Synthesis and characterization of oligodeoxyribonucleotides containing terminal phosphates. NMR, UV spectroscopic and thermodynamic analysis of duplex formation of [d(pGGAATTCC)]2, [d(GGAATTCCp)]2and [d(pGGAATTCCp)]2

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Abstract
Derivatives of the oligomer [d(GGAATTCC)]2 with 5′ (5′-P), 3′ (3′-P) and both 5′ and 3′ (5′, 3′-P2) terminal phosphate groups have been synthesized and studied by temperature dependent UV and NMR spectroscopic methods. Thermo-dynamic studies of the helix to strand transition indicate that addition of 3′ phosphate groups has very little effect on the ΔG° for helix formation at 37°C while addition of 5′ phosphate groups adds approximately -0.5 kcal/mole to the ΔG° for duplex formation. The helix stabilization by 5′ phosphate groups occurs at salt concentrations of 0.1 M and above, and is primarily enthalpic in origin. Tm studies as a function of ionic strength also indicate that the oligomers fall into two groups with the parent and 3′-P derivatives being similar but less stable than the 5′-P and 5′, 3′-P2 derivatives. Imino proton and 31P NMR studies also divide the oligomers into these same two groups based on spectral comparisons and temperature induced chemical shift and linewidth changes. 31P NMR analysis suggests that addition of 5′ phosphate groups results in a small change in phosphodiester torsional angles in the g, t to g, g direction, indicating improved base stacking at the 5′ end of the modified oligomer. No such changes are seen at the 3′ end of the oligomer on adding 3′ phosphate groups.

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