Kinking the double helix by bending deformation

DNA bending and torsional deformations that often occur during its functioning inside the cell can cause local disruptions of the regular helical structure. The disruptions created by negative torsional stress have been studied in detail, but those caused by bending stress have only been analyzed theoretically. By probing the structure of very small DNA circles, we determined that bending stress disrupts the regular helical structure when the radius of DNA curvature is smaller than 3.5 nm. First, we developed an efficient method to obtain covalently closed DNA minicircles. To detect structural disruptions in the minicircles we treated them by single-strand-specific endonucleases. The data showed that the regular DNA structure is disrupted by bending deformation in the 64–65-bp minicircles, but not in the 85–86-bp minicircles. Our results suggest that strong DNA bending initiates kink formation while preserving base pairing.     

Torsional and bending rigidity of the double helix from data on small DNA rings

We have calculated the variance of equilibrium distribution of a circular wormlike polymer chain over the writhing number, [Wr)2), as a function of the number of Kuhn statistical segments, n. For large n these data splice well with our earlier results obtained for a circular freely jointed polymer chain. Assuming that [delta Lk)2) = [delta Tw)2) we have compared our results with experimental data on the chain length dependence of the [delta Lk)2) value recently obtained by Horowitz and Wang for small DNA rings. This comparison has shown an excellent agreement between theory and experiment and yielded a reliable estimate of the torsional and bending rigidity parameters. Namely, the torsional rigidity constant is C = 3.0.10(-19) erg cm, and the bending rigidity as expressed in terms of the DNA persistence length is a = 500 A. The obtained value of C agrees well with earlier estimates by Shore and Baldwin as well as by Horowitz and Wang whereas the a value is in accord with the data of Hagerman. We have found the data of Shore and Baldwin on the chain length dependence of the [delta Lk)2) value to be entirely inconsistent with our theorectical results.     

DNA multimode interaction with berenil and pentamidine; double helix stiffening, unbending and bending

The antitrypanosomal drugs berenil (Ber) and pentamidine (Pm) preferentially bind to DNA in the minor groove of A.T-rich domains. The properties of A.T clusters are essential for sequence-mediated helix bending. Groove binding drugs locally stiffen the DNA helix but may also change intrinsic helix bends or may bend straight DNA. Ligand binding to randomly distributed sites alters the apparent DNA persistence length, a. Criteria permit the distinction of the underlying mechanism(s). Helix bends, if phased with the helix screw, however, generate solenoidal superhelix components mediating an apparent change of the hydrodynamically effective DNA contour length, L. The measurement of relative changes of both, a and L, as induced by Ber or Pm is performed by titration rotational viscometry. The determination of the two quantities requires two independent measurements: the relative change of DNA intrinsic viscosity, deltay, for short (tending to rod-like) DNA molecules and for comparably long (almost coil-like) ones as a function of r, the bound drug molecules per DNA-P, and this under conditions effectively excluding intramolecular DNA-DNA crosslinking effects. At least at r< or =0.05 and < or =0.03, respectively, the two drugs virtually bind completely to a eukaryotic DNA. r ranges of different drug binding strength and, concomitantly, of different specific conformational response, could be resolved. They represent (sub)modes of different DNA sequences... Whereas the mode-specific elongation effects are fairly similar for both systems, there are pronounced quantitative differences in the relative change of DNA persistence length. The sites of highest Ber-binding strength are correlated to unbent alternating helical A.T segments followed by bent and by less bent or unbent dAn.dTn tracts straightened on Ber-binding. For Pm-DNA interaction the ligand bends the sites of highest Pm affinity. Generally, ligand induced and sequence mediated local DNA-bend removal or DNA bending, as observed for several modes of interaction with A.T rich DNA, are considered to be of gene regulatory relevance.     

Electrostatic free energy landscapes for DNA helix bending

Nucleic acids are highly charged polyanionic molecules; thus, the ionic conditions are crucial for nucleic acid structural changes such as bending. We use the tightly bound ion theory, which explicitly accounts for the correlation and ensemble effects for counterions, to calculate the electrostatic free energy landscapes for DNA helix bending. The electrostatic free energy landscapes show that DNA bending energy is strongly dependent on ion concentration, valency, and size. In a Na⁺ solution, DNA bending is electrostatically unfavorable because of the strong charge repulsion on backbone. With the increase of the Na⁺ concentration, the electrostatic bending repulsion is reduced and thus the bending becomes less unfavorable. In contrast, in an Mg²⁺ solution, ion correlation induces a possible attractive force between the different parts of the helical strands, resulting in bending. The electrostatically most favorable and unfavorable bending directions are toward the major and minor grooves, respectively. Decreasing the size of the divalent ions enhances the electrostatic bending attraction, causing an increased bending angle, and shifts the most favorable bending to the direction toward the minor groove. The microscopic analysis on ion-binding distribution reveals that the divalent ion-induced helix bending attraction may come from the correlated distribution of the ions across the grooves in the bending direction.     

Mutual backbone phosphate group interactions promote DNA double helix bending at high salt concentrations in solution

Results of free energy calculations connected with the backbone phosphate group interactions upon local bending and helical twist modifications of A-, B- or Z-DNA at high salt concentrations have been reported recently (Jursa and Kypr 1990). Here we calculate energies necessary for DNA bending, using three models based on experimentally determined persistence length values. A comparison of energies following from the two quite different approaches suggests that high salt concentrations induce A- and mainly B-DNA bending into the double helix minor groove at least up to 10 degrees.     

Cytosine, the double helix and DNA self-assembly

DNA self-assembly has crucial implications in reading out the genetic information in the cell and in nanotechnological applications. In a recent paper, self-assembled DNA crystals displaying spectacular triangular motifs have been described (Zheng et al., 2009). The authors claimed that their data demonstrate the possibility to rationally design well-ordered macromolecular 3D DNA lattice with precise spatial control using sticky ends. However, the authors did not recognize the fundamental features that control DNA self-assembly in the lateral direction. By analysing available crystallographic data and simulating a DNA triangle, we show that the double helix geometry, sequence-specific cytosine–phosphate interactions and divalent cations are in fact responsible for the precise spatial assembly of DNA.     

Tau could protect DNA double helix structure

The hyperchromic effect has been used to detect the effect of tau on the transition of double-stranded DNA to single-stranded DNA. It was shown that tau increased the melting temperature of calf thymus DNA from 67 to 81 degrees C and that of plasmid from 75 to 85 degrees C. Kinetically, rates of increase in absorbance at 260 nm of DNA incubated with tau were markedly slower than those of DNA and DNA/bovine serum albumin used as controls during thermal denaturation. In contrast, rates of decrease in the DNA absorbance with tau were faster than those of controls when samples were immediately transferred from thermal conditions to room temperature. It revealed that tau prevented DNA from thermal denaturation, and improved renaturation of DNA. Circular dichroic spectra results indicated that there were little detectable conformational changes in DNA double helix when tau was added. Furthermore, tau showed its ability to protect DNA from hydroxyl radical (.OH) attacking in vitro, implying that tau functions as a DNA-protecting molecule to the radical.     

Hydrogen-bonding effects and 13C-NMR of the DNA double helix

13C-nmr chemical shifts of the nucleotides in DNA are sensitive to hydrogen bonding, especially for three of the carbons immediately bonded to exocyclic oxygen or nitrogen atoms acting as H-bond acceptors or donors. GuoC2, GuoC6 and ThdC4 are strongly deshielded (about 1 ppm) upon Watson-Crick pairing in oligodeoxynucleotide duplexes, regardless of the base sequence. Deshielding at these sites may be useful to distinguish bases involved in Watson-Crick pairs from unpaired bases.     

Sequence-dependent base pair opening in DNA double helix

Preservation of genetic information in DNA relies on shielding the nucleobases from damage within the double helix. Thermal fluctuations lead to infrequent events of the Watson-Crick basepair opening, or DNA "breathing", thus making normally buried groups available for modification and interaction with proteins. Fluctuational basepair opening implies the disruption of hydrogen bonds between the complementary bases and flipping of the base out of the helical stack. Prediction of sequence-dependent basepair opening probabilities in DNA is based on separation of the two major contributions to the stability of the double helix: lateral pairing between the complementary bases and stacking of the pairs along the helical axis. The partition function calculates the basepair opening probability at every position based on the loss of two stacking interactions and one base-pairing. Our model also includes a term accounting for the unfavorable positioning of the exposed base, which proceeds through a formation of a highly constrained small loop, or a ring. Quantitatively, the ring factor is found as an adjustable parameter from the comparison of the theoretical basepair opening probabilities and the experimental data on short DNA duplexes measured by NMR spectroscopy. We find that these thermodynamic parameters suggest nonobvious sequence dependent basepair opening probabilities.     

Geometric features of the DNA double helix in the supercoiled state

The geometric features of the DNA molecule in the supercoiled state were considered. A model of the supercoiled structure of the DNA molecule was constructed; the model takes into account its natural helicity. The force factors arising in the molecule at various superhelix angles were calculated.     

Phased psoralen cross-links do not bend the DNA double helix

Although the chemical reaction of psoralens with nucleic acids is well understood, the structure of psoralen-DNA cross-linked products is still not clear. Model building studies base on the crystal structure of the psoralen-thymine monoadduct suggest that each cross-link bends the DNA double helix by 46.5 degrees [Pearlman, D. A., Holbrook, S. R., Pirkle, D. H., & Kim, S.-H. (1985) Science (Washington, D.C.) 227, 1304-1308]. On the other hand, Sinden and Hagerman [Sinden, R. R., & Hagerman, P. J. (1984) Biochemistry 23, 6299-6303] find that, in solution, psoralen cross-linked DNA is not bent. Here we use gel electrophoresis to test the validity of the current models. We have synthesized a series of DNA fragments (21-24 base pairs in length), each containing one unique T-A site for 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) cross-linking. Because of an estimated 28 degrees unwinding of the helix by HMT [Wiesehahn, G., & Hearst, J. E. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 2703-2707], one expects that the 22-bp cross-linked fragment will be repeated nearly in phase with the average helical screw when multimerized. In that sequence ligation will maximally amplify any deformation to the double helix. We find that the ligated multimers of cross-linked DNA migrate close to the multimers of non-cross-linked DNA on polyacrylamide gels. Our observations place an upper limit of 10 degrees on DNA bending induced by psoralen cross-linking and indicate unwinding by about 1 bp, as well as stiffening of the double helix. These properties are not unexpected for classical intercalators.     

Complex between triple helix of collagen and double helix of DNA in aqueous solution

We demonstrate in this paper that one example of a biologically important and molecular self-assembling complex system is a collagen–DNA ordered aggregate which spontaneously forms in aqueous solutions. Interaction between the collagen and the DNA leads to destruction of the hydration shell of the triple helix and stabilization of the double helix structure. From a molecular biology point of view this nano-scale self-assembling superstructure could increase the stability of DNA against the nucleases during collagen diseases and the growth of collagen fibrills in the presence of DNA.     

Force-induced melting of the DNA double helix 1. Thermodynamic analysis

The highly cooperative elongation of a single B-DNA molecule to almost twice its contour length upon application of a stretching force is interpreted as force-induced DNA melting. This interpretation is based on the similarity between experimental and calculated stretching profiles, when the force-dependent free energy of melting is obtained directly from the experimental force versus extension curves of double- and single-stranded DNA. The high cooperativity of the overstretching transition is consistent with a melting interpretation. The ability of nicked DNA to withstand forces greater than that at the transition midpoint is explained as a result of the one-dimensional nature of the melting transition, which leads to alternating zones of melted and unmelted DNA even substantially above the melting midpoint. We discuss the relationship between force-induced melting and the B-to-S transition suggested by other authors. The recently measured effect on T7 DNA polymerase activity of the force applied to a ssDNA template is interpreted in terms of preferential stabilization of dsDNA by weak forces approximately equal to 7 pN.