Double-stranded DNA Chains Research Articles

Structural and Mechanical Characterization of DNA-Tethered Membranes on Graphene.

Lipid membranes that are separated from the surface of graphene by DNA tethers were prepared by surface functionalization with pyrene coupled to single-stranded DNA (ssDNA), followed by self-assembly of the mixture of ssDNA-functionalized phospholipid and the matrix phospholipids. The formation of uniform membranes was confirmed by fluorescence microscopy, and the structures of the systems before and after hybridization in the direction perpendicular to the global plane of the membranes were investigated using high-energy X-ray reflectivity. The thickness values of the DNA spacers (15 and 37 bp) calculated from the best-fit results were less than the expected thicknesses of the double-stranded DNA (dsDNA) chains taking the upright conformation, indicating that the DNA spacers are tilted with respect to the direction normal to the surface. The Young's moduli of the DNA-tethered membranes obtained by AFM nanoindentation showed higher values than the membranes with no DNA tethers, which suggests that the DNA layer resists against the compression, lifting up the membrane. Intriguingly, the presence of DNA tethers caused no increase in the yield depth. The smaller thickness values as well as the unchanged yield depth suggest that the dsDNA chains can tilt and rotate, which can be attributed to the flexible pyrene-DNA junction.

Programmable all-DNA hydrogels based on rolling circle and multiprimed chain amplification products.

Soft, biocompatible, and tunable materials offer biomedical engineers and material scientists programmable matrices for a variety of biomedical applications. In this regard, DNA hydrogels have emerged as highly promising biomaterials that offer programmable self-assembly, superior biocompatibility, and the presence of specific molecular identifiable structures. Many types of DNA hydrogels have been developed, yet the programmability of the DNA building blocks has not been fully exploited, and further efforts must be directed toward understanding how to finely tune their properties in a predictable manner. Herein, we develop physically crosslinked all-DNA hydrogels with tunable morphology and controllable biodegradation, based on rolling circle amplification and multiprimed chain amplification products. Through molecular engineering of the DNA sequences and their nano-/microscale architectures, the precursors self-assemble in a controlled manner to produce soft hydrogels in an efficient, cost-effective, and highly tunable manner. Notably, we develop a novel DNA microladder architecture that serves as a framework for modulating the hydrogel properties, including over an order of magnitude change in pore size and up to 50% change in biodegradation rate. Overall, we demonstrate how the properties of this DNA-based biomaterial can be tuned by modulating the amounts of rigid double-stranded DNA chains compared to flexible single-stranded DNA chains, as well as through the precursor architecture. Ultimately, this work opens new avenues for the development of programmable and biodegradable soft materials in which DNA functions not only as a store of genetic information but also as a versatile polymeric biomaterial and molecularly engineered macroscale scaffold.

Insight into the Sensing Behavior of DNA Probes Based on MOF-Nucleic Acid Interaction for Bioanalysis.

Adsorption of DNA probes onto nanomaterials is a promising strategy for bioassay establishment typically using fluorescence or catalytic activities to generate signals. Albeit important, there is currently a lack of systematic understanding of the sensing behaviors building on nanomaterial-DNA interactions, which greatly limits the rational method design and their subsequent applications. Herein, the issue was investigated by employing multifunctional metal-organic frameworks (MOFs) (FeTCPP⊂UiO-66) as a model that was synthesized via integrating heme-like ligand FeTCPP into commonly used MOFs (UiO-66). Our results demonstrated that the fluorescently labeled DNA adsorbed onto FeTCPP⊂UiO-66 was quenched through photoinduced electron transfer, fluorescence resonance energy transfer, and the internal filtration effect. Among different DNA structures, double-stranded DNA and hybridization chain reaction products largely retained their fluorescence due to desorption and conformational variation, respectively. In addition, ssDNA could maximally inhibit the peroxidase activity of FeTCPP⊂UiO-66, and this inhibition was strongly dependent on the strand length but independent of base composition. On the basis of these discoveries, a fluorescence/colorimetric dual-modal detection was designed against aflatoxin B1 with satisfactory performances obtained to further verify our results. This study provided some new insights into the sensing behaviors based on MOF-DNA interactions, indicating promising applications for rational bioassay design and its performance improvement.

Stability and structural evolution of double-stranded DNA molecules under high pressures: A molecular dynamics study

Conformational changes and stability of interacting double-stranded DNA chains under high hydrostatic pressure in biological systems are striking topics of importance to study several biomolecular phenomena. For example, to unravel the physiological conditions at which life might occur and to ensure the right functionality of the biochemical processes into the cell under extreme thermodynamic conditions. Furthermore, such processes could shed light on the physicochemical properties of the DNA under high confinement and how, through different mechanisms, a virus releases its genome in order to infect a cell and, therefore, to promote the process of viral replication. To achieve a few steps toward this direction, we propose an all-atomistic molecular dynamics approach in the NPT isothermal-isobaric ensemble to account for how the interplay of DNA—DNA interaction, hydrogen bonding, and the hydrostatic pressure modifies both the DNA conformational degrees of freedom and the spatial organization of the DNA chains in the available volume. We consider two interacting double-stranded DNA chains immersed in an explicit aqueous solution, i.e., water and ions. Our preliminary results highlight the role of hydrogen bonding and electrostatic interactions between DNA strands to avoid denaturation and, therefore, to provide mechanical stability for the DNA molecules. However, the structural evolution, whose kinetics depends on the relaxation of the stresses induced by the pressure, indicates that almost in all pressure conditions, the equilibrium configuration corresponds to an alignment of the two double-stranded DNA molecules along their main axis of symmetry; the rearrangement between the two approaching DNA dodecamers does not always correspond to complementary base pairs and becomes a function of the thermodynamic conditions.

Hysteresis loop area scaling exponents in DNA unzipping by a periodic force: A Langevin dynamics simulation study.

Using Langevin dynamics simulations, we study the hysteresis in unzipping of longer double-stranded DNA chains whose ends are subjected to a time-dependent periodic force with frequency ω and amplitude G keeping the other end fixed. We find that the area of the hysteresis loop, A_{loop}, scales as 1/ω at higher frequencies, whereas it scales as (G-G_{c})^{α}ω^{β} with exponents α=1 and β=1.25 in the low-frequency regime. These values are same as the exponents obtained in Monte Carlo simulation studies of a directed self-avoiding walk model of a homopolymer DNA [R. Kapri, Phys. Rev. E 90, 062719 (2014)10.1103/PhysRevE.90.062719], and the block copolymer DNA [R.K. Yadav and R. Kapri, Phys. Rev. E 103, 012413 (2021)2470-004510.1103/PhysRevE.103.012413] on a square lattice, and differs from the values reported earlier using Langevin dynamics simulation studies on a much shorter DNA hairpins.

Signal-off photoelectrochemical biosensing platform based on hybridization chain-doped manganese porphyrin quenching on CdSe signal coupling with cyclic amplification for thrombin detection

A novel signal-off photoelectrochemical (PEC) biosensing platform based on hybridization chain-doped manganese porphyrin quenching on PEC signal of CdSe quantum dots (QDs) coupling with cyclic amplification was developed for thrombin detection. Target thrombin firstly induced DNA enzyme-aided cyclic amplification reaction and produced abundant DNA I. Then DNA I hybridized with capture DNA on the TiO 2 /CdSe QDs modified electrode to form DNA bridge, which triggered a linear chain hybridization reaction with S4 and S5. Numerous manganese porphyrin (MnPP) were doped in the long double-stranded DNA chain, which hindered electron transfer and resulted in obvious decrease of QDs PEC signal, achieving a sensitive detection of thrombin. This PEC biosensor exhibits excellent performance with a wide linear range from 1.0 f. to 100.0 nM and detection limit of 0.331 fM, and the recovery value ranged from 95.5% to 103.5%. The results suggest that this PEC biosensor has high sensitivity and precision, showing great application prospect in microbiological analysis of biomolecules and clinical medicine. • A novel signal-off PEC biosensor based on DNA linear chain-doped MnPP quenching to QDs was reported. • CdSe QDs and TiO 2 complex displayed strong PEC signal. • A large amount of manganese porphyrin doped in linear DNA chain greatly amplified PEC signal change. • DNA S1 and S2 specifically bind to thrombin to form the pliers structure with high selectivity.

Insulator-to-Semiconductor-to-Conductor Phase-Like Transition of DNA Chains.

Using a tight-binding model, we study the transport of charge carriers through DNA molecular wires. In double-stranded DNA chains, according to Chargaff's rules, only Adenine-Thymine (AT) and Cytosine-Guanine (CG) pairs are allowed. In our model, a decimation procedure allows us to represent each pair of bases by a single site with one localized electronic state. We consider chains of different lengths with only AT (CG) sites, and ordered and disordered chains with both types of sites. Disordered chains may include short range correlation. Additionally, hydration is considered in the form of a change of the site energy. We find a conductor-to-semiconductor-to-insulator transition as a function of the three effects taken into account: chain size, intrinsic disorder of CG and AT pairs, and hydration. This model predicts that an appropriate choice of chain size and concentration of AT pairs can be used to tailor the electrical behavior of DNA strands.

A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains.

We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on experimental knotting probabilities of short DNA strands, it reproduces the correct persistence length of DNA. This indicates that knots are not only a fine gauge for structural properties, but a promising tool for the design of polymer models.

Current-induced enhancement of DNA bubble creation

Current-induced heating of short double-stranded DNA chains is studied within a two-probe transport setup by using the Langevin approach. The electrons are modeled by a tight-binding Hamiltonian. The DNA atomic motion is described by the Peyrard–Bishop–Dauxois atomic potential, coupled with electrons through the Holstein interaction. The solvent environment is accounted for as a classical heat bath. Voltage biases of can effectively break the base pairs and lead to the melting transition, which can be detected from the resulting significant reduction of the conductance. When the bias increases, the opening of base pairs near the leads with higher chemical potential is suppressed and bubble (localized separation of the double strand) formation becomes asymmetric. Our results suggest that the voltage bias can excite the base pairs, hence increases the chemical activity of DNA.

Influence of the sequence on the ab initio band structures of single and double stranded DNA models

Abstract The solid state physical approach is widely used for the characterization of electronic properties of DNA. In the simplest case the helical symmetry is explicitly utilized with a repeat unit containing only a single nucleotide or nucleotide pair. This model provides a band structure that is easily interpretable and reflects the main characteristic features of the single nucleotide or a nucleotide pair chain, respectively. The chemical variability of the different DNA chains is, however, almost completely neglected in this way. In the present work we have investigated the effect of the different sequences on the band structure of periodic DNA models. For this purpose we have applied the Hartree–Fock crystal orbital method for single and double stranded DNA chains with two different subsequent nucleotides in the repeat unit of former and two different nucleotide pairs in the latter case, respectively. These results are compared to simple helical models with uniform sequences. The valence and conduction bands related to the stacked nucleotide bases of single stranded DNA built up only from guanidine as well as of double stranded DNA built up only from guanidine–cytidine pairs showed special properties different from the other cases. Namely, they had higher conduction and lower valence band positions and this way larger band gaps and smaller widths of these bands. With the introduction of non-uniform guanidine containing sequences band structures became more similar to each other and to the band structures of other sequences without guanidine. The maximal bandwidths of the non-uniform sequences are considerably smaller than in the case of uniform sequences implying smaller charge carrier mobilities both in the conduction and valence bands.

The adsorption-desorption transition of double-stranded DNA interacting with an oppositely charged dendrimer induced by multivalent anions

The adsorption-desorption transition of DNA in DNA-dendrimer solutions is observed when high-valence anions, such as hexavalent anions, are added to the DNA-dendrimer solutions. In the DNA-dendrimer solutions with low-valence anions, dendrimers bind tightly with the V-shaped double-stranded DNA. When high-valence anions, such as pentavalent or hexavalent anions, are added to the DNA-dendrimer solutions, the double-stranded DNA chains can be stretched straightly and the dendrimers are released from the double-stranded DNA chains. In fact, adding high-valence anions to the solutions can change the charge spatial distribution in the DNA-dendrimer solutions, and weaken the electrostatic interactions between the positively charged dendrimers and the oppositely charged DNA chains. Adsorption-desorption transition of DNA is induced by the overcharging of dendrimers. This investigation is capable of helping us understand how to control effectively the release of DNA in gene/drug delivery because an effective gene delivery for dendrimers includes non-covalent DNA-dendrimer binding and the effective release of DNA in gene therapy.

Mechanism of Membranous Tunnelling Nanotube Formation in Viral Genome Delivery

Author SummaryViral survival and propagation depend on the ability of the viruses to transfer their genetic material to a host cell. Viral genome delivery has been described for viruses that directly enclose their genome in a capsid or nucleocapsid, but not for internal membrane-containing viruses in which the genome is protected by a lipid vesicle enclosed by the icosahedral capsid. The latter infect organisms across the three domains of life. We use a range of electron microscopy techniques to reveal how one such virus, the bacteriophage PRD1, which uses gram negative bacteria as its host, delivers its double-stranded DNA to the bacteria across the cell envelope. The PRD1 bacteriophage is special in that it doesn't carry a rigid tail; rather it creates a tube tail when needed at the time of infection to pass its DNA through to the host. We now show that this tube formation is accomplished via concerted restructuring of the icosahedral capsid and remodeling of the internal icosahedral protein-rich virus membrane. We also find that this tail tube is studded with membrane-associated proteins and its internal diameter allows one double-stranded DNA chain to be injected. Finally, we capture PRD1 in 3-D with the proteo-lipidic tail piercing the gram-negative bacterial cell and shuttling its viral genome in vivo. These results provide insights into a new mechanism of viral genome delivery.

Twist–radial normal mode analysis in double-stranded DNA chains

We study the normal modes of a duplex DNA chain at low temperatures. We consider the coupling between the hydrogen-bond radial oscillations and the twisting motion of each base pair within the Peyrard–Bishop–Dauxois model. The coupling is mediated by the stacking interaction between adjacent base pairs along the helix. We explicitly consider different mass values for different nucleotides, extending previous works. We disclose several resonance conditions of interest, determined by the fine-tuning of certain model parameters. The role of these dynamical effects on the DNA chain charge transport properties is discussed.

A transfer integral technique for solving a class of linear integral equations: Convergence and applications to DNA

An eigenvalue problem, the convergence difficulties that arise and a mathematical solution are considered. The eigenvalue problem is motivated by simplified models for the dissociation equilibrium between double-stranded and single-stranded DNA chains induced by temperature (thermal denaturation), and by the application of the so-called transfer integral technique. Namely, we extend the Peyrard–Bishop model for DNA melting from the original one-dimensional model to a three-dimensional one, which gives rise to an eigenvalue problem defined by a linear integral equation whose kernel is not in L2. For the one-dimensional model, the corresponding kernel is not in L2 either, which is related to certain convergence difficulties noticed by previous researchers. Inspired by methods from quantum scattering theory, we transform the three-dimensional eigenvalue problem, obtaining a new L2 kernel which has improved convergence properties.

Gaussian fluctuations in tethered DNA chains

In a recent work [Gao et al., Appl. Phys. Lett. 134, 113902 (2007)], we reported a novel DNA separation method by tethering DNA chains to a solid surface and then stretching the DNA chains with an electric field. The anchor is such designed that the critical force to detach a DNA chain is independent of its length. Because the stretching force is proportional to the DNA net charge, a gradual increase of the electric field leads to size-based removal of the DNA strands from the surface and thus DNA separation. Originally proposed for separation of long double-stranded DNA chains (>10 000 bps), this method has been proven useful also for short single-stranded DNA fragments (<100 bases) for which the fluctuation force induced by the solvent becomes significant. Here we show that the fluctuation force can be approximately represented by a gaussian model for tethered DNA chains. Analytical expressions have been derived to account for the dependence of the fluctuation force on the surface confinement, the polymer chain length, and the DNA tethering potential. The theoretical predictions are found to coincide with experiment.

Separation of single-stranded DNA fragments at a 10-nucleotide resolution by stretching in microfluidic channels

We report a novel DNA separation method by tethering DNA chains to a solid surface and then stretching the DNA chains with an electric field. The anchor is such designed that the critical force to detach a DNA chain is independent of its size. Because the stretching force is proportional to the DNA net charge, a gradual increase of the electric field leads to size-based removal of the DNA strands from the surface and thus DNA separation. Here we show that this method, originally proposed for separation of long double-stranded DNA chains (>10,000 base pairs), is also applicable to single-stranded (ss) DNA fragments with less than 100 nucleotides (nt). Theoretical analysis indicates that the separation resolution is limited by the fluctuation forces on tethered DNA chains. By employing a microfluidic platform with narrow channels filled with a buffer of low ionic conductivity, we are able to apply a strong electric field to the DNA fragments with negligible Joule heating. Upon stepwise increments of the electric field, we demonstrate efficient separation of short ssDNA fragments at a 10-nt resolution.

Interaction of double-stranded DNA with a nanosphere: a coarse-grained molecular dynamics simulation study

Using coarse-grained molecular dynamics simulations, we study the behavior of a DNA-nanosphere complex in the absence and presence of an external stretching force exerted on two ends of DNA chain. In this work, we use an accurate coarse-grained model for double-stranded DNA chain recently developed by Savelyev and Papoian [Biophys. J. 96, 4044 (2009)]. Charged particles are uniformly distributed on the surface of the sphere. Without a stretching force, an ordered or disordered complex is formed depending on the surface charge density and the salt concentration. It is found that DNA wraps randomly around the sphere only at an intermediate salt concentration and high surface charge density. Additionally, the DNA folding around the sphere induces a reduced distance between DNA monomers close to the spherical surface. When an external force is applied, the force-extension relation reveals a discontinuous transition of DNA stretching during the unwrapping process. Moreover, the discrete change becomes more obvious for a higher salt concentration.

Chemically accurate coarse graining of double-stranded DNA.

Coarse-grained (CG) modeling approaches are widely used to simulate many important biological processes involving DNA, including chromatin folding and genomic packaging. The bending propensity of a semiflexible DNA molecule critically influences these processes. However, existing CG DNA models do not retain a sufficient fidelity of the important local chain motions, whose propagation at larger length scales would generate correct DNA persistent lengths, in particular when the solution's ionic strength is widely varied. Here we report on a development of an accurate CG model for the double-stranded DNA chain, with explicit treatment of mobile ions, derived systematically from all-atom molecular dynamics simulations. Our model generates complex local motions of the DNA chain, similar to fully atomistic dynamics, leading also to a quantitative agreement of our simulation results with the experimental data on the dependence of the DNA persistence length on the solution ionic strength. We also predict a structural transition in a torsionally stressed DNA nanocircle as the buffer ionic strength is increased beyond a threshold value.

Mo 6S 3I 6–Au composites: Synthesis, conductance, and applications

A single-step, premixing method was used to directly deposit gold nanoparticles on Mo 6S 3I 6 (MSI) molecular wire bundles. Gold nanoparticles with different sizes and densities were coated on the MSI by changing the concentration of the gold containing salt, HAuCl 4. TEM, SEM, and EDX characterization showed deposition of gold nanoparticles on the MSI nanowire surface. The electrical resistance of these MSI–Au composites was more than 100 times lower than that for pure MSI, and was mainly dependent on the density of the deposited gold nanoparticles. Furthermore, we immobilized thiol group-labeled oligonucleotide on the composites and then hybridized with a fully matched sequence. The resistance of the MSI–Au composites increased during the thiol step, while it decreased by hybridizing, due to the conductance difference between single- and double-stranded DNA chains. These results indicate that this new kind of MSI–Au composite could be used as a platform for different applications, including biosensors.

Probing the Conformational Distributions of Subpersistence Length DNA

We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle x-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average value (as in ensemble fluorescence resonance energy transfer) or an extreme value (as in cyclization), and in principle provides a more robust data set for assessing the suitability of theoretical models. Our experimental results for dsDNA comprising 42–94 basepairs are consistent with a simple wormlike chain model of dsDNA elasticity, whose behavior we have determined from Monte Carlo simulations that explicitly represent nanoparticles and their alkane tethers. A persistence length of 50 nm (150 basepairs) gave a favorable comparison, consistent with the results of single-molecule force-extension experiments on much longer dsDNA chains, but in contrast to recent suggestions of enhanced flexibility at these length scales.