DNA melting and energetics of the double helix

Organic Modulators Enable Morphological Diversity in Colloidal Crystals Engineered with DNA

Colloidal crystal engineering with DNA is a powerful way of generating a wide variety of crystals spanning over 90 different symmetries. However, in many cases, crystals with well-defined habits are difficult, if not impossible, to make, in part due to rapid crystal defect formation and propagation. This is especially true in the case of face-centered cubic (FCC) structures. Herein, we report a strategy that uses formamide as a chemical modulator to slow down colloidal crystal growth, which decreases defect formation and yields higher-quality crystals. Formamide forms hydrogen bonds with DNA bases and destabilizes the DNA duplex; in the context of colloidal crystallization, formamide leads to the disassembly of undercoordinated particles (defect architectures) and facilitates their reassembly into structures with the maximum number of nearest-neighbor contacts and DNA bonds. When targeting an FCC lattice comprised of DNA-modified spherical 20 nm particles, formamide promotes the formation of its Wulff polyhedron (a truncated octahedron), never observed before in colloidal crystal engineering with DNA. Importantly, kinetic habits, including tetrahedra, octahedra, icosahedra, and decahedra, are also observed depending on formamide concentration.

Force-induced melting and S-DNA pathways for DNA overstretching exhibit distinct kinetics

It is widely appreciated that double stranded DNA (dsDNA) is subjected to strong and dynamic mechanical forces in cells. Under increasing tension B-DNA, the most stable double-stranded (ds) form of DNA, undergoes cooperative elongation into a mixture of S-DNA and single stranded DNA (ssDNA). Despite significant effort, the structure, energetics, kinetics and the biological role of S-DNA remains obscure. We here stretch 60 base pair (bp) dsDNA oligonucleotides with a variable number of tricyclic cytosine, tC, modifications using optical tweezers. We observe multiple fast cooperative and reversible two-state transitions between B-DNA and S-DNA. Notably, tC modifications increase the transition force, while reducing the transition extension and free energy due to progressively increasing fraying of the dsDNA ends. We quantify the average number of bps undergoing the B-to-S transition, as well as the free energies and rates. This allows us to reconstruct the B-to-S free energy profiles in absence of force. We conclude that S-DNA is an entirely force-induced state, and that the B-to-S transition is much faster than internal dsDNA melting. We hypothesize that S-DNA may have a role as a transient intermediate in, for example, molecular motor-induced local dsDNA strand separation.

Influence of Cu L-Histidinate Schiff Base Derivatives on Structural Features of Irradiated Rat's DNA

A study of rats liver DNA damages under the influence of X-ray radiation at a dose of 6.5 Gy(LD60) was carried out. The radioprotective properties of newly synthesized Cu(II) L-Schiff Histidinate complexes were also studied. The survival of rats was determined over a 30-day period after exposure to X-rays without pretreatment and also after preadministration of Cu(II) L-Histidinate-Schiff base complexes. The structural defects of rat's liver DNA were detected at 3, 7, 14, and 30 days post-irradiation extracted. The results obtained revealed that irradiation with a 6.5Gy dose in the control group degraded the characteristics of rat liver DNA in comparison to healthy DNA. On all investigated experimental days, a decrease in the melting temperature (Tm), a widening of the melting interval (ΔT), and a decrease in hypochromicity (Δh) were observed in the DNA samples of irradiated animals compared to the norm. The rat's pretreatment by Cu(II) L-Histidinate complexes 1 or 24 hours prior to irradiation improved DNA characteristics. Electrophoretic studies of DNA were in good agreement with the melting data. Based on the study results, it can be concluded that Cu(II) L-Histidinate complexes exhibit radioprotective properties under the studied conditions and can protect DNA from damage.

Selective Formation of Pd-DNA Hybrids Using Tailored Palladium-Mediated Base Pairs: Towards Heteroleptic Pd-DNA Systems

The formation of highly organized metal-DNA structures has significant implications in bioinorganic chemistry, molecular biology and material science due to their unique properties and potential applications. In this study, we report on the conversion of single-stranded polydeoxycytidine (dC15 ) into a Pd-DNA supramolecular structure using the [Pd(Aqa)] complex (Aqa=8-amino-4-hydroxyquinoline-2-carboxylic acid) through a self-assembly process. The resulting Pd-DNA assembly closely resembles a natural double helix, with continuous [Pd(Aqa)(C)] (C=cytosine) units serving as palladium-mediated base pairs, forming interbase hydrogen bonds and intrastrand stacking interactions. Notably, the design of the [Pd(Aqa)] complex favours the interaction with cytosine, distinguishing it from our previously reported [Pd(Cheld)] complex (Cheld=chelidamic acid). This finding opens possibilities for creating heteroleptic Pd-DNA hybrids where different complexes specifically bind to nucleobases. We confirmed the Pd-DNA supramolecular structural assembly and selective binding of the complexes using NMR spectroscopy, circular dichroism, mass spectrometry, isothermal titration calorimetry, and DFT calculations.

Theranostic DNA nanostructure based on phenotype-specific activation of antisense oligonucleotides

Antisense oligonucleotide (ASO) is a powerful agent for gene therapy, designed to form complementary pairs with specific mRNA to inhibit gene expression. However, low specificity limits its potential. To overcome this challenge, we developed a Y-shape DNA nanostructure that enhances the specificity in ASO-based treatment by introducing a detection trigger. The design incorporates the phenotype-specific miR21 activation and the sequential release of Bcl2 ASO. As a result, our Y-shape DNA nanostructure downregulates >50 % Bcl2 mRNA expression and induces >60 % cell death in breast cancer cells. Meanwhile, this approach shows no obvious damage to the non-cancerous cells, indicating the therapeutic potential as a theranostics agent in precision medicine with the combination of biomarker sensing and treatment. Overall, our Y-shape DNA nanostructure serves as a promising strategy providing potential in customized conformation design with specific target sequences in gene therapy.

Accumulation and Stretching of DNA Molecules in Temperature-Induced Concentration Gradients

Temperature fields provide a noninvasive approach for manipulating individual macromolecules in solution. Utilizing thermophoresis and other secondary effects resulting from the inhomogeneous distribution of crowding agents, one may gain valuable insights into the interactions of molecular mixtures. In this report, we examine the steady-state concentration distribution and dynamics of DNA molecules in a poly(ethylene glycol) (PEG)/water solution when exposed to localized temperature gradients generated by optical heating of a thin chrome layer at a liquid-solid boundary. This allowed us to experimentally investigate the interplay between DNA thermophoresis and PEG-induced entropic depletion effects. Our quantitative analysis demonstrates that the depletion effects dominate over DNA thermophoresis, causing the DNA polymers to migrate toward the heat source. Additionally, we explore the transient stretching of individual DNA molecules in thermally induced PEG gradients and estimate the contributing forces.

Equilibrium melting probabilities of a DNA molecule with a defect: An exact solution of the Poland-Scheraga model

In this study we derive analytically the equilibrium melting probabilities for basepairs of a DNA molecule with a defect site. We assume that the defect is characterized by a change in the Watson-Crick basepair energy of the defect basepair, and in the associated two stacking energies for the defect, as compared to the remaining parts of the DNA. The defect site could, for instance, occur due to DNA basepair mismatching, cross-linking, or by the chemical modifications when attaching fluorescent labels, such as fluorescent-quencher pairs, to DNA. Our exact solution of the Poland-Scheraga model for DNA melting provides the probability that the labeled basepair, and its neighbors, are open at different temperatures. Our work is of direct importance, for instance, for studies where fluorophore-quencher pairs are used for studying single basepair fluctuations of designed DNA molecules.

Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome

Long human ultra-conserved non-coding elements (UCNEs) do not have any sequence similarity to each other or other characteristics that make them unalterable during vertebrate evolution. We hypothesized that UCNEs have unique dinucleotide (DN) composition and arrangements compared to the rest of the genome. A total of 4272 human UCNE sequences were analyzed computationally and compared with the whole genomes of human, chicken, zebrafish, and fly. Statistical analysis was performed to assess the non-randomness in DN spacing arrangements within the entire human genome and within UCNEs. Significant non-randomness in DN spacing arrangements was observed in the entire human genome. Additionally, UCNEs exhibited distinct patterns in DN arrangements compared to the rest of the genome. Approximately 83% of all DN pairs within UCNEs showed significant (>10%) non-random genomic arrangements at short distances (2-6 nucleotides) relative to each other. At the extremes, non-randomness in DN spacing distances deviated up to 40% from expected values and were frequently associated with GpC, CpG, ApT, and GpG/CpC dinucleotides. The described peculiarities in DN arrangements have persisted for hundreds of millions of years in vertebrates. These distinctive patterns may suggest that UCNEs have specific DNA conformations.

Planar Chirality for Acid/Base Responsive Macrocyclic Pillararenes Induced by Amino Acid Derivatives: Molecular Dynamics Simulations and Machine Learning

Chirality is ubiquitous in nature, ranging from a DNA helix to a biological macromolecule, snail's shell, and even a galaxy. However, the precise control of chirality at the nanoscale is a challenge due to the structure complexity of supramolecular assemblies, the small energy differences between different enantiomers, and the difficulty in obtaining polymorphic crystals. The planar chirality of water-soluble pillar[5]arenes (called WP5-Na with Na ions in the side chain) host triggered by the addition of chiral L-amino acid hydrochloride (L-AA-OEt) guests and acid/base is rationalized by the relative stability of different chiral isomers, being estimated by molecular dynamics (MD) simulations and quantum chemical calculations. As an increase in the pH value, the change from a positive to a negative value of the free energy difference (ΔG) between two conformations, pR-WP5-Na⊃L-AA-OEt and pS-WP5-Na⊃L-AA-OEt, suggests an inversed preference of the pS-WP5-Na conformer induced by the deprotonated L-arginine ethyl ester (L-Arg-OEt) at pH = 14, which is supported by the circular dichroism (CD) experiments. On the basis of 2256 WP5-Na⊃L-Ala-OEt and 3299 WP5-Na⊃L-Arg-OEt conformers sampled from MD, the gradient boosting regression (GBR) model exhibits a satisfactory performance (R² = 0.91) in predicting the chirality of WP5-Na complexations using host-guest binding descriptors, including the geometry matching and binding sites and modes (electrostatics and hydrogen bonding). The machine learning model also performs well on external tests of different hosts (using different side chains and cavity sizes) with the addition of 22 other different guests, with the average chirality prediction accuracy of ML versus experimental CD determinations of 92.8%. The easily accessible host-guest features, binding position coordination and size matching between the cavity and guest, exhibit a close correlation to the chirality of different macrocyclic molecules, water-soluble pillar[6]arenes (WP6) versus WP5, in complexation with different amino acid guests. The exploration of efficient host-guest features in ML displays the great potential of building a large space of various assembled systems and accelerating the on-demand design of chiral supramolecular systems at the nanoscale.

Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments

Understanding of the pairing statistics in solutions populated by a large number of distinct solute species with mutual interactions is a challenging topic, relevant in modeling the complexity of real biological systems. Here we describe, both experimentally and theoretically, the formation of duplexes in a solution of random-sequence DNA (rsDNA) oligomers of length L = 8, 12, 20 nucleotides. rsDNA solutions are formed by 4^L distinct molecular species, leading to a variety of pairing motifs that depend on sequence complementarity and range from strongly bound, fully paired defectless helices to weakly interacting mismatched duplexes. Experiments and theory coherently combine revealing a hybridization statistics characterized by a prevalence of partially defected duplexes, with a distribution of type and number of pairing errors that depends on temperature. We find that despite the enormous multitude of inter-strand interactions, defectless duplexes are formed, involving a fraction up to 15% of the rsDNA chains at the lowest temperatures. Experiments and theory are limited here to equilibrium conditions.

Several biological processes require that specific partner molecules succeed in binding after negotiating their way through a huge number of interactions with other molecules. How such molecular recognition emerges among millions distinct molecular species is an open problem. We have studied, both experimentally and theoretically, such process of “molecular recognition” in pools of highly diverse random DNA oligomers, which binds preferentially, but not exclusively, to its perfect complementary sequence. We find a complex behavior, in which some perfect pairing takes place with a non-trivial temperature dependence that we understand thorough statistical mechanics modelling. The pairing pattern of short random DNA is relevant in the context of the origin of life since the so-called “RNA World” was most probably based on the mutual recognition of random chains.

Photoswitchable architecture transformation of a DNA-hybrid assembly at the microscopic and macroscopic scale

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks. Oligonucleotide-based nanotechnology and soft-materials benefit from the high information storage density, self-correction, and memory function of DNA. Here we control these beneficial properties with light in a photoresponsive biohybrid hydrogel, adding an extra level of function to the system. An ssDNA template was combined with a complementary photo-responsive unit to reversibly switch between various functional states of the supramolecular assembly using a combination of light and heat. We studied the structural response of the hydrogel at both the microscopic and macroscopic scale using a combination of UV-vis absorption and CD spectroscopy, as well as fluorescence, transmission electron, and atomic force microscopy. The hydrogels grown from these supramolecular self-assembly systems show remarkable shape-memory properties and imprinting shape-behavior while the macroscopic shape of the materials obtained can be further manipulated by irradiation.

Needles in Haystacks: Understanding the Success of Selective Pairing of Nucleic Acids

The effectiveness of several biological and biotechnological processes relies on the remarkably selective pairing of nucleic acids in contexts of molecular complexity. Relevant examples are the on-target binding of primers in genomic PCR and the regulatory efficacy of microRNA via binding on the transcriptome. Here, we propose a statistical framework that enables us to describe and understand such selectivity by means of a model that is extremely cheap from a computational point of view. By re-parametrizing the hybridization thermodynamics on three classes of base pairing errors, we find a convenient way to obtain the free energy of pairwise interactions between nucleic acids. We thus evaluate the hybridization statistics of a given oligonucleotide within a large number of competitive sites that we assume to be random, and we compute the probability of on-target binding. We apply our strategy to PCR amplification and microRNA-based gene regulation, shedding new light on their selectivity. In particular, we show the relevance of the defectless pairing of 3′ terminals imposed by the polymerase in PCR selection. We also evaluate the selectivity afforded by the microRNA seed region, thus quantifying the extra contributions given by mechanisms beyond pairing statistics.

B-DNA Structure and Stability: The Role of Nucleotide Composition and Order

We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.

Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex

Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson-Crick base pairing - consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.

A molecular view of DNA flexibility

DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general 'rules' that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.

Natural DNA Intercalators as Promising Therapeutics for Cancer and Infectious Diseases

Cancer and infectious diseases are one of the greatest challenges of modern medicine. An unhealthy lifestyle, the improper use of drugs, or their abuse are conducive to the increase of morbidity and mortality caused by these diseases. The imperfections of drugs currently used in therapy for these diseases and the increasing problem of drug resistance have forced a search for new substances with therapeutic potential. Throughout history, plants, animals, fungi and microorganisms have been rich sources of biologically active compounds. Even today, despite the development of chemistry and the introduction of many synthetic chemotherapeutics, a substantial part of the new compounds being tested for treatment are still of natural origin. Natural compounds exhibit a great diversity of chemical structures, and thus possess diverse mechanisms of action and molecular targets. Nucleic acids seem to be a good molecular target for substances with anticancer potential in particular, but they may also be a target for antimicrobial compounds. There are many types of interactions of small-molecule ligands with DNA. This publication focuses on the intercalation process. Intercalators are compounds that usually have planar aromatic moieties and can insert themselves between adjacent base pairs in the DNA helix. These types of interactions change the structure of DNA, leading to various types of disorders in the functioning of cells and the cell cycle. This article presents the most promising intercalators of natural origin, which have aroused interest in recent years due to their therapeutic potential.

Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.

Nucleotide spacing distribution analysis for human genome

The distribution of nucleotides spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution has no self-similar (fractal) structure. The results nevertheless revealed several characteristic features: (i) the distribution for short-range spacing is quite similar to the purely stochastic sequences; (ii) the distribution for long-range spacing essentially deviates from the random sequence distribution, showing strong long-range correlations; (iii) the differences between (A, T) and (C, G) nucleotides are quite significant; (iv) the spacing distribution displays tiny oscillations.

pH-dependent sedimentation of DNA in the presence of divalent, but not monovalent, metal ions

Precipitation of DNA is performed frequently in molecular biology laboratories for the purpose of purification and concentration of samples and also for transfer of DNA into cells. Metal ions are used to facilitate these processes, though their precise functions are not well characterized. In the current study we have investigated the precipitation of double-stranded DNA by group 1 and group 2 metal ions. Double-stranded DNAs were not sedimented efficiently by metals alone, even at high concentrations. Increasing the pH to 11 or higher caused strong DNA precipitation in the presence of the divalent group 2 metals magnesium, calcium, strontium and barium, but not group 1 metals. Group 2 sedimentation profiles were distinctly different from that of the transition metal zinc, which caused precipitation at pH 8. Analysis of DNAs recovered from precipitates formed with calcium revealed that structural integrity was retained and that sedimentation efficiency was largely size-independent above 400 bp. Several tests supported a model whereby single-stranded DNA regions formed by denaturation at high pH became bound by the divalent metal cations. Neutralization of negative surface charges reduced the repulsive forces between molecules, leading to formation of insoluble aggregates that could be further stabilized by cation bridging (ionic crosslinking).

Hydrophobic interactions control the self-assembly of DNA and cellulose

Desoxyribosenucleic acid, DNA, and cellulose molecules self-assemble in aqueous systems. This aggregation is the basis of the important functions of these biological macromolecules. Both DNA and cellulose have significant polar and nonpolar parts and there is a delicate balance between hydrophilic and hydrophobic interactions. The hydrophilic interactions related to net charges have been thoroughly studied and are well understood. On the other hand, the detailed roles of hydrogen bonding and hydrophobic interactions have remained controversial. It is found that the contributions of hydrophobic interactions in driving important processes, like the double-helix formation of DNA and the aqueous dissolution of cellulose, are dominating whereas the net contribution from hydrogen bonding is small. In reviewing the roles of different interactions for DNA and cellulose it is useful to compare with the self-assembly features of surfactants, the simplest case of amphiphilic molecules. Pertinent information on the amphiphilic character of cellulose and DNA can be obtained from the association with surfactants, as well as on modifying the hydrophobic interactions by additives.

Dynamics of K+ counterions around DNA double helix in the external electric field: A molecular dynamics study

The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study was performed for the system of DNA double helix with neutralizing K⁺ counterions and for the system of KCl salt solution in an external electric field of different strength (up to 32mV/Å). The analysis of ionic conductivities of these systems has shown that the counterions around the DNA double helix are slowed down compared with the KCl salt solution. The calculated values of ion mobility are within (0.05-0.4)mS/cm depending on the orientation of the external electric field relatively to the double helix. Under the electric field parallel to the macromolecule K⁺ counterions move along the grooves of the double helix staying longer in the places with narrower minor groove. Under the electric field perpendicular to the macromolecule the dynamics of counterions is less affected by DNA atoms, and starting with the electric field values about 30mV/Å the double helix undergoes a phase transition from a double-stranded to a single-strand state.

Base-Pairing and Base-Stacking Contributions to Double-Stranded DNA Formation

Double-stranded (ds)DNA formation and dissociation are of fundamental biological importance. The negative DNA charge influences the dsDNA stability. However, the base pairing and the stacking between neighboring bases are responsible for the sequence-dependent stability of dsDNA. The stability of a dsDNA molecule can be estimated from empirical nearest-neighbor models based on contributions assigned to base-pair steps along the DNA and additional parameters because of DNA termini. In efforts to separate contributions, it has been concluded that base stacking dominates dsDNA stability, whereas base pairing contributes negligibly. Using a different model for dsDNA formation, we reanalyze dsDNA stability contributions and conclude that base stacking contributes already at the level of separate ssDNAs but that pairing contributions drive the dsDNA formation. The theoretical model also predicts that stability contributions of base-pair steps that contain only guanine/cytosine, mixed steps, and steps with only adenine/thymine follow the order 6:5:4, respectively, as expected based on the formed hydrogen bonds. The model is fully consistent with the available stacking data and the nearest-neighbor dsDNA parameters. It allows assigning a narrowly distributed value for the effective free energy contribution per formed hydrogen bond during dsDNA formation of -0.72 kcal·mol^-1 based entirely on the experimental data.

Solid-Phase Synthesis of Sequence-Defined Informational Oligomers

Genetic biopolymers utilize defined sequences and monomer-specific molecular recognition to store and transfer information. Synthetic polymers that mimic these attributes using reversible covalent chemistry for base-pairing pose unique synthetic challenges. Here, we describe a solid-phase synthesis methodology for the efficient construction of ethynyl benzene oligomers with specific sequences of aniline and benzaldehyde subunits. Handling these oligomers is complicated by the fact that they often exhibit multiple conformations because of intra- or intermolecular pairing. We describe conditions that allow the dynamic behavior of these oligomers to be controlled so that they may be manipulated and characterized without needing to mask the recognition units with protecting groups.

Analysis and uncertainty quantification of DNA fluorescence melt data: Applications of affine transformations

Fluorescence-based measurements are a standard tool for characterizing the thermodynamic properties of DNA systems. Nonetheless, experimental melt data obtained from polymerase chain-reaction (PCR) machines (for example) often leads to signals that vary significantly between datasets. In many cases, this lack of reproducibility has led to difficulties in analyzing results and computing reasonable uncertainty estimates. To address this problem, we propose a data analysis procedure based on constrained, convex optimization of affine transformations, which can determine when and how melt curves collapse onto one another. A key aspect of this approach is its ability to provide a reproducible and more objective measure of whether a collection of datasets yields a consistent "universal" signal according to an appropriate model of the raw signals. Importantly, integrating this validation step into the analysis hardens the measurement protocol by allowing one to identify experimental conditions and/or modeling assumptions that may corrupt a measurement. Moreover, this robustness facilitates extraction of thermodynamic information at no additional cost in experimental time. We illustrate and test our approach on experiments of Förster resonance energy transfer (FRET) pairs used study the thermodynamics of DNA loops.

Melting of DNA in confined geometries

The stability of DNA molecules during viral or biotechnological encapsulation is a topic of active current research. We studied the thermal stability of double-stranded DNA molecules of different lengths in a confined space. Using a statistical model, we evaluate the melting profile of DNA molecules in two geometries: conical and cylindrical. Our results show that not only the confinement, but also the geometry of the confined space plays a prominent role in the stability and opening of the DNA duplex. We find that for more confined spaces, cylindrical confinement stabilizes the DNA, but for less confined spaces conical geometry stabilizes the DNA overall. We also analyse the interaction between DNA sequence and stability, and the evenness with which strand separation occurs. Cylindrical and conical geometries enable a better controlled tuning of the stability of DNA encapsulation and the efficiency of its eventual release, compared to spherical or quasi-spherical geometries.

Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA

In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between nitrogenous base pairs on occurrence and open states zones dynamics is investigated. These processes are studied using mathematical modeling, taking into account the number of open states between base pairs. The calculations of the probability of occurrence of open states in different parts of the gene were done depending on the localization of the deuterium atom. The mathematical modeling study demonstrated significant inequality (dependent on single 2H/1H replacement in DNA) among three parts of the gene similar in length of the frequency of occurrence of the open states. In this paper, the new convenient approach of the analysis of the abnormal frequency of open states in different parts of the gene encoding interferon alpha 17 was presented, which took into account both rising and decreasing of them that allowed to make a prediction of the functional instability of the specific DNA regions. One advantage of the new algorithm is diminishing the number of both false positive and false negative results in data filtered by this approach compared to the pure fractile methods, such as deciles or quartiles.

Discrimination between G/C Binding Sites by Olivomycin A Is Determined by Kinetics of the Drug-DNA Interaction

Olivomycin A (OA) exerts its cytotoxic potency due to binding to the minor groove of the G/C-rich DNA and interfering with replication and transcription. Screening of the complete set of tetranucleotide G/C sites by electrophoretic mobility gel shift assay (EMSA) revealed that the sites containing central GC or GG dinucleotides were able to bind OA, whereas the sites with the central CG dinucleotide were not. However, studies of equilibrium OA binding in solution by fluorescence, circular dichroism and isothermal titration calorimetry failed to confirm the sequence preference of OA, indicating instead a similar type of complex and comparable affinity of OA to all G/C binding sites. This discrepancy was resolved by kinetics analysis of the drug–DNA interaction: the dissociation rate significantly differed between SGCS, SGGS and SCGS sites (S stands for G or C), thereby explaining the disintegration of the complexes during EMSA. The functional relevance of the revealed differential kinetics of OA–DNA interaction was demonstrated in an in vitro transcription assay. These findings emphasize the crucial role of kinetics in the mechanism of OA action and provide an important approach to the screening of new drug candidates.

Forster resonance energy transfer for studying nucleic acids denaturation: A chemical and biological sciences laboratory experiment

The Förster resonance energy transfer (FRET) melting assay intends to evaluate the unfolding, denaturation process of DNA secondary structures, and its stabilization using compounds known as DNA binders, some of which are highly specific for G-quadruplex DNAs versus duplex DNAs. First, students determined the melting temperature (T_m ) of DNA sequences double labeled with 5'-FAM (fluorescein) and 3'-TAMRA (tetramethylrhodamine) in the absence of DNA binders. Second, they determined the melting temperature of the DNAs in the presence of DNA binders by monitoring fluorescence. After completing this experiment, students understood that this method allows a semiquantitative analysis to test a variety of DNA binders against DNA secondary structures, and it can be used to rapidly identify the most promising drug candidates in the drug development stages at the basic research level.

Heat Capacity Changes (ΔCp) for Interconversions between Differentially-Ordered DNA States within Physiological Temperature Domains: Implications for Biological Regulatory Switches

Knowledge of differences in heat capacity changes (ΔC_p) between biopolymer states provides essential information about the temperature dependence of the thermodynamic properties of these states, while also revealing insights into the nature of the forces that drive the formation of functional and dysfunctional biopolymer "order." In contrast to proteins, for nucleic acids there is a dearth of direct experimental determination of this information-rich parameter, a deficiency that compromises interpretations of the ever-increasing thermodynamic analyses of nucleic acid properties; particularly as they relate to differential nucleic acid (meta)stability states and their potential biological functions. Here we demonstrate that such heat capacity differences, in fact, exist not only between traditionally measured native to fully unfolded (assumed "random coil") DNA states, but also between competing order-to-order transformations. We illustrate the experimental approach by measuring the heat capacity change between "native"/ordered, sequence homologous, "isomeric" DNA states that differ in conformation but not sequence. Importantly, these heat capacity differences occur within biologically relevant temperature ranges. In short, we describe a new and general method to measure the value of such heat capacity differences anywhere in experimentally accessible conformational and temperature space; in this case, between two metastable bulge loop states, implicated in DNA expansion diseases, and their competing, fully paired, thermodynamically more stable duplex states. This measurement reveals a ΔC_p of 61 ± 7 cal mol_bp ^-1 K ^-1. Such heat capacity differences between competing DNA "native" ensemble states must be considered when evaluating equilibria between different DNA "ordered" conformations, including the assessment of the differential stabilizing forces and potential biological functions of competing DNA "structured" motifs.

Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility

Hybridization chain reaction (HCR) was a significant discovery for the development of nanoscale materials and devices. One key challenge for HCR is the vulnerability to background leakage in the absence of the initiator. Here, we systematically analyze the sources of leakage and refine leak-resistant rule by using molecular thermodynamics and dynamics, biochemical and biophysical methods. Transient melting of DNA hairpin is revealed to be the underlying cause of leakage and that this can be mitigated through careful consideration of the sequence thermodynamics. The transition threshold of the energy barrier is proposed as a testing benchmark of leak-resistance DNA hairpins. The universal design of DNA hairpins is illustrated by the analysis of hsa-miR-21-5p as biomarker when used in conjunction with surface-enhanced Raman spectroscopy. We further extend the strategy for specific signal amplification of miRNA homologs. Significantly, it possibly provides a practical route to improve the accuracy of DNA self-assembly for signal amplification, and that could facilitate the development of sensors for the sensitive detection of interest molecules in biotechnology and clinical medicine.

Pillararene Host-Guest Complexation Induced Chirality Amplification: A New Way to Detect Cryptochiral Compounds

The contradiction between the rising demands of optical chirality sensing and the failure in chiral detection of cryptochiral compounds encourages researchers to find new methods for chirality amplification. Inspired by planar chirality and the host-guest recognition of pillararenes, we establish a new concept for amplifying CD signals of cryptochiral molecules by pillararene host-guest complexation induced chirality amplification. The planar chirality of pillararenes is induced and stabilized in the presence of the chiral guest, which makes the cryptochiral molecule detectable by CD spectroscopy. Several chiral guests are selected in these experiments and the mechanism of chiral amplification is studied with a non-rotatable pillararene derivative and density functional theory calculations. We believe this work affords deeper understanding of chirality and provides a new perspective for chiral sensing.

Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells

This review provides the biophysicochemical background and recent advances in stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells.

Assessment of DNA Susceptibility to Denaturation as a Marker of Chromatin Structure

The susceptibility of DNA in situ to denaturation is modulated by its interactions with histone and nonhistone proteins, as well as with other chromatin components related to the maintenance of the 3D nuclear structure. Measurement of DNA proclivity to denature by cytometry provides insight into chromatin structure and thus can be used to recognize cells in different phases of the cell cycle, including mitosis, quiescence (G₀ ), and apoptosis, as well as to identify the effects of drugs that modify chromatin structure. Particularly useful is the method's ability to detect chromatin changes in sperm cells related to DNA fragmentation and infertility. This article presents a flow cytometric procedure for assessing DNA denaturation based on application of the metachromatic property of acridine orange (AO) to differentially stain single- versus double-stranded DNA. This approach circumvents limitations of biochemical methods of examining DNA denaturation, in particular the fact that the latter destroy higher orders of chromatin structure and that, being applied to bulk cell populations, they cannot detect heterogeneity of individual cells. Because the metachromatic properties of AO have also found application in other cytometric procedures, such as differential staining of RNA versus DNA and assessment of lysosomal proton pump including autophagy, to avert confusion between these approaches and the use of this dye in the DNA denaturation assay, these AO applications are briefly outlined in this unit as well. © 2019 by John Wiley & Sons, Inc. Basic Protocol: Differential staining of single- versus double-stranded DNA with acridine orange.

Determination of nucleobase-pairing free energies from rotamer equilibria of 2-(methylamino)pyrimidines

A fast straightforward method for the determination of free energies of modified nucleobase pairing is proposed. The method is based on the nuclear magnetic resonance (NMR) spectroscopy monitoring of conformational changes of 2-(methylamino)-pyrimidines upon intermolecular binding.

Analysis of the reannealing- instead of melting-curve in the detection of JAK2 V617F mutation by HRM method

BACKGROUND

The Janus kinase 2 (JAK2) has an important role in the intracellular signaling in normal and neoplastic cells. JAK2 mutation, called JAK2 V617F, is frequently found in Philadelphia chromosome-negative myeloproliferative neoplasms. We aimed to assess the analytical efficiency of high-resolution melting (HRM) method using reannealing-curve analysis in comparison with routine melting-curve analysis for JAK2 V617F mutation detection.

METHOD

Twenty-three samples including one negative synthetic standard DNA, two 50% and 75% positive synthetic standard DNA samples, five wild-type samples and 15 samples positive for JAK2 V617F were examined by HRM. Melting and reannealing stages were performed, and then, raw and normalized curves were compared between the two stages.

RESULTS

In melting-curve analysis, the wild-type and mutant samples had different melting temperatures (75/53°C and 75/10°C, respectively). In normalized curves corresponding to reannealing method, mutant samples were better separated from the baseline than in melting method as well as for samples with different mutant DNA burden from each other. Furthermore, wild-type samples were more homogenous in the normalized curves corresponding to reannealing than in melting method. This means that patients with a low allelic burden may be wrongly interpreted as normal in the common melting method.

CONCLUSION

We suggest the use of reannealing instead of the melting-curve analysis for the detection of sequence variations, especially for large-scale mutation and allele burden measurement in clinical settings. However, more evaluations with more sample size will better improve the benefits of reannealing-curve analysis in research and clinic.

Nanomechanics of Diaminopurine-Substituted DNA

2,6-diaminopurine (DAP) is a nucleobase analog of adenine. When incorporated into double-stranded DNA (dsDNA), it forms three hydrogen bonds with thymine. Rare in nature, DAP substitution alters the physical characteristics of a DNA molecule without sacrificing sequence specificity. Here, we show that in addition to stabilizing double-strand hybridization, DAP substitution also changes the mechanical and conformational properties of dsDNA. Thermal melting experiments reveal that DAP substitution raises melting temperatures without diminishing sequence-dependent effects. Using a combination of atomic force microscopy (AFM), magnetic tweezer (MT) nanomechanical assays, and circular dichroism spectroscopy, we demonstrate that DAP substitution increases the flexural rigidity of dsDNA yet also facilitates conformational shifts, which manifest as changes in molecule length. DAP substitution increases both the static and dynamic persistence length of DNA (measured by AFM and MT, respectively). In the static case (AFM), in which tension is not applied to the molecule, the contour length of DAP-DNA appears shorter than wild-type (WT)-DNA; under tension (MT), they have similar dynamic contour lengths. At tensions above 60 pN, WT-DNA undergoes characteristic overstretching because of strand separation (tension-induced melting) and spontaneous adoption of a conformation termed S-DNA. Cyclic overstretching and relaxation of WT-DNA at near-zero loading rates typically yields hysteresis, indicative of tension-induced melting; conversely, cyclic stretching of DAP-DNA showed little or no hysteresis, consistent with the adoption of the S-form, similar to what has been reported for GC-rich sequences. However, DAP-DNA overstretching is distinct from GC-rich overstretching in that it happens at a significantly lower tension. In physiological salt conditions, evenly mixed AT/GC DNA typically overstretches around 60 pN. GC-rich sequences overstretch at similar if not slightly higher tensions. Here, we show that DAP-DNA overstretches at 52 pN. In summary, DAP substitution decreases the overall stability of the B-form double helix, biasing toward non-B-form DNA helix conformations at zero tension and facilitating the B-to-S transition at high tension.

Aflatoxin B₁⁻Formamidopyrimidine DNA Adducts: Relationships between Structures, Free Energies, and Melting Temperatures

Thermal stabilities of DNA duplexes containing Gua (g), α- (a) or β-anomer of formamidopyrimidine-N7-9-hydroxy-aflatoxin B₁ (b) differ markedly (T_m: a<g<b), but the underlying molecular origin of this experimentally observed phenomenon is yet to be identified and determined. Here, by employing explicit-solvent molecular dynamics simulations coupled with free-energy calculations using a combined linear-interaction-energy/linear-response-approximation approach, we explain the quantitative differences in Tm in terms of three structural features (bulkiness, order, and compactness) and three energetical contributions (non-polar, electrostatic, and preorganized-electrostatic), and thus advance the current understanding of the relationships between structures, free energies, and thermal stabilities of DNA double helices.