A Linear Biopolymer in the Vicinity of the Triple Point The Homopolymer Case

Frank‐Kamenetskii, Maxim D.; Chogovadze, G. I.

doi:10.1080/07391102.1984.10507535

Cited by 5 publications

(1 citation statement)

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“…pur-pyr (8), etc. This phenomenon may be explained by the fact that for each boundary between two conformations (helix-coil, B-Z, A-B, ...) there is an energy term which adds a sizable contribution to the difference in free energy between the two conformations (2,4,5,10); thus the number of boundaries is kept to a minimun.…”

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An algorithm for studying cooperative transitions in DNA

et al. 1986

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5UIjZjjBX: Cooperative transitions in DNA (B to Z, B to A, helix to coil, etc.) are known to depend strongly on nucleotide sequence. In general the change in free energy involved in the transition can be expressed as:where oa is a factor arising from the free energy associated with boundaries of different conformations along the molecule.This formula allows to infer a general algorithm with which DNA sequences can be partitioned into well defined domains in which under suitable conditions, base pairs change state cooperatively.The different partitions of the sequence that can be generated by varying the values of the physical parameters involved in the above formula, are shown to be embedded into a binary tree hierarchy.Application to a reliable prediction of Z-DNA antibody binding sites will be illustrated for the 0X174 genome. Possible biological implications are briefly discussed. (*)Nucleic acids may adopt a number of conformations: A, B, Z, coil, etc. and under appropriate physical conditions they can readily switch between two of these conformations: helix to coil, B to Z, B to A, etc. (1-5). These conformations, and transitions between two of them,are highly dependent on base composition since the value of the parameters monitoring the transition point (supercoiling, hydration, temperature etc.) varies over large ranges for different polymers (5-7).In natural DNA, alternating conformations were observed to appear in domains ie. continuous base pair (bp.) stretches with well defined location inside the sequence sharing a given conformation. Domain sequences allow for "mismatches": disrupted GC bp. in an AT rich coiled segment below the poly(GC) melting point (3), Z segments in supercoiled DNA with breaks in the alternance (*) Prograns mentioned in this paper are available on request.

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An algorithm for studying cooperative transitions in DNA

et al. 1986

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Mechanochemical study of conformational transitions and melting of Li‐, Na‐, K‐, and CsDNA fibers in ethanol–water solutions

et al. 1994

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SYNOPSISHighly oriented fibers of Li-, Na-, K-, and CsDNA were prepared with a previously developed wet spinning method. The procedure gave a large number of equivalent fiber bundle samples (reference length, Lo, typically = 12-15 cm) for systematic measurements of the fiber length L in ethanol-water solutions, using a simple mechanochemical set up. The decrease in relative length L / Lo with increasing ethanol concentration at room temperature gave evidence for the B-A transition centered at 76% ( v / v ) ethanol for NaDNA fibers and at 80 and 84% ethanol for Kand CsDNA fibers. A smaller decrease in L / L o of LiDNA fibers was attributed to the B-C transition centered at 80% ethanol. In a second type of experiment with DNA fibers in ethanol-water solutions, the heat-induced helix-coil transition, or melting, revealed itself in a marked contraction of the DNA fibers. The melting temperature T,, decreased linearly with increasing ethanol concentration for fibers in the B-DNA ethanol concentration region. In the B-A transition region, Na-and KUNA fibers showed a local maximum in T,. On further increase of the ethanol concentration, the A-DNA region followed with an even steeper linear decrease in T,. The dependence on the identity of the counterion is discussed with reference to the model for groove binding of cations in B-DNA developed by Skuratovskii and co-workers and to the results from Raman studies of the interhelical bonds in A-DNA performed by Lindsay and co-workers. An attempt to apply the theory of Chogovadze and Frank-Kamenetskii on DNA melting in the B-A transition region to the curves failed. However, for Na-and KDNA the T , dependence in and around the A-B transition region could be expressed as a weighted mean value of T , of Aand B-DNA. On further increase of the ethanol concentration, above 84% ethanol for LiDNA and above about 90% ethanol for Na-, K-, and CsDNA, a drastic change occurred. T , increased and a few percentages higher ethanol concentrations were found to stabilize the DNA fibers so that they did not melt at all, not even at the upper temperature limit of the experiments ( -80°C). This is interpreted as being due to the strong aggregation induced by these high ethanol concentrations and to the formation of P-DNA. Many features of the results are compatible with the counterion-water affinity model. In another series of measurements, T,,, of DNA fibers in 75% ethanol was measured at various salt concentrations. No salt effect was observed (with the exception of LiDNA at low salt concentrations). This result is supported hy calculations within the Poisson-Roltzmann cylindrical cell model.

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[6] A-DNA in solution as studied by diverse approaches

Иванов¹,

Krylov²

1992

Methods in Enzymology

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A Linear Biopolymer in the Vicinity of the Triple Point The Homopolymer Case

Cited by 5 publications

References 11 publications

An algorithm for studying cooperative transitions in DNA

An algorithm for studying cooperative transitions in DNA

Mechanochemical study of conformational transitions and melting of Li‐, Na‐, K‐, and CsDNA fibers in ethanol–water solutions

[6] A-DNA in solution as studied by diverse approaches

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