Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B DNA.
In previous papers of this series the temperature-dependent Raman spectra of poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) were used to characterize structurally the melting and premelting transitions in DNAs containing consecutive A.T and alternating A.T/T.A base pairs. Here, we describe procedures for obtaining thermodynamic parameters from the Raman data. The method exploits base-specific and backbone-specific Raman markers to determine separate thermodynamic contributions of A, T and deoxyribosyl-phosphate moieties to premelting and melting transitions. Key findings include the following: (i) Both poly(dA).poly(dT) and poly(dA-dT). poly(dA-dT) exhibit robust premelting transitions, due predominantly to backbone conformational changes. (ii) The significant van't Hoff premelting enthalpies of poly(dA).poly(dT) [DeltaH(vH)(pm) = 18.0 +/- 1.6 kcal x mol(-1) (kilocalories per mole cooperative unit)] and poly(dA-dT).poly(dA-dT) (DeltaH(vH)(pm) = 13.4 +/- 2.5 kcal x mol(-1)) differ by an amount (approximately 4.6 kcal x mol(-1)) estimated as the contribution from three-centered inter-base hydrogen bonding in (dA)(n).(dT)(n) tracts. (iii) The overall stacking free energy of poly(dA). poly(dT) [-6.88 kcal x mol(bp)(-1) (kilocalories per mole base pair)] is greater than that of poly(dA-dT). poly(dA-dT) (-6.31 kcal x mol(bp)(-1)). (iv) The difference between stacking free energies of A and T is significant in poly(dA).poly(dT) (DeltaDeltaG(st) = 0.8 +/- 0.3 kcal. mol(bp)(-1)), but marginal in poly(dA-dT).poly(dA-dT) (DeltaDeltaG(st) = 0.3 +/- 0.3 kcal x mol(bp)(-1)). (v) In poly(dA). poly(dT), the van't Hoff parameters for melting of A (DeltaH(vH)(A) = 407 +/- 23 kcal.mol(-1), DeltaS(vH)(A) = 1166 +/- 67 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(A) = 60.0 +/- 3.2 kcal x mol(-1)) are clearly distinguished from those of T (DeltaH(vH)(T) = 185 +/- 38 kcal x mol(-1), DeltaS(vH)(T) = 516 +/- 109 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(T) = 27.1 +/- 5.5 kcal x mol(-1)). (vi) Similar relative differences are observed in poly(dA-dT). poly(dA-dT) (DeltaH(vH)(A) = 333 +/- 54 kcal x mol(-1), DeltaS(vH)(A) = 961 +/- 157 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(A) = 45.0 +/- 7.6 kcal x mol(-1); DeltaH(vH)(T) = 213 +/- 30 kcal x mol(-1), DeltaS(vH)(T) = 617 +/- 86 cal. degrees K(-1) x mol(-1), DeltaG(vH(25 degrees C))(T) = 29.3 +/- 4.9 kcal x mol(-1)). The methodology employed here distinguishes thermodynamic contributions of base stacking, base pairing and backbone conformational ordering in the molecular mechanism of double-helical B DNA formation.
Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110-2499, USA.
Liviu
L
Movileanu
James M
JM
Benevides
George J
GJ
Thomas
D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D019277:Entropy; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011067:Poly dA-dT / Q000737:chemistry; D015203:Reproducibility of Results; D013059:Spectrum Analysis, Raman / Q000379:methods; D013696:Temperature; D013816:Thermodynamics
D011067:Poly dA-dT; D004247:DNA