Effect of cations on the volume of the helix-coil transition of poly[d(A-T)]

Najaf-Zadeh, Reza; Wu, Jianqing; Macgregor, Robert B.

doi:10.1016/0167-4781(95)00047-k

Cited by 24 publications

(27 citation statements)

References 24 publications

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“…The volume parameters associated with the DNA helix-coil transition have not been examined using a NN analysis; however, there are studies investigating the effects of chain length, 28 cation type, 29 fraction of G ⅐ C base pairs, 30 and overall transition volumes of other DNA polymers. [31][32][33] In general, at temperatures in the vicinity of the melting temperature, the molar volume of the double stranded form of DNA is 1-3 mL/mol less than that of the denatured state; thus, pressure stabilizes the double stranded form of DNA.…”

Section: Discussionmentioning

confidence: 98%

Volumetric properties of the formation of double stranded DNA: A nearest‐neighbor analysis

Dubins

Macgregor

2003

Biopolymers

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The kinetics of the helix-coil transition have been studied by performing UV-monitored melting and reannealing curves of DNA and analyzing the resultant hysteresis between these curves. The analysis assumes a single-step bimolecular transition with duplex formation defined as the forward reaction. Volume parameters of the helix-coil transition were obtained by measuring the pressure dependence of the rate constants from 5-200 MPa. The data were interpreted in terms of several possible nearest-neighbor models, ranging from one to eleven parameters. Twenty-four oligonucleotide duplexes 22 base pairs in length were used to solve for individual nearest-neighbor activation volumes and transition volumes. Statistically, the most valid fit of the volumetric data was obtained with a six-parameter model in which the directionality of the dinucleotide steps is not considered, for example, 5'AG/CT is the same as 5'GA/TC. The resultant transition volumes at 48 degrees C ranged from -7.1 +/- 0.8 mL/mol (GC/CG) to +2.9 +/- 0.3 mL/mol (AA/TT). The success of the six-parameter model suggests that the relative size of the nearest-neighbor dinucleotides is the most important factor determining the magnitude of the volumetric parameters. The finding that the magnitude of the volumetric parameters correlates with the change in the solvent accessible surface area of the bases during the helix-coil transition corroborates this hypothesis.

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Section: Discussionmentioning

confidence: 98%

Volumetric properties of the formation of double stranded DNA: A nearest‐neighbor analysis

Dubins

Macgregor

2003

Biopolymers

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“…In our analysis of data acquired at high pressure we have assumed that ΔH has no significant pressure dependence. This assumption is supported by the absence of a pressure dependence of the van't Hoff enthalpies for helix-coil transitions [2,20] as well as the data presented in Fig. 2.…”

Section: Helix-coil Transition Of Poly(da)·poly(dt) In Aqueous Solutimentioning

confidence: 59%

“…We have also assumed that the transition enthalpy is not strongly dependent on the nature of the counter-ion (Na + , Cs + ). This has been suggested in the literature [2]. The value of the T m in given in Table 1 is its value at atmosphere pressure (0.…”

Section: Helix-coil Transition Of Poly(da)·poly(dt) In Aqueous Solutimentioning

confidence: 96%

“…We have previously shown that there is a significant difference in the volume of the [2]. In the present study, we further investigate the thermodynamic and volumetric differences in the effect of Na + and Cs + on helix-coil transition of DNA with different sequences, poly[d(A-T)]·poly[d(A-T)] and poly(dA)·poly(dT), and on the intercalation of ethidium bromide (EB) with these two polymers.…”

Section: Introductionmentioning

confidence: 98%

“…We have previously reported that the different alkali metal cations have a significant impact on the volume of helix-coil transition of poly[d(A-T)]·poly[d(A-T)] [2]. The monovalent alkali cations, Na + , K + , Rb + , and Cs + , differ greatly in their ionic radius and consequently in their charge density and the extent to which they are hydrated.…”

Section: Introductionmentioning

confidence: 98%

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Effect of cesium on the volume of the helix–coil transition of dA·dT polymers and their ligand complexes

Shi

Macgregor

2007

Biophysical Chemistry

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Chain length and oligonucleotide stability at high pressure

Macgregor

1998

Biopolymers

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The effect of hydrostatic pressure on the helix‐coil transition temperature (Tm) was measured for the DNA oligomers (dA)n(dT)n, where n = 11, 15, and 19, in 50 mM NaCl. The data were analyzed in light of previously published data for the polymer, poly(dA)·poly(dT) under the same conditions. As has been observed for DNA polymers, increasing the hydrostatic pressure led to an increase in the Tm of the oligomers; however, the effect of pressure diminished with decreasing chain length. The value of dTm/dP decreased linearly with the inverse of the chain length varying from 3.15 × 10−2°C MPa−1 for the polymer to 0.7 × 10−2°C MPa−1 for the 11‐mer. The two‐state or van't Hoff enthalpy (ΔHvH) of the helix‐coil transition was obtained by analysis of the half‐width of the thermal transition. As expected, ΔHvH decreases with decreasing chain length. In contrast to the behavior of the polymer, poly(dA)·poly(dT), and (dA)19(dT)19, the ΔHvH of the two shorter duplex oligonucleotides displayed a small pressure dependence dΔHvH/dP≃−0.4 kJ MPa−1 in both cases. The changes observed in the Tm and ΔHvH were not sufficient to explain the magnitude of the chain‐length dependence of the pressure effect. To interpret the large chain‐length dependence of dTm/dP, we propose that the terminal base pairs contribute a negative volume change to the helix‐coil transition. Base pairs distant from the ends exhibit behavior characterized by the polymer where end effects are assumed to be negligible, i.e., a positive volume change for the helix‐coil transition. The negative volume change of separating terminal bases may originate from the imperfect interactions these base pairs form with water due to the existence of several energetically equivalent conformations. This is reminiscent of one of the mechanisms proposed to be important in the pressure‐induced dissociation of multimeric proteins into their constituent subunits. © 1996 John Wiley & Sons, Inc.

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Effect of cations on the volume of the helix-coil transition of poly[d(A-T)]

Cited by 24 publications

References 24 publications

Volumetric properties of the formation of double stranded DNA: A nearest‐neighbor analysis

Volumetric properties of the formation of double stranded DNA: A nearest‐neighbor analysis

Effect of cesium on the volume of the helix–coil transition of dA·dT polymers and their ligand complexes

Chain length and oligonucleotide stability at high pressure

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