DNA localization and stretching on periodically microstructured lipid membranes

We study the conformational behavior of DNA molecules adsorbed on cationic-lipid membranes that are supported on grooved, one-dimensionally periodic microstructured surfaces. We reveal a striking ability of these periodically structured membranes to stretch DNA coils. We elucidate this DNA stretching phenomenon in terms of surface curvature dependent potential energy attained by the adsorbed DNA molecules. Because of it, DNA molecules undergo a localization transition causing them to stretch by binding to highly curved sections of the supported membranes.     

DNA Intercalation in Neutral Multilamellar Membranes: Experiments and Theory

We report both an experimental and a theoretical work on the effect of confinement on a biological polymer (DNA) incorporated to multilamellar phase. We can see that even when no electrostatic interaction are involved this semi-flexible polymer can be incorporated in between the membranes. X-ray provides experimental evidence for the existence of a mixed DNA/Phospholipid structure. The nature of the DNA ordering is briefly described. A theoretical model is developed to describe the phase diagram. We emphasize the role of the isotropic/nematic transition of the DNA molecules to explain the ability to confine DNA in membranes.     

Effect of spermine and DNase on DNA release from bacteriophage T5

Bacterial viruses (bacteriophages) consist of nucleic acid protected by a protein envelope called capsid. At the start of infection, the phage genome is translocated into the bacterial cytoplasm. In vitro (and also in vivo), this DNA release can be triggered by binding a specific receptor protein to the phage tail. The force responsible for the release arises from energy stored in the capsid due to strong confinement of the DNA. We show that this force can be modified by adding molecules like spermine that affect DNA conformation. The tetravalent cation spermine can reduce the pressure inside the capsid and induce condensation of the released DNA. We examine the effect of spermine on DNA ejection from phage T5 by using light scattering and gel electrophoresis to measure the amount of DNA remaining in the capsid at the end of ejection. We discuss the results in terms of free energy minimization and we demonstrate that the presence of a DNA condensate outside the phage generates an additional force pulling passively on the DNA remaining inside the capsid.     

Mechanically controlled DNA extrusion from a palindromic sequence by single molecule micromanipulation

A magnetic tweezers setup is used to control both the stretching force and the relative linking number DeltaLk of a palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at approximately 1 pN induces the formation of a cruciform DNA structure. Furthermore, once the cruciform DNA structure is formed, the extrusion of several kilo-base pairs of palindromic DNA sequence is directly and reversibly controlled by varying DeltaLk. Indeed the branch point behaves as a nanomechanical gear that links rotation with translation, a feature related to the helicity of DNA. We obtain experimentally a very good linear relationship between the extension of the molecule and DeltaLk. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution: 3.61 +/- 0.03 nm/turn.     

Design rule for colloidal crystals of DNA-functionalized particles

We report a Monte Carlo simulation study of the phase behavior of colloids coated with long, flexible DNA chains. We find that an important change occurs in the phase diagram when the number of DNAs per colloid is decreased below a critical value. In this case, the triple point disappears and the condensed phase that coexists with the vapor is always liquid. Our simulations thus explain why, in the dilute solutions typically used in experiments, colloids coated with a small number of DNA strands cannot crystallize. We understand this behavior in terms of the discrete nature of DNA binding.     

Disentangling DNA molecules

The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.     

Disorder in DNA-linked gold nanoparticle assemblies

We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies. We observed an unusual trend of a nonmonotonic "zigzag" pattern in the melting temperature as a function of DNA linker length. Linker DNA resulting in unequal DNA duplex lengths introduces disorder and lowers the melting temperature of the nanoparticle system. Comparison with free DNA thermodynamics shows that such an anomalous zigzag pattern does not exist for free DNA duplex melting, which suggests that the disorder introduced by unequal DNA duplex lengths results in this unusual collective behavior of DNA-linked nanoparticle assemblies.     

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.     

Chiral electrostatics breaks the mirror symmetry of DNA supercoiling

DNA supercoiling plays a fundamental role in regulating cellular activity and in the packaging of genetic material. In this communication, we analyse the effect of attractive chiral forces on the conformation of a closed circular DNA molecule, arising due to the helical patterns of charges on the DNA. We propose a model for closed loop DNA which uses the results of the recent theory of electrostatic interactions of a braid of two free-ended DNA molecules. Our model reproduces the known features of DNA supercoiling in an environment of low ionic strength. In high salt conditions, and in the presence of counterions that have high affinity to the DNA grooves, helix-specific forces significantly affect the conformation of the molecule by favouring a state characterized by a central left-handed braided section where there is close contact between distant portions of the loop. In such an environment we predict a previously unexplored possibility that nicked or topologically relaxed DNA molecules adopt a writhed state. This prediction suggests an alternative explanation for experiments in which it was assumed that the most stable topoisomer is always an open circle. Our results also give the first plausible explanation for the occurrence of tightly interwound molecules observed in cryo-electron microscopy and atomic force microscopy in a high ionic strength environment. We suggest several new experiments to test the predictions of this theory.     

Optical detection of DNA translocation through silicon nanopore by ultraviolet light

In this paper, we propose a new optical detection scheme for nanopore-based DNA sequencing with high resolution towards eventual base identification. We use ultraviolet light for excitation of a fluorescent probe attached to DNA and a nanopore in the silicon membrane that has a significantly large refractive index and an extinction coefficient at ultraviolet wavelengths. In this study, numerical electromagnetic simulation revealed that the z-polarization component (perpendicular to the membrane plane) of the electric field was dominant near the nanopore and generated a large electric field gradient at the nanopore exit, typically with a decay length of 2 nm for a nanopore with diameter of 7 nm. The large extinction coefficient contributed to reduction in background noise coming from fluorophore-labeled DNA strands that remain behind the membrane (the cis side of the membrane). We observed a high signal-to-noise ratio of single DNA translocation events under the application of an electric field.     

Packing nanomechanics of viral genomes

We investigate the osmotic equilibrium between a bulk polyethylene glycol (PEG) solution and DNA tightly packed in a spherical capsid. We base our analysis on the equations of thermodynamic equilibrium in terms of osmotic pressure. The equality between external osmotic pressure of PEG and osmotic pressure of tightly packed DNA gives us the DNA encapsidation curves. In this way we directly connect the wealth of existing osmotic pressure data for DNA in the bulk with the DNA encapsidation curves within small viral capsids. Specific calculations are made for a monovalent salt, Na(+) -DNA and a divalent salt, Mn(2+) -DNA that have quite different DNA encapsidation behaviors. The main conclusion of our work is that bending energy of DNA is of minor importance regarding the encapsidated DNA length, but has a non-negligible influence on the density distribution of DNA within the capsid.     

The nucleosome: A transparent, slippery, sticky and yet stable DNA-protein complex

Roughly three quarters of eucaryotic DNA are tightly wrapped onto protein cylinders organized in so-called nucleosomes. Despite this fact, the wrapped DNA cannot be inert since DNA is at the heart of many crucial life processes. We focus here on physical mechanisms that might allow nucleosomes to perform a great deal of such processes, specifically 1) on unwrapping fluctuations that give DNA-binding proteins access to the wrapped DNA portions without disrupting the nucleosome as a whole, 2) on corkscrew sliding along DNA and some implications and on 3) tail-bridging-induced attraction between nucleosomes as a means of controlling higher-order folding.     

Stretching and relaxation dynamics in double stranded DNA

We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special attention to the opening–closing dynamics of double-stranded DNA molecules which are forced into non-equilibrium conformations. Mechanical stress imposed at one terminal end of the DNA molecule brings it into a partially opened configuration. We examine the subsequent relaxation dynamics connected with energy exchange processes between the various degrees of freedom and structural rearrangements leading to complete recombination to the double-stranded conformation. The similarities and differences between the relaxation dynamics for a planar ladder-like DNA molecule and a twisted one are discussed in detail. In this way we show that the attainment of a quasi-equilibrium regime proceeds faster in the case of the twisted DNA form than for its thus less flexible ladder counterpart. Furthermore we find that the velocity of the complete recombination of the DNA molecule is lower than the velocity imposed by the forcing unit which is in compliance with the experimental observations for the opening–closing cycle of DNA molecules.     

Finding borders between coding and noncoding DNA regions by an entropic segmentation method

We present a new computational approach to finding borders between coding and noncoding DNA. This approach has two features: (i) DNA sequences are described by a 12-letter alphabet that captures the differential base composition at each codon position, and (ii) the search for the borders is carried out by means of an entropic segmentation method which uses only the general statistical properties of coding DNA. We find that this method is highly accurate in finding borders between coding and noncoding regions and requires no "prior training" on known data sets. Our results appear to be more accurate than those obtained with moving windows in the discrimination of coding from noncoding DNA.     

PROPAGATION OF TWIST SOLITONS IN FULLY INHOMOGENEOUS DNA CHAINS

In the framework of a recently introduced model of DNA torsional dynamics, we argued — on the basis of perturbative considerations — that an inhomogeneous DNA chain could support long-lived soliton-type excitations due to the peculiar geometric structure of DNA and the effect of this on nonlinear torsional dynamics. Here we consider an inhomogeneous version of this model of DNA torsional dynamics, and investigate numerically the propagation of solitons in a DNA chain with a real base sequence (corresponding to the Human Adenovirus 2); this implies inhomogeneities of up to 50% in the base masses and inter-pair interactions. We find that twist solitons propagate for considerable distances (2–10 times their diameters) before stopping due to phonon emission. Our results show that twist solitons may exist in realistic DNA chain models, and on a more general level that solitonic propagation can take place in highly inhomogeneous media. The most relevant feature for general nonlinear dynamics is that we identify the physical mechanisms allowing this behavior and thus the class of models candidate to support long-lived soliton-type excitations in the presence of significant inhomogeneities.     

Mechanics of binding of a single integration-host-factor protein to DNA

We report on a single-molecule experiment where we directly observe local bending of a 76 base pair DNA oligomer caused by specific binding of a single integration-host-factor (IHF) protein. The conformational change of the DNA is detected by optically monitoring the displacement of a micron size bead tethered to a surface by the DNA. Since in the bound state the DNA loops around the IHF, a mechanical tension on the DNA tends to eject the protein. We measure how the rate for the protein to fall off the DNA depends on the mechanical tension in the DNA, gaining insight into the energy landscape for this molecular bond. Our method further demonstrates a new paradigm of molecular detection, where ligand binding is detected through the conformational change induced in the probe molecule. Here this allows the detection of single, unlabeled proteins.     

Scaling in nature: from DNA through heartbeats to weather.

The purpose of this report is to describe some recent progress in applying scaling concepts to various systems in nature. We review several systems characterized by scaling laws such as DNA sequences, heartbeat rates and weather variations. We discuss the finding that the exponent alpha quantifying the scaling in DNA in smaller for coding than for noncoding sequences. We also discuss the application of fractal scaling analysis to the dynamics of heartbeat regulation, and report the recent finding that the scaling exponent alpha is smaller during sleep periods compared to wake periods. We also discuss the recent findings that suggest a universal scaling exponent characterizing the weather fluctuations.     

Direct observation of the formation of DNA triplexes by single-molecule FRET measurements

In this report we investigated the effects of various biological and chemical factors (DNA sequence, pH, ions, and molecularity) on the formation of DNA triplexes through single-molecule FRET technique. Using this method, we determined how the third strand bound to a DNA duplex and how stable the triplex structure was under various conditions. From this study, we not only verified a variety of well-known features of DNA triplex but also discovered or experimentally supported several interesting behaviors: at neutral pH, a pyrimidine-motif triplex can be formed; the parallel arrangement was not only possible but also dominant over the antiparallel arrangement for a purine-motif triplex. We demonstrated that our method is a versatile analytical tool in studying structural aspects of nucleic acids, particularly non-classical DNA structures, and provides insights into physical mechanism of such structures.     

Fractal landscape analysis of DNA walks

By mapping nucleotide sequences onto a "DNA walk", we uncovered remarkably long-range power law correlations [Nature 356 (1992) 168] that imply a new scale invariant property of DNA. We found such long-range correlations in intron-containing genes and in non-transcribed regulatory DNA sequences, but not in cDNA sequences or intron-less genes. In this paper, we present more explicit evidences to support our findings.     

Scaling features of noncoding DNA.

We review evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene, and utilize this fact to build a Coding Sequence Finder Algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. Finally, we describe briefly some recent work adapting to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function, and reporting that noncoding regions in eukaryotes display a larger redundancy than coding regions. Specifically, we consider the possibility that this result is solely a consequence of nucleotide concentration differences as first noted by Bonhoeffer and his collaborators. We find that cytosine-guanine (CG) concentration does have a strong "background" effect on redundancy. However, we find that for the purine-pyrimidine binary mapping rule, which is not affected by the difference in CG concentration, the Shannon redundancy for the set of analyzed sequences is larger for noncoding regions compared to coding regions.