Hexamer oligonucleotide topology and assembly under solution phase NMR and theoretical modeling scrutiny |
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Authors: | Maxim P Evstigneev John A Parkinson Anastasia O Lantushenko Viktor V Kostjukov Valery I Pahomov |
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Institution: | 1. Sevastopol National Technical University, Department of Physics, Sevastopol 99053, Ukraine;2. University of Strathclyde, WestCHEM, Department of Pure and Applied Chemistry, 295 Cathedral Street, Glasgow G1 1XL, United KingdomMaxim P. Evstigneev and John A. Parkinson contributed equally to this work. |
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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 D298 K = (2.0 ± 0.07) × 10?10 m2 s?1 was evaluated across all hexamers except for d(GCGAGC) (D298 K = 1.7 × 10?10 m2 s?1) and d(GCGGGC) (D298 K = 1.2 × 10?10 m2 s?1). Melting under VT analysis (Tm = 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 remaining noncomplementary oligonucleotides adopt equilibria between monomer and duplex, contributed largely by monomer random‐coil forms. Contrastingly, d(GCGAGC) showed preference for tandem sheared GA mismatch duplex formation with an association constant K = 3.9 × 105M?1. No direct evidence was acquired for hairpin formation in any instance although its potential existence is considered possible for d(GCGAGC) on the basis of molecular modeling studies. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 1023–1038, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com |
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Keywords: | hexamer DNA topology diffusion NMR thermodynamics molecular modeling tandem mismatch |
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