The crystal and molecular structure of guanosine-5'-phosphate trihydrate

Spontaneous Assembly of an Organic-Inorganic Nucleic Acid Z-DNA Double-Helix Structure

Herein, we report a hybrid polyoxometalate organic-inorganic compound, Na₂ [(HGMP)₂ Mo₅ O₁₅ ]⋅7 H₂ O (1; where GMP=guanosine monophosphate), which spontaneously assembles into a structure with dimensions that are strikingly similar to those of the naturally occurring left-handed Z-form of DNA. The helical parameters in the crystal structure of the new compound, such as rise per turn and helical twist per dimer, are nearly identical to this DNA conformation, allowing a close comparison of the two structures. Solution circular dichroism studies show that compound 1 also forms extended secondary structures in solution. Gel electrophoresis studies demonstrate the formation of non-covalent adducts with natural plasmids. Thus we show a route by which simple hybrid inorganic-organic monomers, such as compound 1, can spontaneously assemble into a double helix without the need for a covalently connected linear sequence of nucleic acid base pairs.

C–H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study

The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of benzene and pyridine. These results can be very important for molecular recognition of DNA and RNA.

Metal-nucleotide interactions: crystal structures of alkali (Li+, Na+, K+) and alkaline earth (Ca2+, Mg2+) metal complexes of adenosine 2'-monophosphate

Crystal structures of lithium, sodium, potassium, calcium and magnesium salts of adenosine 2'-monophosphate (2'-AMP) have been obtained at atomic resolution by X-ray crystallographic methods. 2'-AMP.Li belongs to the monoclinic space group P2(1) with a = 7.472(3)A, b = 26.853(6) A, c = 9.184(1)A, b = 113.36(1)A and Z= 4. 2'-AMP.Na and 2'-AMP.K crystallize in the trigonal space groups P3(1) and P3(1)21 with a = 8.762(1)A, c = 34.630(5)A, Z= 6 and a = 8.931(4), Ac = 34.852(9)A and Z= 6 respectively while 2'-AMP.Ca and 2'-AMP.Mg belong to space groups P6(5)22 and P2(1) with cell parameters a = 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 10.023(2), c = 16.506(2), beta = 91.1(0) and Z = 2 respectively. All the structures were solved by direct methods and refined by full matrix least-squares to final R factors of 0.033, 0.028, 0.075, 0.069 and 0.030 for 2'-AMP.Li, 2'-AMP.Na, 2'- AMP.K, 2'-AMP.Ca and 2'-AMP.Mg, respectively. The neutral adenine bases in all the structures are in syn conformation stabilized by the O5'-N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry (chiCN = -156.4(2)degrees) in 2'-AMP.Mg. Ribose moieties adopt C2'-endo puckering in 2'-AMP.Li and 2'-AMP.Ca, C2'-endo-C3'-exo twist puckering in 2'-AMP.Na and 2'-AMP.K and a C3'-endo-C2'-exo twist puckering in 2'-AMP.Mg structure. The conformation about the exocyclic C4'-C5' bond is the commonly observed gauche-gauche (g+) in all the structures except the gauche- trans (g-) conformation observed in 2'-AMP.Mg structure. Lithium ions coordinate with water, ribose and phosphate oxygens at distances 1.88 to 1.99A. Na+ ions and K+ ions interact with phosphate and ribose oxygens directly and with N7 indirectly through a water oxygen. A distinct feature of 2'-AMP.Na and 2'-AMP.K structures is the involvement of ribose 04' in metal coordination. The calcium ion situated on a two-fold axis coordinates directly with three oxygens OW1, OW2 and O2 and their symmetry mates at distances 2.18 to 2.42A forming an octahedron. A classic example of an exception to the existence of the O5'-N3 intramolecular hydorgen bond is the 2'-AMP.Mg strucure. Magnesium ion forms an octahedral coordination with three water and three phosphate oxygens at distances ranging from 2.02 to 2.11 A. A noteworthy feature of its coordination is the indirect link with N3 through OW3 oxygen resulting in macrochelation between the base and the phosphate group. Greater affnity of metal clays towards 5' compared to 2' and 3' nucleotides (J. Lawless, E. Edelson, and L. Manning, Am. Chem. Soc. Northwest Region Meeting, Seattle. 1978) due to macrochelation infered from solution studies (S. S. Massoud, H. Sigel, Eur J. Biochem. 179, 451-458 (1989)) and interligand hydrogen bonding induced by metals postulated from metal-nucleotide structures in solid state (V. Swaminathan and M. Sundaralingam, CRC. Crit. Rev. Biochem. 6, 245-336 (1979)) are borne out by our structures also. The stacking patterns of adenine bases of both 2'-AMP.Na and 2'-AMP.K structures resemble the 2'-AMP.NH4 structure reported in the previous article. 2'-AMP.Li, 2'-AMP.Ca and 2'-AMP.Mg structures display base-ribose 04' stacking. An overview of interaction of monovalent and divalent cations with 2' and 5'-nucleotides has been presented.

Computer simulation of aqueous biomolecular systems

Computer simulation techniques are increasingly being used to predict structural and thermodynamic properties of large heterogeneous macromolecule and solvent assemblies. We discuss, with examples from our own studies, some problems we and others have experienced in using these techniques, which were originally devised for simple liquids. In particular, we consider the problems which arise from the large size and heterogeneity of macromolecule water systems, comparisons with experimental data and equilibrium and sampling procedures.

Solvent interactions in nucleic acid crystal hydrates

A detailed knowledge of structural and energetic aspects of water-nucleic acid interactions is essential for understanding the role of solvent in stabilizing the various helical forms of nucleic acids. In this study, computer simulation techniques have been used to predict structural properties of solvent networks in small nucleic acid crystal hydrates. A detailed comparison of predicted and experimental results on the structure of the solvent networks is presented and includes an analysis of both the local environment and hydrogen bond pattern of each water molecule. A correlation between the environment of each unique water molecule and its energetic properties (such a dipole moment and binding energy) is seen. As in the previous studies on small amino acid hydrate crystals, non-pair additive (cooperative) effects are found to be non-negligible. It is concluded that the potential functions used in this initial study lead to simulated solvent networks in reasonable agreement with experimental data. Thus, it is now feasible to use them in studies of hydration of larger helical fragments of nucleic acids of more direct biological interest.