The d ATGCAT 2 Duplex

The d(ATGCAT)2 Duplex. From NMR studies of the d(ATGCAT)2 duplex, it was known that, even at the lowest temperature studied, the terminal AT base-pairs were partially open or frayed . By partitioning the calorimetrically measured enthalpy into contributions from the internal AT and GC pairs using data from the d(GCGCGC)2 duplex and other measurements on AT pairs (not reproduced here), Breslauer and colleagues were able to show that what the NMR spectra interpreted as open pairs were also energetically ruptured. 

Technique Calor vH Calor vH Calor vH Calor vH Calor vH Calor vH 

Abbreviations calor = AH obtained from integration of the integrated DSC curve vH = a van t Hoff enthalpy obtained from UV absorbance or NMR chemical shift measurements unless otherwise noted NR indicates that results were not reported. 

Since a comparison of various van t Hoff enthalpies (calculated by analysis of da/dT at Tm, the slope of /Tm vs In cTot and the shape of the calorimetric curve)0 with the calorimetric enthalpy shows that A// h A//Cai, it was concluded that the melting transition in this duplex is cooperative and well represented by a two-state model. 

The d(CGCGAATTCGCG)2 Duplex. When studied at comparable salt (NaCl) and duplex concentrations, the duplex of d(CGCGAATTCGCG) was found to have about the same Tm by DSC measurements (344 K) and by the temperature-dependent changes in the NMR chemical shifts of nonexchangeable GC and AT protons (345 K). At 0.01 M NaCl, the calorimetric enthalpy was 376 kJ mol-1 of duplex, while the van t Hoff enthalpy evaluated from equation (16.28) was found to be 393 kJ-mol-1 of duplex. At a 10-fold higher salt concentration, the calorimetric enthalpy was 427 kJ-mol-1 of duplex, while the van t Hoff enthalpy was 310 kJ-mol-1 of duplex. From the ratio of the van t Hoff enthalpy to the calorimetric enthalpy at the higher salt concentration, it was estimated that 9 out of 12 base-pairs melt together in the cooperative unit, while all melt simultaneously at the low salt concentrations. 

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