DNA on a tube: electrostatic contribution to stiffness

Lateral migration of electrospun hydrogel nanofilaments in an oscillatory flow

The recent progress in bioengineering has created great interest in the dynamics and manipulation of long, deformable macromolecules interacting with fluid flow. We report experimental data on the cross-flow migration, bending, and buckling of extremely deformable hydrogel nanofilaments conveyed by an oscillatory flow into a microchannel. The changes in migration velocity and filament orientation are related to the flow velocity and the filament's initial position, deformation, and length. The observed migration dynamics of hydrogel filaments qualitatively confirms the validity of the previously developed worm-like bead-chain hydrodynamic model. The experimental data collected may help to verify the role of hydrodynamic interactions in molecular simulations of long molecular chains dynamics.

Measuring shape-dependent looping probability of DNA

Recently, several studies have shown that short doubled-stranded DNA (dsDNA) loops more readily than the wormlike chain model predicts. In most of these experiments, the intrinsic bendedness of dsDNA, which in theory can dramatically influence looping dynamics, was either avoided or unaccounted for. To investigate the effect of the shape of dsDNA on looping dynamics, we characterized the shapes of several synthetic dsDNA molecules of equal length but different sequences using gel electrophoresis. We then measured their looping rates using a FRET (Förster resonance energy transfer)-based assay and extracted the looping probability density known as the J factor (jM). We also used, for comparison, several dinucleotide angular parameter sets derived from the observed electrophoretic mobility to compute the jM predicted by the wormlike chain model. Although we found a strong correlation between curvature and jM, the measured jM was higher than most dinucleotide model predictions. This result suggests that it is difficult to reconcile the looping probability with the observed gel mobility within the wormlike chain model and underscores the importance of determining the intrinsic shape of dsDNA for proper theoretical analysis.

Mechanical properties of DNA-like polymers

The molecular structure of the DNA double helix has been known for 60 years, but we remain surprisingly ignorant of the balance of forces that determine its mechanical properties. The DNA double helix is among the stiffest of all biopolymers, but neither theory nor experiment has provided a coherent understanding of the relative roles of attractive base stacking forces and repulsive electrostatic forces creating this stiffness. To gain insight, we have created a family of double-helical DNA-like polymers where one of the four normal bases is replaced with various cationic, anionic or neutral analogs. We apply DNA ligase-catalyzed cyclization kinetics experiments to measure the bending and twisting flexibilities of these polymers under low salt conditions. Interestingly, we show that these modifications alter DNA bending stiffness by only 20%, but have much stronger (5-fold) effects on twist flexibility. We suggest that rather than modifying DNA stiffness through a mechanism easily interpretable as electrostatic, the more dominant effect of neutral and charged base modifications is their ability to drive transitions to helical conformations different from canonical B-form DNA.

Electrostatic contribution to DNA condensation--application of 'energy minimization' in a simple model in the strong Coulomb coupling regime

The process of bending of straight DNA to a circular form in the presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in a strong Coulomb coupling environment, employing a previously developed energy minimization simulation technique. The inherent characteristics of the simulation technique allow the monitoring of the required electrostatic contribution to the bending. The curvature of the bending has been found to play a crucial role in facilitating the electrostatic attractive potential energy. The total electrostatic potential energy has been found to decrease with bending, which indicates that bending straight DNA to a circular form or to a toroidal form in the presence of neutralizing counterions is energetically favourable and is practically a spontaneous phenomenon.

Torque-induced deformations of charged elastic DNA rods: thin helices, loops, and precursors of DNA supercoiling

We study the deformations of charged elastic rods under applied end forces and torques. For neutral filaments, we analyze the energetics of initial helical deformations and loop formation. We supplement this elastic approach with electrostatic energies of bent filaments and find critical conditions for buckling depending on the ionic strength of the solution. We also study force-induced loop opening, for parameters relevant for DNA. Finally, some applications of this nano-mechanical DNA model to salt-dependent onset of the DNA supercoiling are discussed.

Condensed DNA: condensing the concepts

DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The mechanistic details of DNA packing are essential for its functioning, as revealed by the recent developments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in the bulk of experimental and theoretical details. Here we try to condense some of these concepts and provide interconnections between the different fields. After a brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented. We end up with an extended discussion of the role of DNA condensation in the context of gene regulation and mention potential applications of DNA condensation in gene therapy and biotechnology.

DNA curvature and flexibility in vitro and in vivo

It has been more than 50 years since the elucidation of the structure of double-helical DNA. Despite active research and progress in DNA biology and biochemistry, much remains to be learned in the field of DNA biophysics. Predicting the sequence-dependent curvature and flexibility of DNA is difficult. Applicability of the conventional worm-like chain polymer model of DNA has been challenged. The fundamental forces responsible for the remarkable resistance of DNA to bending and twisting remain controversial. The apparent 'softening' of DNA measured in vivo in the presence of kinking proteins and superhelical strain is incompletely understood. New methods and insights are being applied to these problems. This review places current work on DNA biophysics in historical context and illustrates the ongoing interplay between theory and experiment in this exciting field.

The unique structure of A-tracts and intrinsic DNA bending

Short runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.