Visualisation of a 2′-5′ parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2′,5′-adenosine

X-ray crystallographlc studies on 3′–5′ ollgomers have provided a great deal of information on the stereochemistry and conformational flexibility of nucleic acids and polynucleotides. In contrast, there is very little Information available on 2′–5′ polynucleotides. We have now obtained the crystal structure of Cytidylyl-2′,5′-Adenoslne (C2′p5′A) at atomic resolution to establish the conformational differences between these two classes of polymers. The dlnucleoside phosphate crystallises in the monocllnlc space group C2, with a = 33.912(4)Å, b =16.824(4)Å, c = 12.898(2)Å and 0 = 112.35(1) with two molecules in the asymmetric unit. Spectacularly, the two independent C2′p5′A molecules in the asymmetric unit form right handed miniature parallel stranded double helices with their respective crystallographic two fold (b axis) symmetry mates. Remarkably, the two mini duplexes are almost indistinguishable. The cytosines and adenines form self-pairs with three and two hydrogen bonds respectively. The conformation of the C and A residues about the glycosyl bond is anti same as in the 3′–5′ analog but contrasts the anti and syn geometry of C and A residues in A2′p5′C. The furanose ring conformation is C3′endo, C2′endo mixed puckering as in the C3′p5′A-proflavine complex. A comparison of the backbone torsion angles with other 2′–5′ dinucleoside structures reveals that the major deviations occur in the torsion angles about the C3′–C2′ and C4′-C3′ bonds. A right-handed 2′–5′ parallel stranded double helix having eight base pairs per turn and 45° turn angle between them has been constructed using this dinucleoside phosphate as repeat unit. A discussion on 2′–5′ parallel stranded double helix and its relevance to biological systems is presented.

Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate

The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.

Effect of calcium depletion on the secretion of newly synthesised human chorionic gonadotropin by first trimester human placenta

Depletion of calcium in the extracellular medium used to incubate first trimester human placental minces resulted in a significant decrease in the quantity of immuno-reactive hCG in the medium and a corresponding increase in the tissue. In contrast, when secretion of newly synthesised hCG was monitored in the absence of calcium by using a radioactive amino acid precursor, a significant increase in the secretion of newly synthesised hCG in the medium was noticed. This was true of secretion of other proteins also as evidenced by the increase in the trichloroacetic acid precipitable radioactivity in the medium in the absence of calcium. These results suggest that newly synthesised hCG is preferentially released over stored hormone in the absence of calcium.

Phase relations and thermodynamic properties of condensed phases in the system calcium-copper-oxygen

The isothermal sections of the phase diagram for the system Ca-Cu-0 at 1073 and 1223 K have been determined. Several compositions in the ternary system were quenched after equilibration, and the phases present were identified by optical microscopy, X-ray diffraction, and electron probe microanalysis. Two ternary compounds Ca2CuO3 and Cao.8&uO1.9s were identified at 1073 K. However, only Ca2CuO3 was found to be stable at 1223 K. The thermodynamic properties of the two ternary compounds were determined using solid-state cells incorporating either an oxide or a fluoride solid electrolyte. The results for both types of cells were internally consistent. The compound C ~ O . ~ & U Ow~h.i~ch~ c, a n also be represented as Ca15Cu18035h, as been identified in an earlier investigation as Cao.828CuOz. Using a novel variation of the galvanic cell technique, in which the emf of a cell incorporating a fluoride electrolyte is measured as a function of the oxygen potential of the gas phase in equilibrium with the condensed phase electrodes, it has been confirmed that the compound Cao.828CuO1.93 (Ca15Cu18035d) oes not have significant oxygen nonstoichiometry. Phase relations have been deduced from the thermodynamic data as a function of the partial pressure of oxygen for the system Ca-Cu-0 at 873, 1073, and 1223 K.

Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Structure and conformation of the calcium complex of cyclo(Ala-Leu-Pro-Gly)2 in two crystal forms

Crystal structures of two different forms of the calcium perchlorate complex of cyclo(Ala-Leu-Pro-Gly)2 have been determined and refined using X-ray crystallographic techniques. Orthorhombic form: C32H52N8O8.Ca(ClO4)2.7H2O.2CH3OH, space group C222(1), a = 14.366, b = 18.653, c = 19.824 A, Z = 4, R = 0.068 for 2208 observed reflections. Monoclinic form: C32H52N8O8.Ca(ClO4)2.4H2O, space group C2, a = 21.096, b = 10.182, c = 11.256 A, beta = 103.33 degrees, Z = 2, R = 0.075 for 2165 observed reflections. The cyclic peptide molecule in both the structures has the form of a twofold symmetric, slightly elongated bowl. Type II' beta-turns, involving Gly and Ala at the corners, exist at the two ends of the molecule. The interior of the molecule is substantially hydrophilic, and the external surface of the bowl is largely hydrophobic. The calcium ion is located at the centre of the mouth of the bowl-like molecule. In both crystal forms, four peptide carbonyl oxygens from the cyclic peptide and two solvent oxygens coordinate to the metal ion. The mode of complexation may be described as incomplete encapsulation as, for example, in the case of metal complexes of antamanide. In the crystal structures the complex ions are held together by hydrogen bonds involving perchlorate ions and water molecules. The molecular structure observed in the crystals is entirely consistent with the results of solution studies, which also indicate the conformation of the cyclic peptide in the complex to be similar to that of the uncomplexed molecule.

An electron-spin-resonance study of MN2+ doped calcium hydrazine carboxylate monohydrate

Single crystals of calcium hydrazine carboxylate, monohydrate have been studied by ESR of Mn2+ doped in the calcium sites. X-band ESR indicated a large crystal field splitting necessitating experiments at Q band. The analysis shows two magnetically inequivalent (but chemically equivalent) sites with g(xx) = 2.0042+/-0.0038, g(yy) = 2.0076 +/-00029, g(zz) =2.0314+/-0.001, A(zz) = 0.0099+/-0.0002 cm(-1), A(xx) = 0.0099+/-0.0002 cm(-1), A(yy) = 0.0082+/-0.0002cm(-1), D = 3/2D(zz) = 0.0558+/-0.0006cm(-1), and E = 1/2(D-xx-D-yy) = 0.0127+/-0.0002 cm(-1).One of the principal components of the crystal field, (D-zz), is found to be along the Ca<->Ca direction in the structure and a second one, (D-xx), along the perpendicular to the plane of the triangle formed by three neighbouring calciums. The A tensor is found to have an orientation different from that of the g and D tensors reflecting the low symmetry of the Ca2+ sites.

Calcium ionophore, A23187 and its amino acid complexes: spectroscopic and molecular modeling studies.

The circular dichroism, fluorescence, Nuclear Magnetic Resonance and BLM conductance studies indicate that A23187 forms a stable complex with amino acids at low ionophore concentrations (<10(-4)M). However, A23187 prefers to be in a dimeric structure with no significant binding to amino acids, at concentrations higher than 10(-4)M. It was also observed that at lower concentrations, at which the amino acids bind to the ionophore, the affinity for calcium ions was several orders of magnitude lower than that at higher ionophore concentrations. We have also conducted molecular modeling studies to examine the structure of the A23187 dimer and its amino acid complexes. The results of these modeling studies strongly support our experimental results and validate the formation of a hydrogen bonded and energetically stable A23187 dimer and its amino acid complexes.

Influence of acetyl and bromine substitutions on stacking. Crystal and molecular structures of 8-bromo-2',3',5'-triacetyl adenosine and 8-bromo 2',3',5'-triacetyl guanosine

The three dimensional structures of 8-bromo 2',3',5' triacetyl adenosine (8-Br Tri A) and 8-bromo 2',3',5'-triacetyl guanosine (8-Br Tri G) have been determined by single crystal X-ray diffraction methods to study the combined effect of bromine and acetyl substitutions on molecular conformation and interactions. The ribose puckers differ from those found in unbrominated Tri A and Tri G and unacetylated 8-Br A and 8-Br G analogues