A standard reference frame for the description of nucleic acid base-pair geometry

Mechanical response of double-stranded DNA: Bend, twist, and overwind

We employed all-atom molecular dynamics simulations to explore the mechanical response of bending, twisting, and overwinding for double-stranded DNA (dsDNA). We analyzed the bending and twisting deformations, as well as their stiffnesses, using the tilt, roll, and twist modes under stretching force. Findings indicate that the roll and twist angles vary linearly with the stretching force but show opposite trends. The tilt, roll, and twist elastic moduli are considered constants, while the coupling between roll and twist modes slightly decreases under stretching force. The effect of the stretching force on the roll and twist modes, including both their deformations and elasticities, exhibits sequence-dependence, with symmetry around the base pair step. Furthermore, we examined the overwinding path and mechanism of dsDNA from the perspective of the stiffness matrix, based on the tilt, roll, and twist modes. The correlations among tilt, roll, and twist angles imply an alternative overwinding pathway via twist-roll coupling when dsDNA is stretched, wherein entropic contribution prevails.

Utilizing biological experimental data and molecular dynamics for the classification of mutational hotspots through machine learning

Motivation

Benzo[a]pyrene, a notorious DNA-damaging carcinogen, belongs to the family of polycyclic aromatic hydrocarbons commonly found in tobacco smoke. Surprisingly, nucleotide excision repair (NER) machinery exhibits inefficiency in recognizing specific bulky DNA adducts including Benzo[a]pyrene Diol-Epoxide (BPDE), a Benzo[a]pyrene metabolite. While sequence context is emerging as the leading factor linking the inadequate NER response to BPDE adducts, the precise structural attributes governing these disparities remain inadequately understood. We therefore combined the domains of molecular dynamics and machine learning to conduct a comprehensive assessment of helical distortion caused by BPDE-Guanine adducts in multiple gene contexts. Specifically, we implemented a dual approach involving a random forest classification-based analysis and subsequent feature selection to identify precise topological features that may distinguish adduct sites of variable repair capacity. Our models were trained using helical data extracted from duplexes representing both BPDE hotspot and nonhotspot sites within the TP53 gene, then applied to sites within TP53, cII, and lacZ genes.

Results

We show our optimized model consistently achieved exceptional performance, with accuracy, precision, and f1 scores exceeding 91%. Our feature selection approach uncovered that discernible variance in regional base pair rotation played a pivotal role in informing the decisions of our model. Notably, these disparities were highly conserved among TP53 and lacZ duplexes and appeared to be influenced by the regional GC content. As such, our findings suggest that there are indeed conserved topological features distinguishing hotspots and nonhotpot sites, highlighting regional GC content as a potential biomarker for mutation.

Availability and implementation

Code for comparing machine learning classifiers and evaluating their performance is available at https://github.com/jdavies24/ML-Classifier-Comparison, and code for analysing DNA structure with Curves+ and Canal using Random Forest is available at https://github.com/jdavies24/ML-classification-of-DNA-trajectories.

Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

Mixed double helices formed by RNA and DNA strands, commonly referred to as hybrid duplexes or hybrids, are essential in biological processes like transcription and reverse transcription. They are also important for their applications in CRISPR gene editing and nanotechnology. Yet, despite their significance, the hybrid duplexes have been seldom modeled by atomistic molecular dynamics methodology, and there is no benchmark study systematically assessing the force-field performance. Here, we present an extensive benchmark study of polypurine tract (PPT) and Dickerson-Drew dodecamer hybrid duplexes using contemporary and commonly utilized pairwise additive and polarizable nucleic acid force fields. Our findings indicate that none of the available force-field choices accurately reproduces all the characteristic structural details of the hybrid duplexes. The AMBER force fields are unable to populate the C3'-endo (north) pucker of the DNA strand and underestimate inclination. The CHARMM force field accurately describes the C3'-endo pucker and inclination but shows base pair instability. The polarizable force fields struggle with accurately reproducing the helical parameters. Some force-field combinations even demonstrate a discernible conflict between the RNA and DNA parameters. In this work, we offer a candid assessment of the force-field performance for mixed DNA/RNA duplexes. We provide guidance on selecting utilizable force-field combinations and also highlight potential pitfalls and best practices for obtaining optimal performance.

Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation

Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.

Correct Nucleotide Selection Is Confined at the Binding Site of Polymerase Enzymes

DNA polymerases (Pols) add incoming nucleotides (deoxyribonucleoside triphosphate (dNTPs)) to growing DNA strands, a crucial step for DNA synthesis. The insertion of correct (vs incorrect) nucleotides relates to Pols' fidelity, which defines Pols' ability to faithfully replicate DNA strands in a template-dependent manner. We and others have demonstrated that reactant alignment and correct base pairing at the Pols catalytic site are crucial structural features to fidelity. Here, we first used equilibrium molecular simulations to demonstrate that the local dynamics at the protein-DNA interface in the proximity of the catalytic site is different when correct vs incorrect dNTPs are bound to polymerase β (Pol β). Formation and dynamic stability of specific interatomic interactions around the incoming nucleotide influence the overall binding site architecture. This explains why certain Pols' mutants can affect the local catalytic environment and influence the selection of correct vs incorrect nucleotides. In particular, this is here demonstrated by analyzing the interaction network formed by the residue R283, whose mutant R283A has an experimentally measured lower capacity of differentiating correct (G:dCTP) vs incorrect (G:dATP) base pairing in Pol β. We also used alchemical free-energy calculations to quantify the G:dCTP →G:dATP transformation in Pol β wild-type and mutant R283A. These results correlate well with the experimental trend, thus corroborating our mechanistic insights. Sequence and structural comparisons with other Pols from the same family suggest that these findings may also be valid in similar enzymes.

The Influence of Clustered DNA Damage Containing Iz/Oz and OXOdG on the Charge Transfer through the Double Helix: A Theoretical Study

The genome-the source of life and platform of evolution-is continuously exposed to harmful factors, both extra- and intra-cellular. Their activity causes different types of DNA damage, with approximately 80 different types of lesions having been identified so far. In this paper, the influence of a clustered DNA damage site containing imidazolone (Iz) or oxazolone (Oz) and 7,8-dihydro-8-oxo-2'-deoxyguanosine (OXOdG) on the charge transfer through the double helix as well as their electronic properties were investigated. To this end, the structures of oligo-Iz, d[A1Iz2A3OXOG4A5]*d[T5C4T3C2T1], and oligo-Oz, d[A1Oz2A3OXOG4A5]*d[T5C4T3C2T1], were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using the ONIOM methodology; all the discussed energies were obtained at the M06-2X/6-31++G** level of theory. The non-equilibrated and equilibrated solvent-solute interactions were taken into consideration. The following results were found: (A) In all the discussed cases, OXOdG showed a higher predisposition to radical cation formation, and B) the excess electron migration toward Iz and Oz was preferred. However, in the case of oligo-Oz, the electron transfer from Oz2 to complementary C4 was noted during vertical to adiabatic anion relaxation, while for oligo-Iz, it was settled exclusively on the Iz2 moiety. The above was reflected in the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution. It can be postulated that imidazolone moiety formation within the CDL ds-oligo structure and its conversion to oxazolone can significantly influence the charge migration process, depending on the C2 carbon hybridization sp2 or sp3. The above can confuse the single DNA damage recognition and removal processes, cause an increase in mutagenesis, and harm the effectiveness of anticancer therapy.

The nucleosome reference frame and standard geometries for octasomes

There are over 533 nucleosome structures in the Research Collaboratory for Structural Bioinformatics (RCSB). Collectively, numerous variants and species are present, as are sub-nucleosomal and super-nucleosomal assemblies within the nucleosome family. The organization of the histones and DNA is highly conserved in all standard octasomes containing 145, 146, or 147 base pairs. This observation is used to establish a nucleosome reference frame that enables us to describe and compare the gross structure and organization of all nucleosomes. We observe that cumulative sums of Rise, Twist, and DNA arc length are linear functions of the base pair index withR 2 values exceeding 0.999 for almost all octasome structures. These relationships enable us to readily compare the location and orientation of DNA director frames extracted from the crystal structures to ideal superhelix values. Such comparisons reveal that the DNA superhelix extracted from X-ray structures exhibits a sinusoidal variation with an amplitude of approximately 5Å  about a constant superhelix radius of ∼ 42 Å, in agreement with early descriptions of nucleosome organization as tripartite. There is also a distinct straightening of the nucleosomal DNA over the outermost turn of DNA's double helix. The straightening of the DNA superhelix marks the transition to linker DNA and is easily recognized as a rapid increase in superhelix radius and is concomitant with a change in pitch. This provides a rigorous means of separating nucleosomal DNA from linker DNA. For all X-ray structures, we find that near the dyad, there exists a set of DNA director frames for which the spatial location and orientation are highly conserved. Away from the dyad, the DNA superhelix exhibits "singletrack" and "multipath" regions. In the singletrack region, all structures exhibit a single highly conserved pathway along which all base pairs must track, but at varying rates. In the multipath regions, the base pairs are allowed to map out a limited number of different pathways along the surface of the histone octamer. To demonstrate the utility of the proposed reference geometries, standard and distorted octasome structures, super-nucleosomal structures, nucleosomes with linker DNA, and nucleosomes in closed circular DNA are analyzed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-024-01206-5.

Molecular choreography: Unveiling the dynamic landscape of type IIA DNA topoisomerases before T-segment passage through all-atom simulations

Type IIA DNA topoisomerases are molecular nanomachines responsible for controlling topological states of DNA molecules. Here, we explore the dynamic landscape of yeast topoisomerase IIA during key stages of its catalytic cycle, focusing in particular on the events preceding the passage of the T-segment. To this end, we generated six configurations of fully catalytic yeast topo IIA, strategically inserted a T-segment into the N-gate in relevant configurations, and performed all-atom simulations. The essential motion of topo IIA protein dimer was characterized by rotational gyrating-like movement together with sliding motion within the DNA-gate. Both appear to be inherent properties of the enzyme and an inbuilt feature that allows passage of the T-segment through the cleaved G-segment. Coupled dynamics of the N-gate and DNA-gate residues may be particularly important for controlled and smooth passage of the T-segment and consequently the prevention of DNA double-strand breaks. QTK loop residue Lys367, which interacts with ATP and ADP molecules, is involved in regulating the size and stability of the N-gate. The unveiled features of the simulated configurations provide insights into the catalytic cycle of type IIA topoisomerases and elucidate the molecular choreography governing their ability to modulate the topological states of DNA topology.

The Influence of Oxidized Imino-Allantoin in the Presence of OXOG on Double Helix Charge Transfer: A Theoretical Approach

The genome is continuously exposed to a variety of harmful factors that result in a significant amount of DNA damage. This article examines the influence of a multi-damage site containing oxidized imino-allantoin (OXIa) and 7,8-dihydro-8-oxo-2'-deoxyguanosine (OXOdG) on the spatial geometry, electronic properties, and ds-DNA charge transfer. The ground stage of a d[A1OXIa2A3OXOG4A5]*d[T5C4T3C2T1] structure was obtained at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the condensed phase, with the energies obtained at the M06-2X/6-31++G** level. The non-equilibrated and equilibrated solvent-solute interactions were also considered. Theoretical studies reveal that the radical cation prefers to settle on the OXOG moiety, irrespective of the presence of OXIa in a ds-oligo. The lowest vertical and adiabatic ionization potential values were found for the OXOG:::C base pair (5.94 and 5.52 [eV], respectively). Conversely, the highest vertical and adiabatic electron affinity was assigned for OXIaC as follows: 3.15 and 3.49 [eV]. The charge transfers were analyzed according to Marcus' theory. The highest value of charge transfer rate constant for hole and excess electron migration was found for the process towards the OXOGC moiety. Surprisingly, the values obtained for the driving force and activation energy of electro-transfer towards OXIa2C4 located this process in the Marcus inverted region, which is thermodynamically unfavorable. Therefore, the presence of OXIa can slow down the recognition and removal processes of other DNA lesions. However, with regard to anticancer therapy (radio/chemo), the presence of OXIa in the structure of clustered DNA damage can result in improved cancer treatment outcomes.

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.

Hydration Waters Make Up for the Missing Third Hydrogen Bond in the A·T Base Pair

Base pairing complementarity is central to DNA function. G·C and A·T pair specificity is thought to originate from the different number of hydrogen bonds the pairs make. Quantifying how many hydrogen bonds exist can be difficult because water molecules in the surrounding can make up for or disrupt direct hydrogen bonds, and the hydration structures around A·T and G·C pairs on duplex DNA are distinct. Large-scale computer simulations have been used here to create a detailed map for the hydration structure on A·T and G·C base pairs in water. The contributions of specific hydration waters to the free energy of each of the hydrogen bonds in the A·T and G·C pairs were computed. Using the equilibrium fractions of hydrated versus unhydrated states from the hydration profiles, the impact of specific bound waters on each hydrogen bond can be uniquely quantified using a thermodynamic construction. The findings suggest that hydration water in the minor groove of an A·T pair can provide up to about 2 kcal/mol of free energy advantage, effectively making up for the missing third hydrogen bond in the A·T pair compared to G·C, rendering the intrinsic thermodynamic stability of the A·T pair almost synonymous with G·C.

Influence of temperature on bend, twist and twist-bend coupling of dsDNA

The temperature-dependent bend and twist elasticities of dsDNA, as well as their couplings, were explored through all-atom molecular dynamics simulations. Three rotational parameters, tilt, roll, and twist, were employed to assess the bend and twist elasticities through their stiffness matrix. Our analysis indicates that the bend and twist stiffnesses decrease as the temperature rises, primarily owing to entropic influences stemming from thermodynamic fluctuations. Furthermore, the couplings between these rotational parameters also exhibit a decline with increasing temperature, although the roll-twist coupling displays greater strength than the tilt-roll and tilt-twist couplings, attributed to its more robust correction component. We elucidated the influence of temperature on bend and twist elasticities based on the comparisons between various models and existing data.

The structure and physical properties of a packaged bacteriophage particle

A string of nucleotides confined within a protein capsid contains all the instructions necessary to make a functional virus particle, a virion. Although the structure of the protein capsid is known for many virus species1,2, the three-dimensional organization of viral genomes has mostly eluded experimental probes3,4. Here we report all-atom structural models of an HK97 virion5, including its entire 39,732 base pair genome, obtained through multiresolution simulations. Mimicking the action of a packaging motor6, the genome was gradually loaded into the capsid. The structure of the packaged capsid was then refined through simulations of increasing resolution, which produced a 26 million atom model of the complete virion, including water and ions confined within the capsid. DNA packaging occurs through a loop extrusion mechanism7 that produces globally different configurations of the packaged genome and gives each viral particle individual traits. Multiple microsecond-long all-atom simulations characterized the effect of the packaged genome on capsid structure, internal pressure, electrostatics and diffusion of water, ions and DNA, and revealed the structural imprints of the capsid onto the genome. Our approach can be generalized to obtain complete all-atom structural models of other virus species, thereby potentially revealing new drug targets at the genome-capsid interface.

The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids

The Nucleic Acid Knowledgebase (nakb.org) is a new data resource, updated weekly, for experimentally determined 3D structures containing DNA and/or RNA nucleic acid polymers and their biological assemblies. NAKB indexes nucleic acid-containing structures derived from all major structure determination methods (X-ray, NMR and EM), including all held by the Protein Data Bank (PDB). As the planned successor to the Nucleic Acid Database (NDB), NAKB's design preserves all functionality of the NDB and provides novel nucleic acid-centric content, including structural and functional annotations, as well as annotations from and links to external resources. A variety of custom interactive tools have been developed to enable rapid exploration and drill-down of NAKB's content.

Mechanisms of DNA-Mediated Allostery

Proteins often regulate their activities via allostery-or action at a distance-in which the binding of a ligand at one binding site influences the affinity for another ligand at a distal site. Although less studied than in proteins, allosteric effects have been observed in experiments with DNA as well. In these experiments two or more proteins bind at distinct DNA sites and interact indirectly with each other, via a mechanism mediated by the linker DNA molecule. We develop a mechanical model of DNA/protein interactions which predicts three distinct mechanisms of allostery. Two of these involve an enthalpy-mediated allostery, while a third mechanism is entropy driven. We analyze experiments of DNA allostery and highlight the distinctive signatures allowing one to identify which of the proposed mechanisms best fits the data.

The pseudotorsional space of RNA

The characterization of the conformational landscape of the RNA backbone is rather complex due to the ability of RNA to assume a large variety of conformations. These backbone conformations can be depicted by pseudotorsional angles linking RNA backbone atoms, from which Ramachandran-like plots can be built. We explore here different definitions of these pseudotorsional angles, finding that the most accurate ones are the traditional η (eta) and θ (theta) angles, which represent the relative position of RNA backbone atoms P and C4'. We explore the distribution of η - θ in known experimental structures, comparing the pseudotorsional space generated with structures determined exclusively by one experimental technique. We found that the complete picture only appears when combining data from different sources. The maps provide a quite comprehensive representation of the RNA accessible space, which can be used in RNA-structural predictions. Finally, our results highlight that protein interactions lead to significant changes in the population of the η - θ space, pointing toward the role of induced-fit mechanisms in protein-RNA recognition.

Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA

A triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not known. To understand this, various triplets formed between eight artificial nucleobases (P, Z, J, V, B, S, X, and K) and four natural DNA bases (G, C, A, and T) are studied herein by employing a reliable density functional theoretic (DFT) method. Initially, the triple helix-forming artificial nucleobases interacted with the duplex DNA containing GC and AT base pairs, and subsequently, triple helix-forming natural bases (G and C) interacted with artificial duplex DNA containing PZ, JV, BS, and XK base pairs. Among the different triplets formed in the first category, the C-JV triplet is found to be the most stable with a binding energy of about - 31 kcal/mol. Similarly, among the second category of triplets, the Z-GC and V-GC triplets are the most stable. Interestingly, Z-GC and V-GC are found to be isoenergetic with a binding energy of about - 30 kcal/mol. The C-JV, and Z-GC or V-GC triplets are about 12-14 kcal/mol more stable than the JV and GC base pairs respectively. Microsolvation of these triplets in 5 explicit water molecules further enhanced their stability by 16-21 kcal/mol. These results along with the consecutive stacking of the C-JV triplet (C-JV/C-JV) data indicate that the synthetic nucleobases can form stable semisynthetic triple helical DNA. However, consideration of a full-length DNA containing one or more semisynthetic bases or base pairs is necessary to understand the formation of semisynthetic DNA in living cells.

Nucleosome Array Deformation in Chromatin is Sustained by Bending, Twisting and Kinking of Linker DNA

Chromatin in the nucleus undergoes mechanical stresses from different sources during the various stages of cell life. Here a trinucleosome array is used as the minimal model to study the mechanical response to applied stress at the molecular level. By using large-scale, all-atom steered-molecular dynamics simulations, we show that the largest part of mechanical stress in compression is accommodated by the DNA linkers joining pairs of nucleosomes, which store the elastic energy accumulated by the applied force. Different mechanical instabilities (Euler bending, Brazier kinking, twist-bending) can deform the DNA canonical structure, as a function of the increasing force load. An important role of the histone tails in assisting the DNA deformation is highlighted. The overall response of the smallest chromatin fragment to compressive stress leaves the nucleosome assembly with a substantial plastic deformation and localised defects, which can have a potential impact on DNA transcription, downstream signaling pathways, the regulation of gene expression, and DNA repair.

Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics

DNA deformability and differential hydration are crucial determinants of biological processes ranging from genetic material packaging to gene expression; their associative details, however, remain inadequately understood. Herein, we report investigations of the dynamic and thermodynamic responses of the local hydration of a variety of base pair sequences. Leveraging in silico sampling and our in-house analyses, we first report the local conformational propensity of sequences that are either predisposed toward the canonical A- or B-conformations or are restrained to potential transitory pathways. It is observed that the transition from the unrestrained A-form to the B-form leads to lengthwise structural deformation. The insertion of intermittent -(CG)- base pairs in otherwise homogeneous -(AT)- sequences bears dynamical consequences for the vicinal hydration layer. Calculation of the excess (pair) entropy suggests substantially higher values of hydration water surrounding A conformations over the B- conformations. Applying the Rosenfeld approximation, we project that the diffusivity of water molecules proximal to canonical B conformation is least for the minor groove of the canonical B-conformation. We determine that structure, composition, and conformation specific groove dimension together influence the local hydration characteristics and, therefore, are expected to be important determinants of biological processes.

Unveiling the interdomain dynamics of type II DNA topoisomerase through all-atom simulations: Implications for understanding its catalytic cycle

Type IIA DNA topoisomerases are complex molecular nanomachines that manage topological states of the DNA molecule in the cell and play a crucial role in cellular processes such as cell division and transcription. They are also established targets of cancer chemotherapy. Starting from the available crystal structure of a fully catalytic topoisomerase IIA homodimer from Saccharomyces cerevisiae, we constructed three states of this molecular motor primarily changing the configurations of the DNA segment bound in the DNA gate and performed μs-long all-atom molecular simulations. A comprehensive analysis revealed a sliding motion within the DNA gate and a teamwork between the N-gate and DNA gate that may be associated with the necessary molecular events that allow passage of the T-segment of DNA. The observed movement of the ATPase dimer relative to the DNA domain was reflected in different interaction patterns between the K-loops of the transducer domain and the B-A-B form of the bound DNA. Based on the obtained results, we mapped simulated configurations to the structures in the proposed catalytic cycle through which type IIA topoisomerases exert their function and discussed the possible transition events. The results extend our understanding of the mechanism of action of type IIA topoisomerases and provide an atomistic interpretation of some of the observed features of these molecular motors.

Incorporation of N7-Platinated Guanines into Thermus Aquaticus (Taq) DNA Polymerase: Atomistic Insights from Molecular Dynamics Simulations

In this work, we elucidated some key aspects of the mechanism of action of the cisplatin anticancer drug, cis-[Pt(NH₃)₂Cl₂], involving direct interactions with free nucleotides. A comprehensive in silico molecular modeling analysis was conducted to compare the interactions of Thermus aquaticus (Taq) DNA polymerase with three distinct N7-platinated deoxyguanosine triphosphates: [Pt(dien)(N7-dGTP)] (1), cis-[Pt(NH₃)₂Cl(N7-dGTP)] (2), and cis-[Pt(NH₃)₂(H₂O)(N7-dGTP)] (3) {dien = diethylenetriamine; dGTP = 5'-(2'-deoxy)-guanosine-triphosphate}, using canonical dGTP as a reference, in the presence of DNA. The goal was to elucidate the binding site interactions between Taq DNA polymerase and the tested nucleotide derivatives, providing valuable atomistic insights. Unbiased molecular dynamics simulations (200 ns for each complex) with explicit water molecules were performed on the four ternary complexes, yielding significant findings that contribute to a better understanding of experimental results. The molecular modeling highlighted the crucial role of a specific α-helix (O-helix) within the fingers subdomain, which facilitates the proper geometry for functional contacts between the incoming nucleotide and the DNA template needed for incorporation into the polymerase. The analysis revealed that complex 1 exhibits a much lower affinity for Taq DNA polymerase than complexes 2-3. The affinities of cisplatin metabolites 2-3 for Taq DNA polymerase were found to be quite similar to those of natural dGTP, resulting in a lower incorporation rate for complex 1 compared to complexes 2-3. These findings could have significant implications for the cisplatin mechanism of action, as the high intracellular availability of free nucleobases might promote the competitive incorporation of platinated nucleotides over direct cisplatin attachment to DNA. The study's insights into the incorporation of platinated nucleotides into the Taq DNA polymerase active site suggest that the role of platinated nucleotides in the cisplatin mechanism of action may have been previously underestimated.

Biotite: new tools for a versatile Python bioinformatics library

BACKGROUND

Biotite is a program library for sequence and structural bioinformatics written for the Python programming language. It implements widely used computational methods into a consistent and accessible package. This allows for easy combination of various data analysis, modeling and simulation methods.

RESULTS

This article presents major functionalities introduced into Biotite since its original publication. The fields of application are shown using concrete examples. We show that the computational performance of Biotite for bioinformatics tasks is comparable to individual, special purpose software systems specifically developed for the respective single task.

CONCLUSIONS

The results show that Biotite can be used as program library to either answer specific bioinformatics questions and simultaneously allow the user to write entire, self-contained software applications with sufficient performance for general application.

Structural basis for water modulating RNA duplex formation in the CUG repeats of myotonic dystrophy type 1

Secondary structures formed by expanded CUG RNA are involved in the pathobiology of myotonic dystrophy type 1. Understanding the molecular basis of toxic RNA structures can provide insights into the mechanism of disease pathogenesis and accelerate the drug discovery process. Here, we report the crystal structure of CUG repeat RNA containing three U-U mismatches between C-G and G-C base pairs. The CUG RNA crystallizes as an A-form duplex, with the first and third U-U mismatches adopting a water-mediated asymmetric mirror isoform geometry. We found for the first time that a symmetric, water-bridged U-H₂O-U mismatch is well tolerated within the CUG RNA duplex, which was previously suspected but not observed. The new water-bridged U-U mismatch resulted in high base-pair opening and single-sided cross-strand stacking interactions, which in turn dominate the CUG RNA structure. Furthermore, we performed molecular dynamics (MD) simulations that complemented the structural findings and proposed that the first and third U-U mismatches are interchangeable conformations, while the central water-bridged U-U mismatch represents an intermediate state that modulates the RNA duplex conformation. Collectively, the new structural features provided in this work are important for understanding the recognition of U-U mismatches in CUG repeats by external ligands such as proteins or small molecules.

The Influence of 5′,8-Cyclo-2′-Deoxyguanosine on ds-DNA Charge Transfer Depends on Its Diastereomeric Form: A Theoretical Study

The genetic information stored in the nucleobase sequence is continuously exposed to harmful extra- and intra-cellular factors, which can lead to different types of DNA damage, with more than 70 lesion types identified so far. In this article, the influence of a multi-damage site containing (5′R/S) 5′,8-cyclo-2′-deoxyguanosine (cdG) and 7,8-dihydro-8-oxo-2′-deoxyguanosine (OXOdG) on charge transfer through ds-DNA was taken into consideration. The spatial geometries of oligo-RcdG: d[A1(5′R)cG2A3OXOG4A5]*d[T5C4T3C2T1] and oligo-ScdG: d[A1(5′S)cG2A3OXOG4A5]*d[T5C4T3C2T1] were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using ONIOM methodology. For all the electronic property energies under discussion, the M06-2X/6-31++G** level of theory was used. Additionally, the non-equilibrated and equilibrated solvent-solute interactions were into consideration. The obtained results confirm the predisposition of OXOdG to radical cation formation regardless of the presence of other lesions in a ds-DNA structure. In the case of electron transfer, however, the situation is different. An excess electron migration towards (5′S)cdG was found to be preferred in the case of oligo-ScdG, while in the case of oligo-RcdG, OXOdG was favored. The above observation was confirmed by the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution analysis. The obtained results indicate that 5′,8-cyclo-2′-deoxyguanosine, depending on the C5′ atom chirality, can significantly influence the charge migration process through the double helix. The above can be manifested by the slowdown of DNA lesion recognition and removal processes, which can increase the probability of mutagenesis and subsequent pathological processes. With regard to anticancer therapy (radio/chemo), the presence of (5′S)cdG in the structure of formed clustered DNA damage can lead to improvements in cancer treatment.

Modeling the Infrared Spectroscopy of Oligonucleotides with 13C Isotope Labels

The carbonyl stretching modes have been widely used in linear and two-dimensional infrared (IR) spectroscopy to probe the conformation, interaction, and biological functions of nucleic acids. However, due to their universal appearance in nucleobases, the IR absorption bands of nucleic acids are often highly congested in the 1600-1800 cm^-1 region. Following the fruitful applications in proteins, ¹³C isotope labels have been introduced to the IR measurements of oligonucleotides to reveal their site-specific structural fluctuations and hydrogen bonding conditions. In this work, we combine recently developed frequency and coupling maps to develop a theoretical strategy that models the IR spectra of oligonucleotides with ¹³C labels directly from molecular dynamics simulations. We apply the theoretical method to nucleoside 5'-monophosphates and DNA double helices and demonstrate how elements of the vibrational Hamiltonian determine the spectral features and their changes upon isotope labeling. Using the double helices as examples, we show that the calculated IR spectra are in good agreement with experiments and the ¹³C isotope labeling technique can potentially be applied to characterize the stacking configurations and secondary structures of nucleic acids.

FapydG in the Shadow of OXOdG—A Theoretical Study of Clustered DNA Lesions

Genetic information, irrespective of cell type (normal or cancerous), is exposed to a range of harmful factors, which can lead to more than 80 different types of DNA damage. Of these, oxoG and FapyG have been identified as the most abundant in normoxic and hypoxic conditions, respectively. This article considers d[AFapyGAOXOGA]*[TCTCT] (oligo-FapyG) with clustered DNA lesions (CDLs) containing both the above types of damage at the M06-2x/6-31++G** level of theory in the condensed phase. Furthermore, the electronic properties of oligo-FapyG were analysed in both equilibrated and non-equilibrated solvation–solute interaction modes. The vertical/adiabatic ionization potential (VIP, AIP) and electron affinity (VEA, AEA) of the investigated ds-oligo were found as follows in [eV]: 5.87/5.39 and −1.41/−2.09, respectively. The optimization of the four ds-DNA spatial geometries revealed that the transFapydG was energetically privileged. Additionally, CDLs were found to have little influence on the ds-oligo structure. Furthermore, for the FapyGC base-pair isolated from the discussed ds-oligo, the ionization potential and electron affinity values were higher than those assigned to OXOGC. Finally, a comparison of the influence of FapyGC and OXOGC on charge transfer revealed that, in contrast to the OXOGC base-pair, which, as expected, acted as a radical cation/anion sink in the oligo-FapyG structure, FapyGC did not significantly affect charge transfer (electron–hole and excess–electron). The results presented below indicate that 7,8-dihydro-8-oxo-2′-deoxyguanosine plays a significant role in charge transfer through ds-DNA containing CDL and indirectly has an influence on the DNA lesion recognition and repair process. In contrast, the electronic properties obtained for 2,6-diamino-4-hydroxy-5-foramido-2′deoxypyrimidine were found to be too weak to compete with OXOG to influence charge transfer through the discussed ds-DNA containing CDL. Because increases in multi-damage site formation are observed during radio- or chemotherapy, understanding their role in the above processes can be crucial for the efficiency and safety of medical cancer treatment.

Temperature dependence of DNA elasticity: An all-atom molecular dynamics simulation study

We used all-atom molecular dynamics simulation to investigate the elastic properties of double-stranded DNA (dsDNA). We focused on the influences of temperature on the stretch, bend, and twist elasticities, as well as the twist-stretch coupling, of the dsDNA over a wide range of temperature. The results showed that the bending and twist persistence lengths, together with the stretch and twist moduli, decrease linearly with temperature. However, the twist-stretch coupling behaves in a positive correction and enhances as the temperature increases. The potential mechanisms of how temperature affects dsDNA elasticity and coupling were investigated by using the trajectories from atomistic simulation, in which thermal fluctuations in structural parameters were analyzed in detail. We analyzed the simulation results by comparing them with previous simulation and experimental data, which are in good agreement. The prediction about the temperature dependence of dsDNA elastic properties provides a deeper understanding of DNA elasticities in biological environments and potentially helps in the further development of DNA nanotechnology.

The 2Ih and OXOG Proximity Consequences on Charge Transfer through ds-DNA: Theoretical Studies of Clustered DNA Damage

Genetic information is continuously exposed to harmful factors, both intra- and extracellular. Their activity can lead to the formation of different types of DNA damage. Clustered lesions (CDL) are problematic for DNA repair systems. In this study, the short ds-oligos with a CDL containing (R) or (S) 2Ih and OXOG in their structure were chosen as the most frequent in vitro lesions. In the condensed phase, the spatial structure was optimized at the M062x/D95**:M026x/sto-3G level of theory, while the electronic properties were optimized at the M062x/6-31++G** level. The influence of equilibrated and non-equilibrated solvent-solute interactions was then discussed. It was found that the presence of (R)2Ih in the ds-oligo structure causes a greater increase in structure sensitivity towards charge adoption than (S)2Ih, while OXOG shows high stability. Moreover, the analysis of charge and spin distribution reveals the different effects of 2Ih diastereomers. Additionally, the adiabatic ionization potential was found as follows for (R)-2Ih and (S)-2Ih in eV: 7.02 and 6.94. This was in good agreement with the AIP of the investigated ds-oligos. It was found that the presence of (R)-2Ih has a negative influence on excess electron migration through ds-DNA. Finally, according to the Marcus theory, the charge transfer constant was calculated. The results presented in the article show that both diastereomers of 5-carboxamido-5-formamido-2-iminohydantoin should play a significant role in the CDL recognition process via electron transfer. Moreover, it should be pointed out that even though the cellular level of (R and S)-2Ih has been obscured, their mutagenic potential should be at the same level as other similar guanine lesions found in different cancer cells.

Rigid Base Biasing in Molecular Dynamics Enables Enhanced Sampling of DNA Conformations

All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution, however, comes at a heavy computational cost, and, within the time scales of simulations, nucleic acids weakly fluctuate around their ideal structure exploring a limited set of conformations. We introduce the RBB-NA algorithm (available as a package in the Open Source Library PLUMED), which is capable of controlling rigid base parameters in all-atom simulations of nucleic acids. With suitable biasing potentials, this algorithm can "force" a DNA or RNA molecule to assume specific values of the six rotational (tilt, roll, twist, buckle, propeller, opening) and/or the six translational parameters (shift, slide, rise, shear, stretch, stagger). The algorithm enables the use of advanced sampling techniques to probe the structure and dynamics of locally strongly deformed nucleic acids. We illustrate its performance showing some examples in which DNA is strongly twisted, bent, or locally buckled. In these examples, RBB-NA reproduces well the unconstrained simulations data and other known features of DNA mechanics, but it also allows one to explore the anharmonic behavior characterizing the mechanics of nucleic acids in the high deformation regime.

Coarse Graining DNA: Symmetry, Nonlocal Elasticity, and Persistence Length

While the behavior of double-stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein interactions and the nucleosome diffusion mechanism. Here, by employing the rigid base-pair model, we connect its microscopic parameters to the persistence length. Combined with all-atom molecular dynamic simulations, our scheme identifies relevant couplings between different degrees of freedom at each coarse-graining step. This allows us to clarify how the scale dependence of the elastic moduli is determined in a systematic way encompassing the role of previously unnoticed off-site couplings between deformations with different parity.

Maturation of siRNA by strand separation: Steered molecular dynamics study

RNA interference, particularly siRNA induced gene silencing is becoming an important avenue of modern therapeutics. The siRNA is delivered to the cells as short double helical RNA which becomes single stranded for forming the RISC complex. Significant experimental evidence is available for most of the steps except the process of the separation of the two strands. We have attempted to understand the pathway for double stranded siRNA (dsRNA) to single stranded (ssRNA) molecules using steered molecular dynamics simulations. As the process is completely unexplored we have applied force from all possible directions restraining all possible residues to convert dsRNA to ssRNA. We found pulling one strand along the helical axis direction restraining the far end of the other strand demands excessive force for ssRNA formation. Pulling a central residue of one strand, in a direction perpendicular to the helix axis, while keeping the base paired residue fixed requires intermediate force for strand separation. Moreover, we found that in this process the force requirement is quite high for the first bubble formation (nucleation energy) and the bubble propagation energies are quite small. We believe the success rate of the design of siRNA sequences for gene silencing may increase if this mechanistic knowledge is utilized for such a design process.Communicated by Ramaswamy H. Sarma.

Insights into DNA solvation found in protein-DNA structures

The proteins that bind double-helical DNA present various microenvironments that sense and/or induce signals in the genetic material. The high-resolution structures of protein-DNA complexes reveal the nature of both the microenvironments and the conformational responses in DNA and protein. Complex networks of interactions within the structures somehow tie the protein and DNA together and induce the observed spatial forms. Here we show how the cumulative buildup of amino acid atoms around the sugars, phosphates, and bases in different protein-DNA complexes produces a binding cloud around the double helix and how different types of atoms fill that cloud. Rather than focusing on the principles of molecular binding and recognition suggested by the arrangements of amino acids and nucleotides in the macromolecular complexes, we consider the proteins in contact with DNA as organized solvents. We describe differences in the mix of atoms that come in closest contact with DNA, subtle sequence-dependent features in the microenvironment of the sugar-phosphate backbone, a direct link between the localized buildup of ionic species and the electrostatic potential surfaces of the DNA bases, and sites of atomic buildup above and below the basepair planes that transmit the unique features of the base environments along the chain backbone. The inferences about solvation that can be drawn from the survey provide new stimuli for improvement of nucleic acid force fields and fresh ideas for exploration of the properties of DNA in solution.

Oligonucleotides Featuring a Covalently Mercurated 6-Phenylcarbazole Residue as High-Affinity Hybridization Probes for Thiopyrimidine-Containing Sequences

Short oligonucleotides incorporating either 1-mercuri-6-phenylcarbazole, 8-mercuri-6-phenylcarbazole, or 1,8-dimercuri-6-phenylcarbazole C-nucleoside in the middle of the chain have been synthesized and studied for their potential as hybridization probes for sequences containing thiopyrimidine nucleobases. All of these oligonucleotides formed very stable duplexes with complementary sequences pairing the organometallic moiety with either 2- or 4-thiothymine. The isomeric monomercurated oligonucleotides were also able to discriminate between 2- and 4-thiothymine based on the different melting temperatures of the respective duplexes. DFT-optimized structures of the most stable mononuclear HgII -mediated base pairs featured a coordinated covalent bond between HgII and either S2 or S4 and a hydrogen bond between the carbazole nitrogen and N3. The dinuclear HgII -mediated base pairs, in turn, were geometrically very similar to the one previously reported to form between 1,8-dimercuri-6-phenylcarbazole and thymine and had one HgII ion coordinated to a thio and the other one to an oxo substituent.

Sarcin/Ricin Domain RNA Retains Its Structure Better Than A-RNA in Adaptively Biased Molecular Dynamics Simulations

Less than one in thirty of the RNA sequences transcribed in humans are translated into protein. The noncoding RNA (ncRNA) functions in catalysis, structure, regulation, and more. However, for the most part, these functions are poorly characterized. RNA is modular and described by motifs that include helical A-RNA with canonical Watson-Crick base-pairing as well as structures with only noncanonical base pairs. Understanding the structure and dynamics of motifs will aid in deciphering functions of specific ncRNAs. We present computational studies on a standard sarcin/ricin domain (SRD), citrus bark cracking viroid SRD, as well as A-RNA. We have applied enhanced molecular dynamics techniques that construct an inverse free-energy surface (iFES) determined by collective variables that monitor base-pairing and backbone conformation. Each SRD RNA is flanked on each side by A-RNA, allowing comparison of the behavior of these motifs in the same molecule. The RNA iFESs have single peaks, indicating that the combined motifs should denature as a single cohesive unit, rather than by regional melting. Local root-mean-square deviation (RMSD) analysis and communication propensity (CProp, variance in distances between residue pairs) reveal distinct motif properties. Our analysis indicates that the standard SRD is more stable than the viroid SRD, which is more stable than A-RNA. Base pairs at SRD to A-RNA transitions have limited flexibility. Application of CProp reveals extraordinary stiffness of the SRD, allowing residues on opposite sides of the motif to sense each other's motions.

DNA Sequence-Dependent Properties of Nucleosome Positioning in Regions of Distinct Chromatin States in Mouse Embryonic Stem Cells

Chromatin architecture is orchestrated, and plays crucial roles during the developmental process by regulating gene expression. In embryonic stem cells (ESCs), three types of chromatin states, including active, repressive and poised states, were previously identified and characterized with specific chromatin modification marks and different transcription activity, but it is largely unknown how nucleosomes are organized in these chromatin states. In this study, by using a DNA deformation energy model, we investigated the sequence-dependent nucleosome organization within the chromatin states in mouse ESCs. The results revealed that: (1) compared with poised genes, active genes are characterized with a higher level of nucleosome occupancy around their transcription start sites (TSS) and transcription termination sites (TTS), and both types of genes do not have a nucleosome-depleted region at their TTS, contrasting with the MNase-seq based result; (2) based on our previous DNA bending energy model, we developed an improved model capable of predicting both rotational positioning and nucleosome occupancy determined by a chemical mapping approach; (3) DNA bending-energy-based analyses demonstrated that the fragile nucleosomes positioned at both gene ends could be explained largely by enhanced rotational positioning signals encoded in DNA, but nucleosome phasing around the TSS of active genes was not determined by sequence preference; (4) the nucleosome occupancy landscape around the binding sites of some developmentally important transcription factors known to bind with different chromatin contexts, was also successfully predicted; (5) the difference of nucleosome occupancy around the TSS between CpG-rich and CpG-poor promoters was partly captured by our sequence-dependent model. Taken together, by developing an improved deformation-energy-based model, we revealed some sequence-dependent properties of the nucleosome arrangements in regions of distinct chromatin states in mouse ESCs.

Helicene Structure between DNA and Cyanuric Acid: The Role of Noncovalent Interactions

The self-assembly between DNA and small organic molecules can expand the structural space of and introduce novel functionalities to DNA nanomaterials. In particular, it was demonstrated that poly(adenosine) DNA self-assembles with cyanuric acid (CA) to form a triplex helical structure. Previous molecular dynamics simulations showed that the DNA-CA assemblies adopt a novel noncovalent helicene structure that has a continuous helical hydrogen bond network. This article explores why the assemblies adopt the helicene geometry instead of an alternative planar hexameric rosette geometry. Analysis of the hydrogen bonding and stacking interaction energies indicates that constraining the system to the hexameric rosette geometry strains the hydrogen bonds without significantly improving the interaction energy. Molecular dynamics simulations for the assemblies between adenosine nucleosides and CA confirm that the formation of helicene structure is primarily driven by base-pair interactions and not because of the DNA backbone.

The Impact of Inflammation-Induced Tumor Plasticity during Myeloid Transformation

Clonal hematopoiesis (CH) is an aging-associated condition characterized by the clonal outgrowth of mutated preleukemic cells. Individuals with CH are at an increased risk of developing hematopoietic malignancies. Here, we describe a novel animal model carrying a recurrent TET2 missense mutation frequently found in patients with CH and leukemia. In a fashion similar to CH, animals show signs of disease late in life when they develop a wide range of myeloid neoplasms, including acute myeloid leukemia (AML). Using single-cell transcriptomic profiling of the bone marrow, we show that disease progression in aged animals correlates with an enhanced inflammatory response and the emergence of an aberrant inflammatory monocytic cell population. The gene signature characteristic of this inflammatory population is associated with poor prognosis in patients with AML. Our study illustrates an example of collaboration between a genetic lesion found in CH and inflammation, leading to transformation and the establishment of blood neoplasms.

SIGNIFICANCE

Progression from a preleukemic state to transformation, in the presence of TET2 mutations, is coupled with the emergence of inflammation and a novel population of inflammatory monocytes. Genes characteristic of this inflammatory population are associated with the worst prognosis in patients with AML. These studies connect inflammation to progression to leukemia. See related commentary by Pietras and DeGregori, p. 2234 . This article is highlighted in the In This Issue feature, p. 2221.

MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution

The linear sequence of DNA provides invaluable information about genes and their regulatory elements along chromosomes. However, to fully understand gene function and regulation, we need to dissect how genes physically fold in the three-dimensional nuclear space. Here we describe immuno-OligoSTORM, an imaging strategy that reveals the distribution of nucleosomes within specific genes in super-resolution, through the simultaneous visualization of DNA and histones. We combine immuno-OligoSTORM with restraint-based and coarse-grained modeling approaches to integrate super-resolution imaging data with Hi-C contact frequencies and deconvoluted micrococcal nuclease-sequencing information. The resulting method, called Modeling immuno-OligoSTORM, allows quantitative modeling of genes with nucleosome resolution and provides information about chromatin accessibility for regulatory factors, such as RNA polymerase II. With Modeling immuno-OligoSTORM, we explore intercellular variability, transcriptional-dependent gene conformation, and folding of housekeeping and pluripotency-related genes in human pluripotent and differentiated cells, thereby obtaining the highest degree of data integration achieved so far to our knowledge.

RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction

The stable three-dimensional structure of RNA is known to play several important biochemical roles, from post-transcriptional gene regulation to enzymatic action. These structures contain double-helical regions, which often have different types of non-canonical base pairs in addition to Watson-Crick base pairs. Hence, it is important to study their structures from experimentally obtained or even predicted ones, to understand their role, or to develop a drug against the potential targets. Molecular Modeling of RNA double helices containing non-canonical base pairs is a difficult process, particularly due to the unavailability of structural features of non-Watson-Crick base pairs. Here we show a composite web-server with an associated database that allows one to generate the structure of RNA double helix containing non-canonical base pairs using consensus parameters obtained from the database. The database classification is followed by an evaluation of the central tendency of the structural parameters as well as a quantitative estimation of interaction strengths. These parameters are used to construct three-dimensional structures of double helices composed of Watson-Crick and/or non-canonical base pairs. Our benchmark study to regenerate double-helical fragments of many experimentally derived RNA structures indicate very high accuracy. This composite server is expected to be highly useful in understanding functions of various pre-miRNA by modeling structures of the molecules and estimating binding efficiency. The database can be accessed from http://hdrnas.saha.ac.in/rnabpdb .

Structural Analysis of the Poly(thymidine)-Melamine Assembly

Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.

Implementing accelerated dynamics to unravel the effects of high-fidelity Cas9 mutants on target DNA and guide RNA hybrid stability

The clustered regularly interspersed short palindromic repeats (CRISPR) and its associated nuclease (Cas9) offers a unique and easily reprogrammable system for editing eukaryotic genomes. Cas9 is guided to the target by an RNA strand, and precise edits are created by introducing double-stranded breaks. However, nuclease activity of Cas9 is also triggered at other sites other than the target sit, which is a major limitation for various applications. Cas9 variants have been designed to improve the efficacy of the tool by introducing certain mutations. However, the on-target activity of such Cas9 variants is often seen as compromised. Hence, understanding the sub-molecular differences in the variants is essential to elucidate the factors that contribute to efficiency. The study reveals distortions in the PAM-distal regions of the nucleic hybrids as well as changes in the interactions between the Cas9 variants and RNA-DNA hybrid, contributing to the explanation for differences in on-target activity.Communicated by Ramaswamy H. Sarma.

First High-Resolution Crystal Structures of DNA:2′-O-Methyl-RNA Heteroduplexes

Heteroduplexes composed of all-DNA and all-2′-OMe RNA strands do not occur in nature, but they have found application in the development of molecular beacons and could also be used as aptamers or elements of nucleic acid-based nanostructures that will contain such structural motifs. The crystallization experiments performed have shown that the introduction of overhangs at the ends of the duplex has a great influence on the success of crystallization, as well as on the DNA:2′-OMe-RNA heteroduplex crystal packing. The molecular and crystal structure of the DNA:2′-O-methyl-RNA heteroduplex in its overhanging and blunt-ended versions was determined at 100 K using synchrotron radiation with a resolution of 1.91 and 1.55 Å, respectively. The Zn-SAD method was used to resolve the original duplex structure when molecular replacement by many existing models of duplex structures failed. Both molecules analyzed adopted a conformation close to the A-RNA double helix. The presented structures provide the first insight into this type of heteroduplexes and allowed a comparative analysis with existing nucleic acid homo- and heteroduplex structures. The results of our research expand the knowledge of the structural properties of new heteroduplexes and may be useful for future applications, such as therapies using this class of compounds.

Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration

DNA carries more than the list of biochemical ingredients that drive the basic functions of living systems. The sequence of base pairs includes a multitude of structural and energetic signals, which determine the degree to which the long, threadlike molecule moves and how it responds to proteins and other molecules that control its processing and govern its packaging. The chemical composition of base pairs directs the spatial disposition and fluctuations of successive residues. The observed arrangements of these moieties in high-resolution protein–DNA crystal structures provide one of the best available estimates of the natural, sequence-dependent structure and deformability of the double-helical molecule. Here, we update the set of knowledge-based elastic potentials designed to describe the observed equilibrium structures and configurational fluctuations of the ten unique base-pair steps. The large number of currently available structures makes it possible to characterize the configurational preferences of the DNA base-pair steps within the context of their immediate neighbors, i.e., tetrameric context. Use of these knowledge-based potentials shows promise in accounting for known effects of sequence in long chain molecules, e.g., the degree of curvature reported in classic gel mobility studies and the recently reported sequence-dependent responses of supercoiled minicircles to nuclease cleavage.

Developing Community Resources for Nucleic Acid Structures

In this review, we describe the creation of the Nucleic Acid Database (NDB) at Rutgers University and how it became a testbed for the current infrastructure of the RCSB Protein Data Bank. We describe some of the special features of the NDB and how it has been used to enable research. Plans for the next phase as the Nucleic Acid Knowledgebase (NAKB) are summarized.

Selective and stable base pairing by alkynylated nucleosides featuring a spatially-separated recognition interface

Unnatural base pairs (UBPs) which exhibit a selectivity against pairing with canonical nucleobases provide a powerful tool for the development of nucleic acid-based technologies. As an alternative strategy to the conventional UBP designs, which involve utility of different recognition modes at the Watson–Crick interface, we now report that the exclusive base pairing can be achieved through the spatial separation of recognition units. The design concept was demonstrated with the alkynylated purine (^NPu, ^OPu) and pyridazine (^NPz, ^OPz) nucleosides endowed with nucleobase-like 2-aminopyrimidine or 2-pyridone (‘pseudo-nucleobases’) on their major groove side. These alkynylated purines and pyridazines exhibited exclusive and stable pairing properties by the formation of complementary hydrogen bonds between the pseudo-nucleobases in the DNA major groove as revealed by comprehensive T_m measurements, 2D-NMR analyses, and MD simulations. Moreover, the alkynylated purine-pyridazine pairs enabled dramatic stabilization of the DNA duplex upon consecutive incorporation while maintaining a high sequence-specificity. The present study showcases the separation of the recognition interface as a promising strategy for developing new types of UBPs.

RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems

Kink-turns are highly bent internal loop motifs commonly found in the ribosome and other RNA complexes. They frequently act as binding sites for proteins and mediate tertiary interactions in larger RNA structures. Kink-turns have been a topic of intense research, but their elastic properties in the folded state are still poorly understood. Here we use extensive all-atom molecular dynamics simulations to parameterize a model of kink-turn in which the two flanking helical stems are represented by effective rigid bodies. Time series of the full set of six interhelical coordinates enable us to extract minimum energy shapes and harmonic stiffness constants for kink-turns from different RNA functional classes. The analysis suggests that kink-turns exhibit isotropic bending stiffness but are highly anisotropic with respect to lateral displacement of the stems. The most flexible lateral displacement mode is perpendicular to the plane of the static bend. These results may help understand the structural adaptation and mechanical signal transmission by kink-turns in complex natural and artificial RNA structures.

Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state

Chromatin remodelers are ATP-dependent enzymes that reorganize nucleosomes within all eukaryotic genomes. Here we report a complex of the Chd1 remodeler bound to a nucleosome in a nucleotide-free state, determined by cryo-EM to 2.3 Å resolution. The remodeler stimulates the nucleosome to absorb an additional nucleotide on each strand at two different locations: on the tracking strand within the ATPase binding site and on the guide strand one helical turn from the ATPase motor. Remarkably, the additional nucleotide on the tracking strand is associated with a local transformation toward an A-form geometry, explaining how sequential ratcheting of each DNA strand occurs. The structure also reveals a histone-binding motif, ChEx, which can block opposing remodelers on the nucleosome and may allow Chd1 to participate in histone reorganization during transcription.

Predicting the configuration and energy of DNA in a nucleosome by coarse-grain modelling

We present a novel algorithm which uses a coarse-grained model and an energy minimisation procedure to predict the sequence-dependent DNA configuration in a nucleosome together with its energetic cost.