Determination of DNA cooperativity factor

Amirikyan, B. R.; Vologodskii, Alexander; Lyubchenko, Yu. L.

doi:10.1093/nar/9.20.5469

Cited by 43 publications

(45 citation statements)

References 11 publications

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“…We fit the structural transition using the same general model as for B-Z transitions (Fig. 3A), notably yielding a lower value for the boundary penalty J than is generally obtained for denaturation of matched duplexes (2,27,32), and lower than we obtained for B-Z transitions (Table 1 and Table S2). The twist persistence length of strand-separated DNA inferred from these measurements is approximately 7 bp at 1.6 pN of tension.…”

Section: Resultsmentioning

confidence: 93%

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

Oberstrass

Fernandes

Bryant

2012

Proc. Natl. Acad. Sci. U.S.A.

117

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B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of alternative conformations including strand-separated DNA and Z-DNA. Localized sequence-dependent structural transitions are important for the regulation of biological processes such as DNA replication and transcription. To directly probe the effect of sequence on structural transitions driven by torque, we have measured the torsional response of a panel of DNA sequences using single molecule assays that employ nanosphere rotational probes to achieve high torque resolution. The responses of Z-forming d(pGpC) n sequences match our predictions based on a theoretical treatment of cooperative transitions in helical polymers. “Bubble” templates containing 50–100 bp mismatch regions show cooperative structural transitions similar to B-DNA, although less torque is required to disrupt strand–strand interactions. Our mechanical measurements, including direct characterization of the torsional rigidity of strand-separated DNA, establish a framework for quantitative predictions of the complex torsional response of arbitrary sequences in their biological context.

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Section: Resultsmentioning

confidence: 93%

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

Oberstrass

Fernandes

Bryant

2012

Proc. Natl. Acad. Sci. U.S.A.

117

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“…Of course the main term in Eq. (31) is s N , which may be predicted on the basis of a quite simple consideration. However, as may be seen below, the contribution from the less trivial denominator terms is also significant in many cases, especially when s is very close to unity.…”

Section: Application To the Problem Of Nucleic Acid Meltingmentioning

confidence: 99%

“…Because of the nucleation of unwinding inside a molecule having N -lo?, the time of unwinding for such a molecule may be roughly estimated from Eq. (31) with the N value somewhere between lo2 and lo3. At the same time, the value of s( T,) to be substituted into Eq.…”

Section: ~N ( T )mentioning

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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“…2. One has to have two DNA preparations with identical sequences, one with the terminal melting region, and the other with the same melting region located inside the helix.…”

Section: Introductionmentioning

confidence: 99%

The Ionic Strength Dependence of the Cooperativity Factor for DNA Melting

Kozyavkin

Mirkin

Amirikyan

1987

Journal of Biomolecular Structure and Dynamics

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The melting temperature for the d(AT)24.d(AT)24 stretch, located inside the DNA helix and terminally, have been determined in a wide range of ionic strength values (0.01 - 1 M Na+). The cooperativity factor was calculated from the shifts in the melting temperature of the stretch due to its different boundary conditions. With the sodium concentration decreasing from 1 M to 0.01 M the cooperativity factor dropped by three orders of magnitude, its change being less marked at high than at low ionic strength.

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Determination of DNA cooperativity factor

Cited by 43 publications

References 11 publications

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

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

The Ionic Strength Dependence of the Cooperativity Factor for DNA Melting

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