Theory of DNA melting curves

Fixman, Marshall; Freire, Juan J.

doi:10.1002/bip.1977.360161209

Cited by 213 publications

(149 citation statements)

References 6 publications

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“…Finally, the formation of a flexible bubble includes an entropy loss corresponding to the returning probability of a random walk [3,[11][12]. For DNA-bubbles, one usually assumes the form F(n) = (n + D) −c where the offset D accounts for persistence length effects [19], and c is the loop closure exponent [3,11,10]. For D, a standard choice is D = 1 [14], while the value of c depends on the boundary conditions; for a dilute solution, c ≈ 1.76 is assumed [14], while other values have been suggested [20,21].…”

Section: Poland-scheraga Free Energy One-bubble Casementioning

confidence: 99%

Dynamic Approach to DNA Breathing

Metzler¹,

Ambjörnsson²

2005

J Biol Phys

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Abstract.Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic quantities such as the lifetime, an important measure for the description of the interaction of a breathing DNA molecule and selectively single-stranded DNA binding proteins. Our approach is consistent with recent single molecule measurements of bubble fluctuation. We also introduce a master equation approach to model DNA breathing, and discuss its differences from the continuous Fokker-Planck description.

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Section: Poland-scheraga Free Energy One-bubble Casementioning

confidence: 99%

Dynamic Approach to DNA Breathing

Metzler¹,

Ambjörnsson²

2005

J Biol Phys

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“…Fig. 1 shows thermal stability maps calculated by the algorithm of Poland-Fixman-Freire [5,6], with parameters TAT = 53.1"C, TGC = 94.1"C, AS = -24.54 e.u., oi = 6 x 10e6 (1+450)-'.75, and/Z0 = 10m7. The gaps are located near intron positions indicated by arrows.…”

Section: Resultsmentioning

confidence: 99%

Vestiges of lost introns in the thermal stability map of DNA

1988

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The absence of introns in prokaryotic genes has been explained by intron loss on various bases. Here we report another piece of evidence on intron loss, which was found in the thermal stability map of DNA. We calculated the local melting temperature of cDNA sequences and found that (i) gaps in thermal stability tend to occur near intron positions with a statistical significance, and (ii) one-third of the gaps far from intron positions can be assigned to lost introns. From these results we conclude that the gaps of thermal stability in protein coding regions are the vestiges of lost introns.

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“…The distribution of thermal stability along each molecule was computed using our program MELT (8) approximation of Poland's sequence-specific, two-state theory of the helix-random chain transition (9,10).…”

Section: Materials Amd Methodsmentioning

confidence: 99%

Intramolecular DNA melting between stable helical segments: melting theory and metastable states

Abrams¹,

Murdaugh²,

Lerman³

1995

Nucl Acids Res

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Melting of DNA in a segment bounded at both ends by regions of greater stability during electphoresis in denaturing gradient gels shows complex properties, not accommodated within standard meiting theory. Compact bands of some DNA molecules become anomalously broadened at the retardation level in a denaturing gradient, or double bands may appear in a uniform denaturant concentration. These properties are associated only with molecules for which the distribution of stability calculated by the Poland-Fixman-Freire algorithms indicates that the region of lowest stability does not extend to an end of the molecule. Retention of helicity at the ends is shown by the difference in the effect of base substitution in the end domains and in the least stable domain. Both the appearance of double bands and band broadening can be explained by invoking a hypothetical metastable intermediate in meiting, which is converted into the equilibrium melted form at a relatively slow rate, depending on both denaturant concentration and field strength. A kinetic model permits plausible rate constants to be inferred from the pattems. Despite the increased band width, sequence variants with base changes in the least stable domain result in readily detectable band shifts in the gradient. INTRODUCTIONThe stepwise melting of DNA molecules of length >100 bp in a gradually increasing denaturing environment is attributable to strong cooperativity and suppression of the unraveling of short interior loops or bubbles. The steps correspond to the concurrent melting within a narrow temperature interval of a large number of contiguous bases, called domains. Denaturing gradient gel electrophoresis (DGGE) is sufficiently sensitive to detect and measure the change in melting temperature of a domain resulting from substitution of a single base. It provides a general means for detection of gene mutations and polymorphisms.Electrophoresis in a denaturing gradient differs from conventional gel electrophoresis in that the mobility of a fragment is not constant,

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Theory of DNA melting curves

Cited by 213 publications

References 6 publications

Dynamic Approach to DNA Breathing

Dynamic Approach to DNA Breathing

Vestiges of lost introns in the thermal stability map of DNA

Intramolecular DNA melting between stable helical segments: melting theory and metastable states

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