Hysteresis of denaturation of DNA in the melting range

Hoff, A. J.; Roos, A.

doi:10.1002/bip.1972.360110612

Cited by 36 publications

(14 citation statements)

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“…Hoff and Roos's model (5) allowed to obtain a satisfactory explanation of the hysteresis phenomena occuring at a low ionic strength. However, it is hard to understand from this model why the denaturation of a section flanked by melted regions proceeds so slowly at the equilibrium melting temperature Tm, for denaturation does not require nucleation.…”

Section: Resultsmentioning

confidence: 99%

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The nonequilibrium character of DNA melting: effects of the heating rate on the fine structure of melting curves

Kozyavkin

Lyubchenko

1984

Nucl Acids Res

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SUMMARYTo investigate the effects of heating rate on the DNA melting profile and to test the predictions of the theory of slow relaxation processes in DNA melting (1) concerning these effects, we obtained differential melting curves for the Bsp I Cl fragment of T7 DNA (1461 bp) and the Sma I-Eco RI fragment of Col El DNA (1291 bp) at heating Sates of 0.05 and 0.5 deg/min. At low ionic strength (0.02 M Na ) the heating rate has been shown to affect the position of the third peak in melting curve for Cl fragment.According to the melting maps (2), this peak corresponds to the unwinding of the section between the end of the molecule and Vhe region already melted.At high ionic strength (0.2 M Na ), when the melting of this DNA is reversible (3), the position of the peaks does not depend on the heating rate.In the case of the Col El DNA fragment the heating rate affects, as might be expected from the melting maps (4), only the last peak, as the melting of the last section is always nonequilibrium. The results of the study are in good qualitative agreement and in satisfactory quantitative agreement with the theoretical predictions (1).

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Section: Resultsmentioning

confidence: 99%

“…A comparison of high resolution differential curves for the partial melting and subsequent renaturation of DNA with the data on their melting topography (3) yielded the definitive proof of the model accounting for irreversibility (5).…”

Section: Introductionmentioning

confidence: 86%

The nonequilibrium character of DNA melting: effects of the heating rate on the fine structure of melting curves

Kozyavkin

Lyubchenko

1984

Nucl Acids Res

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“…Of the above points, perhaps most difficult to reconcile is the variety of DNA samples that have been studied. Data from melting studies of short (6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16) bps) linear synthetic DNAs,~ DNA restriction fragments -150-6000 bps in length, 1,3,s~10 and long repeating copolymers 1,2 has been utilized to evaluate the n-n stacking interactions in DNA. Unfortu-nately, these samples have features that can obscure interpretation of melting curves in terms of n-n sequence stability.…”

Section: Introductionmentioning

confidence: 99%

Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T₄ endloops: Evaluation of the nearest‐neighbor stacking interactions in DNA

Doktycz¹,

Goldstein²,

Paner³

et al. 1992

Biopolymers

121

116

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Seventeen DNA dumbbells were constructed that have duplex sequences ranging in length from 14 to 18 base pairs linked on the ends by T4 single-strand loops. Fifteen of the molecules have the core duplexes with the sequences 5'G-T-A-T-C-C-(W-X-Y-Z)-G-G-A-T-A-C3', where (W-X-Y-Z) represents a unique combination of A.T, T.A, G.C, and C.G base pairs. The remaining two molecules have the central sequence (W-X-Y-Z) = A-C and A-C-A-C-A-C. These duplex sequences were designed such that the central sequences include different combinations of the 10 possible nearest-neighbor (n-n) stacks in DNA. In this sense the set of molecules is complete and serves as a model system for evaluating sequence-dependent local stability of DNA. Optical melting curves of the samples were collected in 25, 55, 85, and 115 mM [Na+], and showed, regardless of solvent ionic strength, that the transition temperatures of the dumbbells vary by as much as 14 degrees for different molecules of the set. Results of melting experiments analyzed in terms of a n-n sequence-dependent model allowed evaluation of nine independent linear combinations of the n-n stacking interactions in DNA as a function of solvent ionic strength. Although there are in principle 10 possible different n-n interactions in DNA, these 10 are not linearly independent and therefore can not be uniquely determined. For molecules with ends, there are 9 linearly independent combinations, as opposed to circular or semiinfinite repeating copolymers where only 8 linear combinations of the 10 possible n-n interactions are linearly independent. The n-n interactions are presented as combinations of the deviations from average stacking for the 5'-3' base-pair doublets, delta Gi, and reveal several interesting features: (1) Titratable changes in the values of delta Gi with changing salt environment are observed. In all salts the most stable unique combination is delta G4 = (delta GGpC+delta GCpG)/2, and the least stable is the GpG/CpC stack, delta G2 = delta GGpG/CpC. (2) The chi 2 values of the fits of the evaluated delta Gi's to experimental data increased with decreasing [Na+], suggesting that significant interactions beyond nearest neighbors become more pronounced, particularly at 25 nM Na+.(ABSTRACT TRUNCATED AT 400 WORDS)

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“…[9] However,t his alternative approach has not been explored to amplify nucleic acids,which possibly is due to the predominant use of thermal cycling for historical reasons that restrict explorations in other directions. [10] Moreover,c hanging the solution pH in an automated way is difficult. Herein, we develop an ionmediated PCR (IM-PCR) strategy to amplify nucleic acids with pH cycling at ac onstant temperature (Scheme 1).…”

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Ion‐Mediated Polymerase Chain Reactions Performed with an Electronically Driven Microfluidic Device

Zeng

Guo

et al. 2016

Angew Chem Int Ed

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The polymerase chain reaction (PCR) is a powerful method for exponentially amplifying very low amounts of target DNA from genetic, clinical, and forensic samples. However, the heating and cooling steps in PCR largely hamper the miniaturization of thermocyclers for on-site detection of pathogens and point-of-care tests. Herein, we devise an ion-mediated PCR (IM-PCR) strategy by exploiting ion-induced DNA denaturation/renaturation cycles. DNA duplexes are effectively denatured in alkaline solutions; whereas, the denatured single-stranded DNA strands readily reform duplexes at neutral pH. By using an integrated microchip that can programmably control the solution pH simply switching the potential in a range of several hundred millivolts, we can trigger IM-PCR at a constant temperature. Analogously to thermal cycling, 30 cycles of pH-induced denaturation/renaturation were used to amplify protein DNA fragments as confirmed by DNA sequencing. We anticipate that this portable, low-cost, and scalable IM-PCR holds great promise for widespread biological, clinical, and environmental applications.

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Hysteresis of denaturation of DNA in the melting range

Cited by 36 publications

References 9 publications

The nonequilibrium character of DNA melting: effects of the heating rate on the fine structure of melting curves

The nonequilibrium character of DNA melting: effects of the heating rate on the fine structure of melting curves

Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T₄ endloops: Evaluation of the nearest‐neighbor stacking interactions in DNA

Ion‐Mediated Polymerase Chain Reactions Performed with an Electronically Driven Microfluidic Device

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Hysteresis of denaturation of DNA in the melting range

Cited by 36 publications

References 9 publications

The nonequilibrium character of DNA melting: effects of the heating rate on the fine structure of melting curves

The nonequilibrium character of DNA melting: effects of the heating rate on the fine structure of melting curves

Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: Evaluation of the nearest‐neighbor stacking interactions in DNA

Ion‐Mediated Polymerase Chain Reactions Performed with an Electronically Driven Microfluidic Device

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Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T₄ endloops: Evaluation of the nearest‐neighbor stacking interactions in DNA