DNA base pair hybridization and water-mediated metastable structures studied by molecular dynamics simulations

The base pair hybridization of a DNA segment was studied using molecular dynamics simulation. The results show the obvious correlation between the probability of successful hybridization and the accessible surface area to water of two successive base pairs, including the unpaired base pair adjacent to paired base pair and this adjacent paired base pair. Importantly, two metastable structures in an A-T base pair were discovered by the analysis of the free energy landscape. Both structures involved addition of a water molecule to the linkage between the two nucleobases in one base pair. The existence of the metastable structures provide potential barriers to the Watson-Crick base pair, and numerical simulations show that those potential barriers can be surmounted by thermal fluctuations at higher temperatures. These studies contribute an important step toward the understanding of the mechanism in DNA hybridization, particularly the effect of temperature on DNA hybridization and polymerase chain reaction. These observations are expected to be helpful for facilitating experimental bio/nanotechnology designs involving fast hybridization.

Potential ecological risks of thermal-treated waste recombination DNA discharged into an aquatic environment

It has been shown that thermal-treatment at 100 ° C can denature deoxyribonucleic acid (DNA), yet this does not cause it to break down completely. To clarify the risk of gene pollution from thermal-treated recombinant DNA, the renaturation characteristics of thermal-denatured plasmid pET-28b and its persistence in aquatic environments were investigated. The results revealed that the double-stranded structure and transforming activity of the thermal-treated plasmid DNA could be recovered even if the thermal-treatment was conducted at 120 ° C. The presence of sodium chloride (NaCl) and ethylenediamine tetraacetic acid (EDTA) led to the increase of renaturation efficiency of the denatured DNA. When thermal-treated plasmid DNA was discharged into simulated aquatic environments with pH values from 5 to 9, it showed a longer persistence at pH 7 and 8 than that at 5, 6 and 9; however, the denatured plasmid DNA could persist for more than 33 min at any pH. Moreover, a higher ionic strength further protected the thermal-denatured plasmids from degradation in the simulated aquatic environment. These results indicated that when the thermal-treated DNA was discharged into an aquatic environment, it might not break down completely in a short period. Therefore, there is the potential for the discarded DNA to renature and transform, which might result in gene pollution.

Mechanism of thermal renaturation and hybridization of nucleic acids: Kramers' process and universality in Watson-Crick base pairing

Renaturation and hybridization reactions lead to the pairing of complementary single-stranded nucleic acids. We present here a theoretical investigation of the mechanism of these reactions in vitro under thermal conditions (dilute solutions of single-stranded chains, in the presence of molar concentrations of monovalent salts and at elevated temperatures). The mechanism follows a Kramers' process, whereby the complementary chains overcome a potential barrier through Brownian motion. The barrier originates from a single rate-limiting nucleation event in which the first complementary base pairs are formed. The reaction then proceeds through a fast growth of the double helix. For the DNA of bacteriophages T7, T4, and phiX174, as well as for Escherichia coli DNA, the bimolecular rate k2 of the reaction increases as a power law of the average degree of polymerization <N> of the reacting single-strands: k2 is proportional to <N> alpha. This relationship holds for 100 < or = <N> < or = 50,000 with an experimentally determined exponent alpha = 0.51 +/- 0.01. The length dependence results from a thermodynamic excluded-volume effect. The reacting single-stranded chains are predicted to be in universal good solvent conditions, and the scaling law is determined by the relevant equilibrium monomer contact probability. The value theoretically predicted for the exponent is alpha = 1 - nutheta2, where nu is Flory's swelling exponent (nu approximately equal 0.588), and theta2 is a critical exponent introduced by des Cloizeaux (theta2 approximately equal 0.82), yielding alpha = 0.52 +/- 0.01, in agreement with the experimental results.

How adsorption influences DNA denaturation

The thermally induced denaturation of DNA in the presence of an attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the surface, the denaturation phase transition disappears. Instead, there is a smooth crossover to a weakly naturated state. Our second conclusion is that even when the interstrand attraction alone is too weak for creating a naturated state at the given temperature and also when the surface-strand attraction alone is too weak for creating an adsorbed state, the combined effect of the two attractions can lead to a naturated and adsorbed state.

Aggregation and adsorption at the air-water interface of bacteriophage phiX174 single-stranded DNA

We study the phase behavior of phage phiX174 single-stranded DNA in very dilute solutions in the presence of monovalent and multivalent salts, in both water (H(2)O) and heavy water (D(2)O). DNA solubility depends on the nature of the salts, their concentrations, and the nature of the solvent. The appearance of attractive interactions between the monomers of the DNA chains in the bulk of the solution is correlated with an adsorption of the chains at the air-water interface. We characterize this correlation in two types of aggregation processes: the condensation of DNA induced by the trivalent cation spermidine and its salting out in the presence of high concentrations (molar and above) of monovalent (sodium) cations, both in water and in heavy water. The overall solubility of single-stranded DNA is decreased in D(2)O compared to H(2)O, pointing to a role of DNA hydration in addition to electrostatic factors in the observed phase separations. DNA adsorption involves attractive van der Waals forces, and these forces are also operating in the bulk aggregation process.

Effect of external fluctuations on the affinity-specificity negative correlation in DNA-probe interactions

We show that the site-specific interaction of a probe DNA with the template DNA can be well modeled as an unbiased random jump process, where the probe molecule first nonspecifically binds to the template DNA and then searches for the specific site via unbiased random jump motion on the template DNA. By investigating the effects of increasing the jump size, and the fluctuations in the position of the specific site and the fluctuations in the specific site interval on the affinity-specificity negative correlation, we show that (1) increasing the jump size will in turn increase the affinity of the probe toward its target site on the template DNA, however, with a limiting value--the maximum affinity condition; (2) the degree of supercoiling or condensation of the template DNA as well as the electrostatic interactions between the probe and the template in turn control the jump size associated with the dynamics of the probe on the template DNA; (3) under a maximum specificity condition (therefore with minimum affinity), by introducing an external fluctuation in the relative position of the target site on the template DNA with respect to the probe, one can still improve the affinity rate; (4) on the other hand, one can improve the specificity of the probe toward the target site on the template DNA by introducing external fluctuations in the target-site interval. Finally, we propose the design strategies and optimum experimental conditions to simultaneously enhance the affinity as well as the specificity of probe toward its target site on the template DNA.

Spermine-induced aggregation of DNA, nucleosome, and chromatin

We have analyzed the conditions of aggregation or precipitation of DNA in four different states: double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), mononucleosome core particles (NCP), and H1-depleted chromatin fragments (ChF) in the presence of the multivalent cation spermine (4+). In an intermediate regime of DNA concentration, these conditions are identical for the four states. This result demonstrates that the mechanism involved is general from flexible chains to rigid rods and quasi-colloidal states. It is dominated by local electrostatic attractions that are considered, for instance, by the "ion-bridging" model. The onset of precipitation does not require the electroneutrality of the DNA chains. Above a given spermine concentration dsDNA aggregates remain neutral, whereas NCP aggregates turn positively charged. The difference is thought to originate from the extension of the positively charged proteic tails of the NCP. This suggests that local fluctuations of polyamine concentrations can induce either positively or negatively charged chromatin domains.

Cyclization of globular DNA. Implications for DNA-DNA interactions in vivo

The rate of cyclization of lambda DNA varies over more than 6 orders of magnitude, from 3.2 x 10(-7) s-1 to 2 s-1, in a Tris-EDTA buffer as a function of spermidine concentration. This variation is strictly correlated with the conformation of the chain. The highest rates are obtained when the chain is collapsed into a dense globular state. The effective concentration of the chain ends in the reaction is then 87 000-fold greater than in the random coil state. These results show that DNA globularity must be taken into account to understand biological processes involving intramolecular DNA-DNA interactions.