing a quantification of the molecular rate constants for single particles. Our findings demonstrate that DNA receptor density and the presence of spacer strands profoundly impact association kinetics, with short spacers enhancing association rates by up to ∼15-fold. In contrast, dissociation kinetics are largely unaffected by receptor density within the studied range. Single-particle analysis directly reveals variability in hybridization kinetics, which is analyzed in terms of intra- and inter-particle heterogeneity. A coarse-grained DNA model that quantifies hybridization kinetics on densely coated surfaces further corroborates our experimental results, additionally shedding light on how transient base pairing within the DNA coating influences kinetics. This integrated approach underscores the value of single-molecule studies and simulations for understanding DNA dynamics on densely coated nanoparticle surfaces, offering guidance for designing DNA-functionalized nanoparticles in sensor applications.

Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations

Double-strand breaks (DSBs), i.e., the covalent cut of the DNA backbone over both strands, are a detrimental outcome of cell irradiation, bearing chromosomal aberrations and leading to cell apoptosis. In the early stages of the evolution of a DSB, the disruption of the residual interactions between the DNA moieties drives the fracture of the helical layout; in spite of its biological significance, the details of this process are still largely uncertain. Here, we address the mechanical rupture of DNA by DSBs via coarse-grained molecular dynamics simulations: the setup involves a 3855-bp DNA filament and diverse DSB motifs, i.e., within a range of distances between strand breaks (or DSB distance). By employing a coarse-grained model of DNA, we access the molecular details and characteristic timescales of the rupturing process. A sequence-nonspecific, linear correlation is observed between the DSB distance and the internal energy contribution to the disruption of the residual (Watson-Crick and stacking) contacts between DNA moieties, which is seemingly driven by an abrupt, cooperative process. Moreover, we infer an exponential dependence of the characteristic rupture times on the DSB distances, which we associate to an Arrhenius-like law of thermally-activated processes. This work lays the foundations of a detailed, mechanistic assessment of DSBs in silico as a benchmark to both numerical simulations and data from single-molecule experiments.

Molecular features underlying phase separation of protein-nucleic acid condensates revealed by a new coarse-grained DNA model.

Recent advances in residue-level coarse-grained (CG) computational models for proteins have enabled molecular-level insights into the properties of protein condensates. However, most of the existing CG nucleic acid models include anisotropic potentials between bases that are computationally demanding and are not fully compatible with the existing CG protein models. Here, we present a new CG DNA model that utilizes isotropic potentials between bases and can be used for investigating protein-DNA complexes and nucleosome arrays, thereby enabling a mechanistic understanding of how molecular information is propagated up at the genome level in a computationally tractable manner. To demonstrate the suitability of our model to facilitate large-scale simulations with a molecular resolution, we simulate nucleosomes (mono, di, etc.) to generate equilibrium conformational ensembles. The simulation data provide essential insights into the role of chromatin in the liquid-liquid phase separation of HP1α protein. We find an extensive network of interactions between HP1α, DNA, and flexible histone tails in the condensates formed by these different biomolecules. The findings of this work illuminate the complex molecular framework that contributes to heterochromatin regulation and function.

Influence of ionic conditions on knotting in a coarse-grained model for DNA.

We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers. We find that the occurrence of knots in DNA can be reinforced considerably by high salt conditions and confinement between plates. Likewise, knots can almost be dissolved completely in a low salt scenario. Comparisons with recent experiments confirm that the coarse-grained model is able to capture and quantitatively predict topological features of DNA and can be used for guiding future experiments on DNA knots.

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.

Role of Hoogsteen interaction in the stability of different phases of triplex DNA.

A simple coarse-grained model of DNA which includes both Watson-Crick and Hoogsteen base pairing has been used to study the melting and unzipping of triplex DNA. Using Langevin dynamics simulations, we reproduce the qualitative features of one-step and two-step thermal melting of triplex as seen in experiments. The thermal melting phase diagram shows the existence of a stable interchain three-strand complex (bubble-bound state). Our studies based on the mechanical unzipping of a triplex revealed that it is mechanically more stable compared to an isolated duplex-DNA.

Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.

We introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar, at the base moiety, and at the phosphate group, respectively. The sequence dependence is included by considering a step-dependent parametrization of the bonded interactions, which are tuned in order to reproduce the values of key observables obtained from exhaustive atomistic simulations from the literature. The predictions of the model are benchmarked against an independent set of all-atom simulations, showing that it captures with high fidelity the sequence dependence of conformational and elastic features beyond the single step considered in its formulation. A remarkably good agreement with experiments is found for both sequence-averaged and sequence-dependent conformational and elastic features, including the stretching and torsion moduli, the twist–stretch and twist–bend couplings, the persistence length, and the helical pitch. Overall, for the inspected quantities, the model has a precision comparable to atomistic simulations, hence providing a reliable coarse-grained description for the rationalization of single-molecule experiments and the study of cellular processes involving dsDNA. Owing to the simplicity of its formulation, MADna can be straightforwardly included in common simulation engines. Particularly, an implementation of the model in LAMMPS is made available on an online repository to ease its usage within the DNA research community.

Monte Carlo molecular simulation of solution and surface-bound DNA hybridization of short oligomers at varying surface densities

DNA microarrays utilize surface bound sequences to probe for target sequences in samples of interest, and density of surface coverage plays an important role in any duplex formation and subsequent detection. Here, Monte Carlo molecular simulations utilize a modified coarse-grained DNA model to calculate the impact of binding density and arrangement as well as temperature on duplex structure and hydrogen bonding patterns for two different undecamer sequences. Results indicate a modest, sequence-dependent increase in dissociation related to the proximity of neighboring duplexes but little impact on duplex structure or hydrogen bonding pattern.

Mechanism of translocation by bacteriophage T7 helicase gp4 using AWSEM-Suite

In the process of DNA replication, the efficient unwinding of the duplex parental DNA is mediated by DNA helicases. Helicases are chemo-mechanic motors that use the energy of ATP hydrolysis to translocate unidirectionally along with DNA. Helicase gp4 from bacteriophage T7 is a model system for studying helicase in DNA replication. However, how ATP hydrolysis drives the conformational changes and the unidirectional translocation remains elusive. Here, molecular dynamics simulations using coarse-grained protein model AWSEM-Suite and DNA model 3SPN2 were applied to explore the global energy landscape of the helicase gp4 translocation along ssDNA.

Solution properties of spherical gold nanoparticles with grafted DNA chains from simulation and theory.

There has been a rapidly growing interest in the use of functionalized Au nanoparticles (NPs) as platforms in multiple applications in medicine and manufacturing. The sensing and targeting characteristics of these NPs, and the realization of precisely organized structures in manufacturing applications using such NPs, depend on the control of their surface functionalization. NP functionalization typically takes the form of polymer grafted layers, and a detailed knowledge of the chemical and structural properties of these layers is required to molecularly engineer the particle characteristics for specific applications. However, the prediction and experimental determination of these properties to enable the rational engineering of these particles is a persistent problem in the development of this class of materials. To address this situation, molecular dynamic simulations were performed based on a previously established coarse-grained single-stranded DNA (ssDNA) model to determine basic solution properties of model ssDNA-grafted NP-layers under a wide range of conditions. In particular, we emphasize the calculation of the hydrodynamic radius for ssDNA-grafted Au NPs as a function of structural parameters such as ssDNA length, NP core size, and surface coverage. We also numerically estimate the radius of gyration and the intrinsic viscosity of these NPs, which in combination with hydrodynamic radius estimates, provide valuable information about the fluctuating structure of the grafted polymer layers. We may then understand the origin of the commonly reported variation in effective NP “size” by different measurement methods, and then exploit this information in connection to material design and characterization in connection with the ever-growing number of applications utilizing polymer-grafted NPs.

Potential of Mean Force for DNA Wrapping Around a Cationic Nanoparticle.

Sharp bending and wrapping of DNA around proteins and nanoparticles (NPs) has been of extensive research interest. Here, we present the potential of mean force (PMF) for wrapping a DNA double helix around a cationic NP using coarse-grained models of a double-stranded DNA and a cationic NP. Starting from a NP wrapped around by DNA, the PMF was calculated along the distance between the center of the NP and one end of the DNA molecule. A relationship between the distance and the extent of DNA wrapping is used to calculate the PMF as a function of DNA wrapping around a NP. In particular, the PMF was compared for two DNA sequences of (AT)25/(AT)25 and (AC)25/(GT)25, for which the persistence lengths are different by ∼10 nm. The simulation results provide solid evidence of the thermodynamic preference for complex formation of a cationic NP with more flexible DNA over the less flexible DNA. Furthermore, we estimated the elastic energy of DNA bending, which was in good order-of-magnitude agreement with the theoretical prediction of elastic rods. This work suggests that the variation of sequence-dependent DNA flexibility can be utilized in DNA nanotechnologies, in which the position and dynamics of NPs are regulated on large-scale DNA structures, or the structural transformation of DNA is triggered by the sequence-dependent binding of NPs.

Understanding sequence effect in DNA bending elasticity by molecular dynamic simulations

Structural elasticity of double-strand DNAs is very important for their biological functions such as DNA-ligand binding and DNA-protein recognition. By all-atom molecular dynamics simulations, we investigated the bending elasticity of DNA with three typical sequences including poly(A)-poly(T) (AA-TT), poly(AT)-poly(TA) (AT-TA), and a generic sequence (GENE). Our calculations indicate that, AA-TT has an apparently larger bending persistence length (P ∼63 nm) than GENE (P ∼49 nm) and AT-TA (P ∼48 nm) while the persistence length of AT-TA is only very slightly smaller than that of GENE, which agrees well with those from existing works. Moreover, through extensive electrostatic calculations, we found that the sequence-dependent bending elasticity is attributed to the sequence-dependent electrostatic bending energy for AA-TT, AT-TA and GENE, which is coupled to their backbone structures. Particularly, the apparently stronger bending stiffness of AA-TT is attributed to its narrower minor groove. Interestingly, for the three DNAs, we predicted the non-electrostatic persistence length of ∼17 nm, thus electrostatic interaction makes the major contribution to DNA bending elasticity. The mechanism of electrostatic energy dominating sequence effect in DNA bending elasticity is furtherly illustrated through the electrostatic calculations for a grooved coarse-grained DNA model where minor groove width and other microscopic structural parameters can be artificially adjusted.

Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling

We study the effect of transcription on the kinetics of DNA supercoiling in three dimensions by means of Brownian dynamics simulations of a single-nucleotide-resolution coarse-grained model for double-stranded DNA. By explicitly accounting for the action of a transcribing RNA polymerase (RNAP), we characterize the geometry and nonequilibrium dynamics of the ensuing twin supercoiling domains. Contrary to the typical textbook picture, we find that the generation of twist by RNAP results in the formation of plectonemes (writhed DNA) some distance away. We further demonstrate that this translates into an "action at a distance" on DNA-binding proteins; for instance, positive supercoils downstream of an elongating RNAP destabilize nucleosomes long before the transcriptional machinery reaches the histone octamer. We also analyze the relaxation dynamics of supercoiled double-stranded DNA, and characterize the widely different timescales of twist diffusion, which is a simple and fast process, and writhe relaxation, which is much slower and entails multiple steps.

Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA

We introduce MADna, a sequence-dependent coarse-grained model of double-stranded DNA (dsDNA), where each nucleotide is described by three beads localized at the sugar and base moieties, and at the phosphate group. The sequence dependence is included by considering a step-dependent parameterization of the bonded interactions, which are tuned in order to reproduce the values of key observables obtained from exhaustive atomistic simulations from literature. The predictions of the model are benchmarked against an independent set of all-atom simulations, showing that it captures with high fidelity the sequence dependence of conformational and elastic features beyond the single step considered in its formulation. A remarkably good agreement with experiments is found for both sequence-averaged and sequence-dependent conformational and elastic features, including the stretching and torsion moduli, the twist-stretch and twist-bend couplings, the persistence length and the helical pitch. Overall, for the inspected quantities, the model has a precision comparable to atomistic simulations, hence providing a reliable coarse-grained description for the rationalization of single-molecule experiments and the study of cellular processes involving dsDNA. Owing to the simplicity of its formulation, MADna can be straightforwardly included in common simulation engines.

Thermal Conductivity of B-DNA.

The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical molecular dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1D model or a coarse-grained model of DNA to reduce simulation times, full atomistic simulations are employed to understand the thermal conduction in B-DNA. Thermal conductivities at different temperatures from 100 to 400 K are investigated using the Einstein-Green-Kubo equilibrium and Müller-Plathe non-equilibrium formalisms. The thermal conductivity of B-DNA at room temperature is found to be 1.5 W/m·K in equilibrium and 1.225 W/m·K in the non-equilibrium approach. In addition, the denaturation regime of B-DNA is obtained from the variation of thermal conductivity with temperature. It is in agreement with previous studies using the Peyrard-Bishop-Dauxois model at a temperature of around 350 K. The quantum heat capacity (Cvq) has given additional clues regarding the Debye and denaturation temperature of 12-bp B-DNA.

Understanding DNA interactions in crowded environments with a coarse-grained model.

Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetics and thermodynamics of DNA duplex and hairpin formation in crowded environments. We find that crowders can increase the melting temperature of both an 8-mer DNA duplex and a hairpin with a stem of 6-nt depending on the excluded volume fraction of crowders in solution and the crowder size. The crowding induced stability originates from the entropic effect caused by the crowding particles in the system. Additionally, we study the hybridization kinetics of DNA duplex formation and the formation of hairpin stems, finding that the reaction rate kon is increased by the crowding effect, while koff is changed only moderately. The increase in kon mostly comes from increasing the probability of reaching a transition state with one base pair formed. A DNA strand displacement reaction in a crowded environment is also studied with the model and we find that rate of toehold association is increased, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnology.

Translational nucleosome positioning: A computational study.

About three-quarters of eukaryotic DNA is wrapped into nucleosomes; DNA spools with a protein core. The affinity of a given DNA stretch to be incorporated into a nucleosome is known to depend on the base-pair sequence-dependent geometry and elasticity of the DNA double helix. This causes the rotational and translational positioning of nucleosomes. In this study we ask the question whether the latter can be predicted by a simple coarse-grained DNA model with sequence-dependent elasticity, the rigid base-pair model. Whereas this model is known to be rather robust in predicting rotational nucleosome positioning, we show that the translational positioning is a rather subtle effect that is dominated by the guanine-cytosine content dependence of entropy rather than energy. A correct qualitative prediction within the rigid base-pair framework can only be achieved by assuming that DNA elasticity effectively changes on complexation into the nucleosome complex. With that extra assumption we arrive at a model which gives an excellent quantitative agreement to experimental in vitro nucleosome maps, under the additional assumption that nucleosomes equilibrate their positions only locally.

Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model.

DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. While the wormlike chain model provides a good description of small to moderate bending fluctuations, it is expected to break down for large bending. Recent cyclization experiments on strongly bent shorter molecules indeed suggest enhanced flexibility over and above that expected from the wormlike chain. Here, we use a coarse-grained model of DNA to investigate the subtle thermodynamics of DNA cyclization for molecules ranging from 30 to 210 base pairs. As the molecules get shorter, we find increasing deviations between our computed equilibrium j-factor and the classic wormlike chain predictions of Shimada and Yamakawa for a torsionally aligned looped molecule. These deviations are due to sharp kinking, first at nicks, and only subsequently in the body of the duplex. At the shortest lengths, substantial fraying at the ends of duplex domains is the dominant method of relaxation. We also estimate the dynamic j-factor measured in recent FRET experiments. We find that the dynamic j-factor is systematically larger than its equilibrium counterpart—with the deviation larger for shorter molecules—because not all the stress present in the fully cyclized state is present in the transition state. These observations are important for the interpretation of recent cyclization experiments, suggesting that measured anomalously high j-factors may not necessarily indicate non-WLC behavior in the body of duplexes.