Theoretical melting profiles and denaturation maps of DNA with known sequence: fd DNA

Vologodskii, Alexander; Frank‐Kamenetskii, Maxim D.

doi:10.1093/nar/5.7.2547

Cited by 22 publications

(9 citation statements)

References 7 publications

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“…In particular, we have discovered that the overstretching force plateau does indeed weakly depend on the pulling rate, and this dependence becomes stronger with faster pulling and in lower salt. This result is analogous to the well-known weak dependence of the DNA melting temperature on heating rate [37], and is a consequence of the highly cooperative melting of long (~100 bp) regions of heterogeneous dsDNA, leading to large sequence-determined peaks in the differential melting profiles [38]. While many direct analogies between thermal and force-induced DNA melting exist, our experiments and theory point out their major differences.…”

supporting

confidence: 70%

DNA stretching as a probe for nucleic acid interactions

McCauley

Chaurasiya

Paramanathan

et al. 2010

Physics of Life Reviews

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We would like to thank the authors of the thoughtful commentaries on various aspects of our review. These commentaries represent a diverse set of opinions on the field of single molecule force spectroscopy. We are unable to address all of the detailed issues brought up in the commentaries due to space constraints. Therefore what follows is a more general view of the most commonly addressed issues.An isolated DNA molecule yields a lattice of binding sites, representing a microlab for the study of DNA-ligand interactions. Increasing tension along the double-stranded DNA (dsDNA) molecule disrupts tertiary DNA-ligand structures, then dislocates base pairing and stacking and ultimately separates the opposite strands to form single-stranded DNA (ssDNA). Varying the applied force alters the free energy to favor ligands that bind preferentially to DNA in one of these forms. These biophysical experiments not only discern the mode of DNA binding, but may also quantify the biochemistry of protein-DNA interactions [1,2]. These types of experiments offer particular advantages over bulk solution measurements, though important caveats remain. Specific issues surrounding DNA characterization and modeling, protein-DNA interactions under force and the ongoing discussion about overstretching highlight important questions that merit further comment and will hopefully propel additional study [2][3][4][5][6][7][8].In any review, some subjects may only be dealt with briefly, while others must regrettably be omitted altogether. The section on DNA models treats well known descriptions of polymer elasticity; the Worm-Like Chain and Freely-Jointed Chain models. These models are used specifically to quantify DNA-protein interactions in the stretching experiments described further in the review [1], but not as a review of the much larger and interesting field of molecular dynamics simulations. The sophistication of computational techniques has increased rapidly in the last few years, enabling fruitful comparisons between theory and experiment [4,9,10]. Further advances in theoretical treatments of DNA have shed light upon even finer structures

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supporting

confidence: 70%

DNA stretching as a probe for nucleic acid interactions

McCauley

Chaurasiya

Paramanathan

et al. 2010

Physics of Life Reviews

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“…There is a critical involvement of the flanking sequences in this mechanism, for which the presence of at least one A+T rich sequence is required. A+T rich sequences have a lower helical stability than those of higher G+C content [15][16][17][18][19] Figure 7. The interconversion of kinetic character of cruciform extrusion by perturbation of helix stability.…”

Section: Duss1onmentioning

confidence: 99%

“…All the sequences found so far which successfully confer C-type character are very A+T rich. Such sequences become denatured at relatively low temperatures [15][16][17][18][19], and suggest that their role may be associated with locally lowered helix stability. We have already proposed [11] that the contextual influence may be related to telestability effects observed in thermal melting experiments [20].…”

mentioning

confidence: 99%

Helix stability and the mechanism of cruciform extrusion in supercoiled DNA molecules

Sullivan

Lilley

1988

Nucl Acids Res

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The kinetic properties of cruciform extrusion in supercoiled DNA molecules fall into two main classes. C-type cruciforms extrude in the absence of added salt, at relatively low temperatures, with large activation energies, while S-type cruciforms exhibit no extrusion in the absence of salt, and maximal rates at 50 mM NaCl, with activation energies about one quarter those of the C-type. These diverse properties are believed to reflect two distinct pathways for the extrusion process, and are determined by the nature of the sequences which form the context of the inverted repeat. C-type kinetics are conferred by A + T rich sequences, implying a role of helix stability in the selection. In this study we have shown that: 1. Helix-destabilising solvents (dimethyl formamide and formamide) facilitate extrusion by normally S-type molecules at low temperatures in the absence of salt. 2. C-type extrusion is strongly suppressed by low concentrations (2-4 microM) distamycin, at which concentrations S-type extrusion is enhanced. 3. Some extrusion occurs in a C-type construct in the presence of 50 mM NaCl. This is increased by addition of 3 microM distamycin, under which conditions extrusion becomes effectively S-type. Thus S-type constructs can behave in a quasi-C-type manner in the presence of helix-destabilising solvents, and C-type extrusion is suppressed by binding a compound which stabilises A + T rich regions of DNA. Helix destabilisation leads to C-type behaviour, while helix stabilisation results in S-type properties. These studies demonstrate the influence of contextual helix stability on the selection of kinetic mechanism of cruciform extrusion.

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“…If the value ATlo is much greater than the relaxation time tN(T,), which corresponds to the temperature T , , we should observe equilibrium melting. By contrast, if tN(Tm) >> ATlu (33) the polymer would not melt a t T , and it would melt at a higher temperature, Tk, which is defined by the equation…”

Section: Dna Fragmentsmentioning

confidence: 99%

Slow relaxational processes in the melting of linear biopolymers: A theory and its application to nucleic acids

et al. 1984

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SynopsisWe treat the problem of the mean time of complete separation of complementary chains of a duplex containing N base pairs. A combination of analytical and computer methods is used to obtain the exact solution in the form of a compact expression. This expression is used to analyze the limits of application of the equilibrium theory of helix-coil transition in oligoand polynucleotides. It also allows the melting behavior of a biopolymer to be predicted when its melting is nonequilibrium. In the case of oligonucleotides for which the equilibrium melting takes place at a high value of the stability constants, the general expression turns into the equation of Craig, Crothers, and Doty, used by them to determine the rate constant hi of the growth of a helical region from temperature-jump experiments. For the case of fragmented DNA with N -lo', the melting process is shown to be completely nonequilibrium, and as a result, the observed melting temperature should be higher than that for the equilibrium. A simple equation is obtained that makes possible calculation of the real, "kinetic" melting temperature Tk. As N increases, the observed melting temperature should approach the equilibrium value, T,. This analysis has explained quantitatively the peculiar chainlength dependence of the experimentally observed shift in the DNA melting temperature during fragmentation. A thorough analysis is given of the nonequilibrium effects in the melting process of long DNA molecules ( N 2 lo3)). The main conclusion is that even in the presence of profound hysteresis phenomena, the melting profile observed on heating may differ only slightly from the equilibrium profile.

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Theoretical melting profiles and denaturation maps of DNA with known sequence: fd DNA

Cited by 22 publications

References 7 publications

DNA stretching as a probe for nucleic acid interactions

DNA stretching as a probe for nucleic acid interactions

Helix stability and the mechanism of cruciform extrusion in supercoiled DNA molecules

Slow relaxational processes in the melting of linear biopolymers: A theory and its application to nucleic acids

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