Twisting DNA by salt

Isotope-Edited Variable Temperature Infrared Spectroscopy for Measuring Transition Temperatures of Single A-T Watson-Crick Base Pairs in DNA Duplexes

Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2═O stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is ∼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL ∼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is ∼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL ∼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.

Effects of monovalent and divalent cations on the rheology of entangled DNA

In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled λDNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by stabilising linear concatenation of λDNA "monomers" via hybridisation of their sticky ends. On the contrary, divalent cations have a far more complex and dramatic effect on the rheology of the solution and we observe evidence of inter-molecular DNA-DNA bridging by Mg2+. We argue that these results may be interesting in the context of dense solutions of single and double stranded DNA, e.g. in vivo or in biotechnology applications such as DNA origami and DNA hydrogels.

Revealing the Molecular Origin of Anisotropy around Chloride Ions in Bulk Water

A clear picture of the local solvation structure around halide anions in liquid water remains elusive. This discussion has been stimulated by pioneering simulation results that proposed a "hydrophobic cavity" around anions in the bulk, which is analogous to air at the air-water interface. However, there is also sound experimental and theoretical evidence that halide ions are rather symmetrically solvated in the bulk, leading to a different viewpoint. Using extensive ab initio molecular dynamics simulations of an aqueous Cl- solution, we indeed find an anisotropic arrangement of H-bonded versus interstitial water molecules. The latter are not H-bonded to the anions and thus do not couple much electronically to Cl-. The resulting purely electronic anisotropy of the local solvation environment correlates with that structural anisotropy, which however should not be understood as an empty cavity─as it would be at the air-water interface─but rather contains interstitial water molecules.

The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations

The subtle differences in the chemical structures of double-stranded (ds) RNA and DNA lead to significant variations in their biological roles and medical implications, largely due to their distinct biophysical properties, such as bending stiffness. Although it is well known that A-form dsRNA is stiffer than B-form dsDNA under physiological salt conditions, the underlying cause of this difference remains unclear. In this study, we employ high-precision magnetic-tweezer experiments along with molecular dynamics simulations and reveal that the relative bending stiffness between dsRNA and dsDNA is primarily determined by the structure- and salt-concentration-dependent ion distribution around their helical structures. At near-physiological salt conditions, dsRNA shows a sparser ion distribution surrounding its phosphate groups compared to dsDNA, causing its greater stiffness. However, at very high monovalent salt concentrations, phosphate groups in both dsRNA and dsDNA become fully neutralized by excess ions, resulting in a similar intrinsic bending persistence length of approximately 39 nm. This similarity in intrinsic bending stiffness of dsRNA and dsDNA is coupled to the analogous fluctuations in their total groove widths and further coupled to the similar fluctuation of base-pair inclination, despite their distinct A-form and B-form helical structures.

Hierarchical Assembly of Single-Stranded RNA

Single-stranded RNA (ssRNA) plays a major role in the flow of genetic information-most notably, in the form of messenger RNA (mRNA)-and in the regulation of biological processes. The highly dynamic nature of chains of unpaired nucleobases challenges structural characterizations of ssRNA by experiments or molecular dynamics (MD) simulations alike. Here, we use hierarchical chain growth (HCG) to construct ensembles of ssRNA chains. HCG assembles the structures of protein and nucleic acid chains from fragment libraries created by MD simulations. Applied to homo- and heteropolymeric ssRNAs of different lengths, we find that HCG produces structural ensembles that overall are in good agreement with diverse experiments, including nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET). The agreement can be further improved by ensemble refinement using Bayesian inference of ensembles (BioEn). HCG can also be used to assemble RNA structures that combine base-paired and base-unpaired regions, as illustrated for the 5' untranslated region (UTR) of SARS-CoV-2 RNA.

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

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

Temperature-dependent elasticity of DNA, RNA, and hybrid double helices

Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003-0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.

Assessing the feasibility of free DNA for disaster victim identification and forensic applications

In tropical disaster victim identification (DVI) scenarios, challenging environmental conditions lead to accelerated DNA degradation in remains. To further enhance the utilization of leached DNA from tissue in the preservative solution (termed "free DNA") as an alternative source, we incorporated new results by assessing its integrity in postmortem and decomposing cadavers preserved in DNA/RNA Shield™ and modified TENT, with silica-based purification (QIAquick®) for faster processing. The psoas muscle tissues of one decomposed and ten cadavers were preserved in each solution at 25 °C and 35 °C for 3 months. Free DNA efficiency was compared with individual reference samples for reliable results in quantity, quality, and STR profiles. The findings revealed that DNA/RNA Shield™ effectively preserves free DNA integrity for extended storage, while modified TENT is more suitable for short-term storage due to higher degradation levels. Moreover, the use of free DNA samples with massive parallel sequencing displays potential for forensic DNA analysis. Successful amplification of the mtDNA control region enables variant calling and heteroplasmy analysis while also serving as quality control using ACTB and enabling differentiation within the 16S rRNA region for microbiome analysis. The simplicity of handling free DNA for PCR-based forensic analysis adds to its potential for various applications, including DVI and field-based analysis of biological evidence.

Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations

RNA plays critical roles in the transmission and regulation of genetic information and is increasingly used in biomedical and biotechnological applications. Functional RNAs contain extended double-stranded regions, and the structure of double-stranded RNA (dsRNA) has been revealed at high resolution. However, the dependence of the properties of the RNA double helix on environmental effects, notably temperature, is still poorly understood. Here, we use single-molecule magnetic tweezer measurements to determine the dependence of the dsRNA twist on temperature. We find that dsRNA unwinds with increasing temperature, even more than DNA, with ΔTwRNA = -14.4 ± 0.7°/(°C·kbp), compared to ΔTwDNA = -11.0 ± 1.2°/(°C·kbp). All-atom molecular dynamics (MD) simulations using a range of nucleic acid force fields, ion parameters, and water models correctly predict that dsRNA unwinds with rising temperature but significantly underestimate the magnitude of the effect. These MD data, together with additional MD simulations involving DNA and DNA-RNA hybrid duplexes, reveal a linear correlation between the twist temperature decrease and the helical rise, in line with DNA but at variance with RNA experimental data. We speculate that this discrepancy might be caused by some unknown bias in the RNA force fields tested or by as yet undiscovered transient alternative structures in the RNA duplex. Our results provide a baseline to model more complex RNA assemblies and to test and develop new parametrizations for RNA simulations. They may also inspire physical models of the temperature-dependent dsRNA structure.

RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy

The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes (rG4s). Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two on-pathway intermediates. We hypothesize that conformational entropy is a hallmark of rG4 folding. Conformational entropy leads to the observed branched multi-pathway folding process for TERRA25. We corroborate this hypothesis by presenting the free energy landscapes and folding pathways of four rG4 systems with varying loop length.

Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type

Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.

Unusual similarity of DNA solvation dynamics in high-salinity crowding with divalent cations of varying concentrations

Double-stranded DNA bears the highest linear negative charge density (2e- per base-pair) among all biopolymers, leading to strong interactions with cations and dipolar water, resulting in the formation of a dense 'condensation layer' around DNA. Interactions involving proteins and ligands binding to DNA are primarily governed by strong electrostatic forces. Increased salt concentrations impede such electrostatic interactions - a situation that prevails in oceanic species due to their cytoplasm being enriched with salts. Nevertheless, how these interactions' dynamics are affected in crowded hypersaline environments remains largely unexplored. Here, we employ steady-state and time-resolved fluorescence Stokes shifts (TRFSS) of a DNA-bound ligand (DAPI) to investigate the static and dynamic solvation properties of DNA in the presence of two divalent cations, magnesium (Mg2+), and calcium (Ca2+) at varying high to very-high concentrations of 0.15 M, 1 M and 2 M. We compare the results to those obtained in physiological concentrations (0.15 M) of monovalent Na+ ions. Combining data from fluorescence femtosecond optical gating (FOG) and time-correlated single photon counting (TCSPC) techniques, dynamic fluorescence Stokes shifts in DNA are analysed over a broad range of time-scales, from 100 fs to 10 ns. We find that while divalent cation crowding strongly influences the DNA stability and ligand binding affinity to DNA, the dynamics of DNA solvation remain remarkably similar across a broad range of five decades in time, even in a high-salinity crowded environment with divalent cations, as compared to the physiological concentration of the Na+ ion. Steady-state and time-resolved data of the DNA-groove-bound ligand are seemingly unaffected by ion-crowding in hypersaline solution, possibly due to ions being mostly displaced by the DNA-bound ligand. Furthermore, the dynamic coupling of cations with nearby water may possibly contribute to a net-neutral effect on the overall collective solvation dynamics in DNA, owing to the strong anti-correlation of their electrostatic interaction energy fluctuations. Such dynamic scenarios may persist within the cellular environment of marine life and other biological cells that experience hypersaline conditions.

Why Na+ has higher propensity than K+ to condense DNA in a crowded environment

Experimentally, in the presence of the crowding agent polyethylene glycol (PEG), sodium ions compact double-stranded DNA more readily than potassium ions. Here, we have used molecular dynamics simulations and the "ion binding shells model" of DNA condensation to provide an explanation for the observed variations in condensation of short DNA duplexes in solutions containing different monovalent cations and PEG; several predictions are made. According to the model we use, externally bound ions contribute the most to the ion-induced aggregation of DNA duplexes. The simulations reveal that for two adjacent DNA duplexes, the number of externally bound Na+ ions is larger than the number of K+ ions over a wide range of chloride concentrations in the presence of PEG, providing a qualitative explanation for the higher propensity of sodium ions to compact DNA under crowded conditions. The qualitative picture is confirmed by an estimate of the corresponding free energy of DNA aggregation that is at least 0.2kBT per base pair more favorable in solution with NaCl than with KCl at the same ion concentration. The estimated attraction free energy of DNA duplexes in the presence of Na+ depends noticeably on the DNA sequence; we predict that AT-rich DNA duplexes are more readily condensed than GC-rich ones in the presence of Na+. Counter-intuitively, the addition of a small amount of a crowding agent with high affinity for the specific condensing ion may lead to the weakening of the ion-mediated DNA-DNA attraction, shifting the equilibrium away from the DNA condensed phase.

Experimental detection of conformational transitions between forms of DNA: problems and prospects

Under different conditions, the DNA double helix can take different geometric forms. Of the large number of its conformations, in addition to the "canonical" B form, the A, C, and Z forms are widely known, and the D, Hoogsteen, and X forms are less known. DNA locally takes the A, C, and Z forms in the cell, in complexes with proteins. We compare different methods for detecting non-canonical DNA conformations: X-ray, IR, and Raman spectroscopy, linear and circular dichroism in both the infrared and ultraviolet regions, as well as NMR (measurement of chemical shifts and their anisotropy, scalar and residual dipolar couplings and inter-proton distances from NOESY (nuclear Overhauser effect spectroscopy) data). We discuss the difficulties in applying these methods, the problems of theoretical interpretation of the experimental results, and the prospects for reliable identification of non-canonical DNA conformations.

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

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

A new DNA extraction method (HV-CTAB-PCI) for amplification of nuclear markers from open ocean-retrieved faeces of an herbivorous marine mammal, the dugong

Non-invasively collected faecal samples are an alternative source of DNA to tissue samples, that may be used in genetic studies of wildlife when direct sampling of animals is difficult. Although several faecal DNA extraction methods exist, their efficacy varies between species. Previous attempts to amplify mitochondrial DNA (mtDNA) markers from faeces of wild dugongs (Dugong dugon) have met with limited success and nuclear markers (microsatellites) have been unsuccessful. This study aimed to establish a tool for sampling both mtDNA and nuclear DNA (nDNA) from dugong faeces by modifying approaches used in studies of other large herbivores. First, a streamlined, cost-effective DNA extraction method that enabled the amplification of both mitochondrial and nuclear markers from large quantities of dugong faeces was developed. Faecal DNA extracted using a new 'High Volume- Cetyltrimethyl Ammonium Bromide- Phenol-Chloroform-Isoamyl Alcohol' (HV-CTAB-PCI) method was found to achieve comparable amplification results to extraction of DNA from dugong skin. As most prevailing practices advocate sampling from the outer surface of a stool to maximise capture of sloughed intestinal cells, this study compared amplification success of mtDNA between the outer and inner layers of faeces, but no difference in amplification was found. Assessment of the impacts of faecal age or degradation on extraction, however, demonstrated that fresher faeces with shorter duration of environmental (seawater) exposure amplified both markers better than eroded scats. Using the HV-CTAB-PCI method, nuclear markers were successfully amplified for the first time from dugong faeces. The successful amplification of single nucleotide polymorphism (SNP) markers represents a proof-of-concept showing that DNA from dugong faeces can potentially be utilised in population genetic studies. This novel DNA extraction protocol offers a new tool that will facilitate genetic studies of dugongs and other large and cryptic marine herbivores in remote locations.

Markedly Different Effects of Monovalent Cations on the Efficiency of Gene Expression

The effect of monovalent cations on a cell-free transcription-translation (TX-TL) system is examined using a luciferase assay. It is found that the potency for all ions analyzed here is in the order Rb⁺  > K⁺  > Cs⁺  > Na⁺  ≈ Li⁺  > (CH₃ )₄ N⁺ , where Rb⁺ is most efficient at promoting TX-TL and the ions of Li⁺ , Na⁺ , and (CH₃ )₄ N⁺ exhibit an inhibitory effect. Similar promotion/inhibition effects are observed for cell-free TL alone with an mRNA template.

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

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

Extracting and characterizing protein-free megabase-pair DNA for in vitro experiments

Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the native proteins. Mass spectrometry indicated that 97%-100% of DNA-binding proteins are removed from the sample. Fluorescence microscopy analysis showed an increase in the radius of gyration of the DNA polymers, while the DNA length remained megabase-pair sized. In proof-of-concept experiments using these deproteinated long DNA molecules, we observed DNA compaction upon adding the DNA-binding protein Fis or PEG crowding agents and showed that it is possible to track the motion of a fluorescently labeled DNA locus. These results indicate the practical feasibility of a "genome-in-a-box" approach to study chromosome organization from the bottom up.

RNA Captures More Cations than DNA: Insights from Molecular Dynamics Simulations

The distribution of cations around nucleic acids is essential for a broad variety of processes ranging from DNA condensation and RNA folding to the detection of biomolecules in biosensors. Predicting the exact distribution of ions remains challenging since the distribution and, hence, a broad variety of nucleic acid properties depend on the salt concentration, the valency of the ions, and the ion type. Despite the importance, a general theory to quantify ion-specific effects for highly charged biomolecules is still lacking. Moreover, recent experiments reveal that despite their similar building blocks, DNA and RNA duplexes can react differently to the same ionic conditions. The aim of our current work is to provide a comprehensive set of molecular dynamics simulations using more than 180 μs of simulation time. For the mono- and divalent cations Li⁺, Na⁺, K⁺, Cs⁺, Ca²⁺, Sr²⁺, and Ba²⁺, the simulations allow us to reveal the ion-specific distributions and binding patterns for DNA and RNA duplexes. The microscopic insights from the simulations display the origin of ion-specificity and shed light on the question of why DNA and RNA show opposing behavior in the same ionic conditions. Finally, the detailed binding patterns from the simulations reveal why RNA can capture more cations than DNA.

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

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

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

Heavy Metal Ions Detection Using Nanomaterials-Based Aptasensors

Heavy metals ions as metallic pollutants are a growing global issue due to their adverse effects on the aquatic ecosystem, and human health. Unfortunately, conventional detection methods such as atomic absorption spectrometry exhibit a relatively low limit of detection and hold numerous disadvantages, and therefore, the development of an efficient method for in-situ and real-time detection of heavy metal residues is of great importance. The aptamer-based sensors offer distinct advantages over antibodies and emerged as a robust sensing platform against various heavy metals due to their high sensitivity, ease of production, simple operations, excellent specificity, better stability, low immunogenicity, and cost-effectiveness. The nucleic acid aptamers in conjugation with nanomaterials can bind to the metal ions with good specificity/selectivity and can be used for on-site monitoring of metal ion residues. This review aimed to provide background information about nanomaterials-based aptasensor, recent advancements in aptamer conjunction on nanomaterials surface, the role of nanomaterials in improving signal transduction, recent progress of nanomaterials-based aptasening procedures (from 2010 to 2022), and future perspectives toward the practical applications of nanomaterials-based aptasensors against hazardous metal ions for food safety and environmental monitoring.

Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter

Transcription initiation is the first step in gene expression, and is therefore strongly regulated in all domains of life. The RNA polymerase (RNAP) first associates with the initiation factor \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sigma$\end{document} to form a holoenzyme, which binds, bends and opens the promoter in a succession of reversible states. These states are critical for transcription regulation, but remain poorly understood. Here, we addressed the mechanism of open complex formation by monitoring its assembly/disassembly kinetics on individual consensus lacUV5 promoters using high-throughput single-molecule magnetic tweezers. We probed the key protein–DNA interactions governing the open-complex formation and dissociation pathway by modulating the dynamics at different concentrations of monovalent salts and varying temperatures. Consistent with ensemble studies, we observed that RNAP-promoter open (RP_O) complex is a stable, slowly reversible state that is preceded by a kinetically significant open intermediate (RP_I), from which the holoenzyme dissociates. A strong anion concentration and type dependence indicates that the RP_O stabilization may involve sequence-independent interactions between the DNA and the holoenzyme, driven by a non-Coulombic effect consistent with the non-template DNA strand interacting with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sigma$\end{document} and the RNAP \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\beta$\end{document} subunit. The temperature dependence provides the energy scale of open-complex formation and further supports the existence of additional intermediates.