Phosphorus Chemical Shifts in a Nucleic Acid Backbone from Combined Molecular Dynamics and Density Functional Calculations JanaPrˇecechte ˇ lova ´, † Petr Nova ´k, † Marke ´ta L. Munzarova ´, † Martin Kaupp, ‡ and Vladimı ´r Sklena ´ rˇ* ,† National Centre for Biomolecular Research, Faculty of Science, Masaryk UniVersity, Kotla ´r ˇska ´ 2, CZ-61137 Brno, Czech Republic, and Institut fu ¨r Chemie, Technische UniVersita ¨t Berlin, Strasse des 17. Juni 135, D-10623 Berlin, Germany Received May 31, 2010; E-mail: sklenar@chemi.muni.cz Abstract: A comprehensive quantum chemical analysis of the influence of backbone torsion angles on 31 P chemical shifts in DNAs has been carried out. An extensive DFT study employed snapshots obtained from the molecular dynamics simulation of [d(CGCGAATTCGCG)] 2 to construct geometries of a hydrated dimethyl phosphate, which was used as a model for the phosphodiester linkage. Our calculations provided differences of 2.1 ( 0.3 and 1.6 ( 0.3 ppm between the B I and B II chemical shifts in two B-DNA residues of interest, which is in a very good agreement with the difference of 1.6 ppm inferred from experimental data. A more negative 31 P chemical shift for a residue in pure B I conformation compared to residues in mixed B I /B II conformation states is provided by DFT, in agreement with the NMR experiment. Statistical analysis of the MD/DFT data revealed a large dispersion of chemical shifts in both B I and B II regions of DNA structures. δP ranges within 3.5 ( 0.8 ppm in the B I region and within 4.5 ( 1.5 ppm in the B II region. While the 31 P chemical shift becomes more negative with increasing R in B I -DNA, it has the opposite trend in B II -DNA when both R and  increase simultaneously. The 31 P chemical shift is dominated by the torsion angles R and , while an implicit treatment of  and ε is sufficient. The presence of an explicit solvent leads to a damping and a 2-3 ppm upfield shift of the torsion angle dependences. Introduction Numerous 31 P NMR experiments revealed the sensitivity of the 31 P chemical shift (δP) to the conformation of the sugar-phosphate backbone in nucleic acids (NA), demonstrating thus the potential of δP to provide valuable structural informa- tion. 1 Although spin-spin coupling constants are primarily used to obtain the restraints for torsion angles in biomolecules, such an approach can only be applied to a limited extent in the case of the NA backbone. 2 Six torsion angles define the conformation of the phosphodiester linkage in oligonucleotides (Figure 1). 3 While Karplus equations are available for , γ, δ, and ε, the torsion angles around P-O bonds cannot be determined since 3 J OPOC values are not accessible via experiment. 2,4 The relation- ships between δP and R/ are therefore of particular interest as they could be used to derive restraints unattainable from other sources. The phosphate groups connecting the sugar moieties undergo a dynamic interconversion between the -gauche/-gauche (R )-60° ( 30°,  )-60° ( 30°) and -gauche/trans (R) -60° ( 30°,  ) 180° ( 30°) substates, which are also frequently referred to as B I - and B II -DNA. 5,6 Sincesaccording to molecular dynamicssthe conformational exchange occurs on a nanosecond time scale 7 and since the two substates differ in δP, 1 the experimentally measured values of δ iso represent time averages over both conformations. In order to derive the populations of B I and B II states, one would have to know the † Masaryk University. ‡ Technische Universita ¨t Berlin. (1) Gorenstein, D. G. Chem. ReV. 1994, 94, 1315–1338. (2) Wijmenga, S. S.; van Buuren, B. N. M. Prog. Nucl. Magn. Reson. Spectrosc. 1998, 32, 287–387. (3) Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984. (4) Sychrovsky ´, V.; Voka ´c ˇova ´, Z.; S ˇ poner, J.; S ˇ packova ´, N.; Schneider, B. J. Phys. Chem. B 2006, 110, 22894–22902. (5) Schneider, B.; Neidle, S.; Berman, H. M. Biopolymers 1997, 42, 113– 124. (6) Fratini, A.; Kopka, M.; Drew, H.; Dickerson, R. J. Biol. Chem. 1982, 257, 4686–4707. (7) Trieb, M.; Rauch, C.; Wellenzohn, B.; Wibowo, F.; Loerting, T.; Liedl, K. R. J. Phys. Chem. B 2004, 108, 2470–2476. Figure 1. Nucleic acid backbone torsion angles: R (O3′-P-O5′-C5′),  (P-O5′-C5′-C4′), γ (O5′-C5′-C4′-C3′), δ (C5′-C4′-C3′-O3′), ε (C4′-C3′-O3′-P), and  (C3′-O3′-P-O5′). Published on Web 11/12/2010 10.1021/ja104564g  2010 American Chemical Society J. AM. CHEM. SOC. 2010, 132, 17139–17148 9 17139