Helix coil transitions of d (A)n·d(T)n, d(A‐T)n·d(A‐T)n, and d(A‐A‐T)n·d(A‐T‐T)n; evaluation of parameters governing DNA stability

Oliver, Adrian L.; Wartell, Roger M.; Ratliff, Robert L.

doi:10.1002/bip.1977.360160512

Cited by 35 publications

(10 citation statements)

References 35 publications

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“…Its most accurate determination was performed by Blake and Delcourt [19] who analyzed the melting of several tandemly repeated inserts on a linearized plasmid DNA and found that the value σ = 1.26 × 10 −5 fits best the experimental melting curves. This value is consistent with previous estimates [1,20,21,22].…”

Section: Entropy Of a Loop Embedded In A Chainsupporting

confidence: 93%

Reparametrizing the loop entropy weights: Effect on DNA melting curves

2003

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Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior loop melting. So far, in the modeling of DNA melting, the entropy of denaturated loops has been estimated from the number of configurations of a closed self-avoiding walk. It is well understood now that a loop embedded in a chain is characterized by a loop closure exponent c which is higher than that of an isolated loop. Here we report an analysis of DNA melting curves for sequences of a broad range of lengths (from 10 to 10 6 base pairs) calculated with a program based on the algorithms underlying MELTSIM. Using the embedded loop exponent we find that the cooperativity parameter is one order of magnitude bigger than current estimates. We argue that in the melting region the double helix persistence length is greatly reduced compared to its room temperature value, so that the use of the embedded loop closure exponent for real DNA sequences is justified.

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Section: Entropy Of a Loop Embedded In A Chainsupporting

confidence: 93%

Reparametrizing the loop entropy weights: Effect on DNA melting curves

2003

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“…As earlier (3), in our calculations we have used the method of Fixman and Freire (7) and the standard set of parameters, corresponding to the conditions of 0.1 SSC (see ref (3) and references therein). Note that the correctness of our choice of paraLmeters was confirmed recently in (8), where these parameters (cooperativity factor d and loop-weighting factor Z ) have been determined from the data on the melting of synthetic polynucleotides with periodic sequences.…”

mentioning

confidence: 61%

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

Vologodskii

Frank‐Kamenetskii

1978

Nucl Acids Res

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Differential melting profiles and denaturation maps are calculated for fdDNA whose sequence of nucleotides has been determined recently. The melting profiles for the total DNA and a number of its restriction fragments are compared with experimental data taken from literature. The comparison enables one to correlate a number of peaks on experimental melting profiles with the melting out of concrete regions of the nucleotide sequence. For three fragments very strong end effects are demonstrated on both theoretical and experimental profiles. These anomalous end effects are shown to be connected with a region highly enriched with AT-pairs. A possible influence of the heterogeneity of stacking interaction on the results obtained is discussed in detail.

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“…Digested plasmid DNA samples, approximately 1 ,Lg, were mixed with ficol loading buffer, placed in the 10 mm wide gel lanes, and electrophoresed. The volume loaded per lane was [15][16][17][18][19][20] Al.…”

Section: +1 +10 +20mentioning

confidence: 99%

Detecting base pair substitutions in DNA fragments by temperature-gradient gel electrophoresis

Wartell¹,

Hosseini²,

Moran³

1990

Nucl Acids Res

101

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A vertical gel electrophoresis apparatus is described which can distinguish DNA fragments differing by single base pair substitutions. The system employs a homogenous polyacrylamide gel containing urea-formamide and a temperature gradient which runs either perpendicular or parallel to the direction of electrophoresis. The temperature-gradient system simplifies several features of the denaturant-gradient system (1) and is relatively inexpensive to construct. Eight homologous 373 bp DNAs differing by one, two, or nine base pair substitutions were examined. DNA electrophoretic mobility changed abruptly with the temperature induced unwinding of DNA domains. GC to AT substitutions at different locations within the first melting domain, as well as an AT to TA transversion were separated with temperature gradients parallel to the electrophoretic direction. The relative stabilities of the DNAs observed in the gels were compared to predictions of DNA melting theory. General agreement was observed however complete correspondence was not obtained.

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Helix coil transitions of d (A)_n·d(T)_n, d(A‐T)_n·d(A‐T)_n, and d(A‐A‐T)_n·d(A‐T‐T)_n; evaluation of parameters governing DNA stability

Cited by 35 publications

References 35 publications

Reparametrizing the loop entropy weights: Effect on DNA melting curves

Reparametrizing the loop entropy weights: Effect on DNA melting curves

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

Detecting base pair substitutions in DNA fragments by temperature-gradient gel electrophoresis

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