Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutiny
Abstract
The entire family of noncomplementary hexamer oligodeoxyribonucleotides d(GCXYGC) (X and Y = A, G, C, or T) were assessed for topological indicators and equilibrium thermodynamics using a priori molecular modeling and solution phase NMR spectroscopy. Feasible modeled hairpin structures formed a basis from which solution structure and equilibria for each oligonucleotide were considered. ¹H and ³¹P variable temperature-dependent (VT) and concentration-dependent NMR data, NMR signal assignments, and diffusion parameters led to d(GCGAGC) and d(GCGGGC) being understood as exceptions within the family in terms of self-association and topological character. A mean diffusion coefficient D(298 K) = (2.0 ± 0.07) × 10⁻¹⁰ m² s⁻¹ was evaluated across all hexamers except for d(GCGAGC) (D(298 K) = 1.7 × 10⁻¹⁰ m² s⁻¹) and d(GCGGGC) (D(298 K) = 1.2 × 10⁻¹⁰ m² s⁻¹). Melting under VT analysis (T(m) = 323 K) combined with supporting NMR evidence confirmed d(GCGAGC) as the shortest tandem sheared GA mismatched duplex. Diffusion measurements were used to conclude that d(GCGGGC) preferentially exists as the shortest stable quadruplex structure. Thermodynamic analysis of all data led to the assertion that, with the exception of XY = GA and GG, the rem...Continue Reading
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