DNA Fragment Conformations

The helix‐coil transition, conformations and dynamic structures of d(A‐C‐A‐T‐G‐T) we re investigated as a function of temperature by 1 H‐NMR spectroscopy at various frequencies (400, 276, 250 arid 90 MHz). Imino exchangeable protons of the d(A‐C‐A‐T‐G‐T) duplex were observed between 5°C and 25°C at 276 MHz. The results suggest that the fraying process mainly consists of two stages: the extreme dA · cT base pairs open at first; the internal dG · dC and central dA · dT base pairs then open simultaneously at higher temperatures. This conclusion was supported by the midpoint temperature measurements: a t 1/2 value of 32 2 °C was obtained for the extreme residues; the same t 1/2 value of 43± 3 °C was obtained for the internal and central base pairs. The helix and coil proportions and the dissociation constant were determined as a function of temperature from the $=f (t) curves corresponding to the non‐exchangeable protons of the internal and central residues. An enthalpy of 150 kJ/mol was found for the helix‐coil transition. At 400 MHz, all the non‐exchangeable proton resonances were assigned and most of the coupling constants were determined. The H‐1' resonance of the dC residue is particularly broad compared with that of the other H‐' protons at I > 42°C. This was attributed to the fact this proton is located in the proximity of the hydrogen bond between C= 0 of cytidine and H 2 of guanine. Several sugar protons, in particular H‐2', exhibited large chemical shift variations (between 20–72°C) which decrease from the central to the extreme residues; this seems to indicate a maximum helical distorsion for the residues. Comparison between the chemical shifts and tempereture‐dependent behaviours associated with d(A‐C‐A‐T‐G‐T) and d(A‐T‐G‐C‐A‐T) protons enabled the H‐1' and thymine H‐6 resonances of d(A‐T‐G‐C‐A‐T) to be assigned. The average sugar conformations of the d(A‐C‐A‐T‐G‐T) residues are very similar for both the helix and coil forms. The large predominance of the S conformation for all d(A‐C‐A‐T‐G‐T) residues and the insignificant chemical shift variation of the guanine 1–8 proton with increasing temperature are consistent with the B‐helical conformation. The initial relaxation time T 1 of the base protons was measured as a function of tem;perature at 90 and 250 MHz. At 250 MHz, the T 1 values vary slightly with temperature (T) , while at 90 MHz most of the curves of log T 1 = f (T −1 ) present a break point corresponding to the midpoint temperature for the hielix‐coil transition. The T 1 values of the adenine H‐8, H‐2 and thymine H‐6 protons are longer for the extreme than for the internal residues whatever the frequency and temperature. The correlation time for the coil form was determined at high temperatures from the proton TI ratios, T 1 (90 Hz)/Tl (250 Hz); t c = 0.2 ns at 65°C. For the helix state, the mobility appears to be different for the purine and pyrimidine bases: the former show a greater base‐sugar flexibility and the latter a stronger anisotropic character.