Thermodynamics and Kinetics of Base‐Stacking Interactions

FEBS Journal - Tập 26 Số 4 - Trang 490-498 - 1972
Dietmar Pörschke1, F. Eggers1
1Max-Planck-Institut für Biophysikalische Chemie BRD-3400 Göttingen, Am Faßberg German Federal Republic

Tóm tắt

The thermodynamics and kinetics of the self‐association of N6, N9‐dimethyladenine has been studied as a model system for base stacking. Molal osmotic coefficients have been determined by vapor pressure osmometry in aqueous solutions at four different temperatures. These data, indicating a very high degree of association much beyond the dimer stage, are consistent with a series of consecutive equivalent association processes. The analysis is performed with an isodesmic model, which allows for cooperativity of the first binding step. Cooperativity can almost be neglected in the present case; the thermodynamic parameters for the formation of stacks are ΔH°=– 8.7 (° 1.5) kcal/mol and ΔS°=– 21.6 cal/K resulting in a stability constant K= 60 at 20°C.The kinetics of base stacking has been investigated by means of sound absorption techniques in the 10–100 MHz frequency range. The excess absorption profiles are only slightly broader than theoretically expected for a single relaxation process. The data can be explained by an isodesmic kinetic model. Formation of stacks proceeds with a rate constant of about 109 M−1 sec−1 and an activation enthalpy of + 6 kcal/mol. Evaluation of the amplitudes leads to a volume change of 6.8 ml (at 25°C) per mol of stacking sites. The volume change decreases with increasing temperature. Optical measurements in a pressure cell show that the volume decreases with increasing number of stacks.These results are discussed with respect to current theories of base stacking. Both ΔH and ΔV found for the stacking equilibrium are in contrast to the thermodynamic parameters of hydro‐phobic interactions according to the standard view. The present data demonstrate a characteristic difference of hydrophobic interactions between unpolar, unpolarisable particles like simple hydrocarbons and between compounds like nucleic acid bases with high polarisability and a dipole structure.

Từ khóa


Tài liệu tham khảo

10.1146/annurev.bi.36.070167.002203

10.1063/1.1723985

10.1016/S0065-3233(08)60608-7

10.1063/1.1732473

10.1021/j100816a004

Sinanoglu O., 1965, Fed. Proc., 24, S‐12

10.1021/ja00892a016

10.1021/ja01073a054

10.1021/ja00990a047

10.1021/ja01048a033

10.1016/0022-2836(68)90281-7

10.1016/0005-2787(68)90079-8

10.1016/S0006-291X(67)80132-3

10.1016/0022-5193(69)90007-1

10.1016/0005-2787(70)90622-2

Eigen M., 1963, Techniques of Organic Chemistry

10.1021/bi00845a029

10.1016/0005-2787(68)90079-8

10.1002/ange.19670790603

10.1021/bi00853a042

Eggers F., 1969, Methods Enzymol., 16, 74

Eggers F., 1972, Ultrasonic Measurements with Milliliter-Liquid Samples in the 0.5 to 100 MHz Range

Thông tin
Thông tin xuất bản

FEBS Journal

Tập 26 Số 4

490-498

Thông tin tác giả