Chain length and oligonucleotide stability at high pressure.
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) center dot 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 x 10(-2) degrees C MPa-1 for the polymer to 0.7 x 10(-2) degrees C MPa-1 for the 11-mer. The two-state or van't Hoff enthalpy (DeltaHvH) of the helix-coil transition was obtained by analysis of the half-width of the thermal transition. As expected, DeltaHvH decreases with decreasing chain length. In contrast to the behavior of the polymer, poly(dA) center dot poly(dT), and (dA)19(dT)19, the DeltaHvH of the two shorter duplex oligonucleotides displayed a small pressure dependence dDeltaHvH/dP approximately equal -0.4 kJ MPa-1 in both cases. The changes observed in the Tm and DeltaHvH 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.
Faculty of Pharmacy, University of Toronto, Ontario, Canada.
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D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004247:DNA / Q000737:chemistry*; D004355:Drug Stability; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D011312:Pressure; D013329:Structure-Activity Relationship
D009841:Oligonucleotides; D004247:DNA