The Ionic Strength Dependence of the Cooperativity Factor for DNA Melting

Kozyavkin, Sergei A.; Mirkin, Sergei M.; Amirikyan, B. R.

doi:10.1080/07391102.1987.10506380

Cited by 27 publications

(9 citation statements)

References 10 publications

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“…The values of these parameters obtained for different ionic strengths are listed in Table I By fitting the dumbbells D-62 theoretical profiles to the experimental ones one can find the value ofr 0 • Using the value of(4) obtained for hairpins one can find the statistical weight ofr 0 and rc for different ionic strengths are listed in Table I. With ionic strength falling by an order of magnitude, rc decreases 10 times, which is consistent with the data obtained in (23) where the effect of ionic strength on DNA cooperativity factor on was studied. It was shown (23) that this parameter is sharply diminishes with decreasing ionic strength.…”

Section: Thermodynamic Parameters Of Hairpins and Dumbbellssupporting

confidence: 81%

Melting of Oligodeoxynucleotides with Various Structures

YuL

1991

Journal of Biomolecular Structure and Dynamics

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Effects of DNA fragments end structures on their melting profiles were studied experimentally and theoretically. We examined melting of hairpins and dumbbells obtained from 62-bp-long linear DNA duplex which is a perfect palindromic sequence. To fit theoretical melting profile to experimental ones additional theoretical parameters were incorporated into the standard statistical mechanical helix-coil transition theory. From comparison theoretical and experimental melting profiles theoretical parameters connected with end-structure effects were evaluated. Analysis revealed the stabilization effect of the hairpin loops and helix ends with respect to DNA duplex melting. Both type of ends make melting these oligodeoxynucleotides more cooperative than predicted by the standard helix-coil transition theory. At low ionic strength ([Na+] less than 0.04 M) this effect becomes so pronounced that melting of the DNA duplexes 30-40 bp-long conforms to the two state model. From the analysis experimental data obtained for dumbbell structures loop-weighting factor for single-stranded loop consisting of 132 nucleotides was determined. This parameter decreases 10 times with the ionic strength decreasing by an order of magnitude from 0.2 to 0.02 M Na+.

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Section: Thermodynamic Parameters Of Hairpins and Dumbbellssupporting

confidence: 81%

Melting of Oligodeoxynucleotides with Various Structures

YuL

1991

Journal of Biomolecular Structure and Dynamics

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“…Nevertheless, we did not adjust the value of F~ in our calculations, for the experimental data available to date do not warrant a reliable assessment of the relation between palindrome size and F~. The parameters ~fAT and ~foe for the TBE buffer and 20°C were found on the basis of the DNA melting data (19).…”

Section: Values Of Parametersmentioning

confidence: 99%

“…Pn{l) = L Pn{l,k); [18] k the probability of the n-th residue being in state 1, and the (n+ 1)-th link being in state 1' [19] Downloaded by [New York University] at 04:02 08 January 2015…”

Section: I'mentioning

confidence: 99%

A Theoretical Study of Formation of DNA Noncanonical Structures Under Negative Superhelical Stress

Anshelevich

Vologodskii

Frank‐Kamenetskii

1988

Journal of Biomolecular Structure and Dynamics

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The development of statistical mechanical models of the formation of noncanonical structures in circular DNA and the finding of the energy parameters for these models made it possible to predict the appearance of such structures in a DNA with any given sequence. It does not seem feasible, however, to perform such calculations for DNA sequences of considerable length by allowing for all the possible states. We propose a special algorithm for calculating the thermodynamic characteristics of various conformational rearrangements in DNA that occur under negative supercoilings, allowing for several possible states of each base pair in the chain. Calculations have been performed for a number of natural DNAs. According to these calculations, the most likely noncanonical structures in DNA under normal conditions are cruciform structures and the Z form. The results of the calculations are compared with the experimental data reported in the literature. State diagrams have been computed for a number of inserts in circular DNA that can adopt both the cruciform conformation and the left-handed helical Z form.

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“…The loop coefficient, a, influences the cooperativity and the half width of each transition. a is dependent on the ionic strength and may be varied between 1 and 1.E -7 (16)(17)(18)(19).…”

Section: System and Methodsmentioning

confidence: 99%