Endo Pucker Research Articles

Stereochemistry of 2′,5′ Nucleic Acids and Their Constituents

Shape and dimension of the preferred nucleotide repeats in nucleic acids are found to depend on whether the sugar-phosphate linkage is of 2′,5′ or 3′,5′ type. It is shown that a nucleotide which is “compact” in 3′,5′ nucleic acids is rendered “extended” and vice versa for a given sugar pucker. It is interesting that this feature is accompanied by a switch in the preferred sugar ring conformation in 3′,5′ and 2′,5′ nucleic acids. 3′ ribose and 3′ deoxyribose rings (in 2′,5′ linkages) tend to favour C2′ endo and C3′ endo puckers respectively in contrast to C3′ endo and C2′ endo puckers favored by 2′ ribose and 2′ deoxyribose sugars (in 3′,5′ linkages).The distinguishable features between the nucleotide repeats of 3′,5′ and 2′,5′ nucleic acids need to be recognised while discussing their structural properties, as well as those of a variety of complexes that could be formed involving 2′,5′ and 3′,5′ strands of DNA and RNA. Ability and stability, or lack of them, for formation of a specific combination of these complexes may be directly related to the stereochemical constraints imposed as a consequence of conformationally homogeneous or heterogeneous nature of the repeating nucleotides of the complexing chains. As a first step towards delineating stereochemical features that distinguish 2′,5′ nucleic acids from their naturally occurring isomer A and B type helices have been modelled using the new concept of “compact” and “extended” nucleotide repeat that seemingly unifies helix generation of both types of linkages. Helical models for 2′,5′ RNA with “dinucleotide” repeat based on the crystal structure of 2′,5′ ApU have also been obtained.

Molecular Dynamics and Continuum Solvent Studies of the Stability of PolyG-PolyC and PolyA-PolyT DNA Duplexes in Solution

Molecular dynamics simulation in explicit solvent and continuum solvent models are applied to investigate the relative stability of A- and B-form helices for two DNA sequences, dA10−dT10 and dG10−dC10 in three structural forms. One structural form is based on an unrestrained molecular dynamics (MD) trajectory starting from a canonical B-DNA structure, the second is based on a MD trajectory starting in a canonical B-DNA structure with the sugars constrained to be C2′-endo and the third simulation started from a canonical A-DNA structure with the sugars constrained to C3′-endo puckers. For the energetic analysis, structures were taken as snapshots from nanosecond length molecular dynamics simulations computed in a consistent fashion in explicit solvent, applying the particle mesh Ewald method and the Cornell et al, force field. The electrostatic contributions to solvation free energies are computed using both, a finite-difference Poisson-Boltzmann model and a pairwise Generalized Bom model. The non-electrostatic contributions to the solvation free energies are estimated with a solvent accessible surface area dependent term. To estimate the gas phase component of the relative free energy between the various structures, the mean solute internal energies (determined with the Cornell et al, molecular mechanics potential including all pairwise interactions within the solute) and estimates of the solute entropy (using a harmonic approximation) were used. Consistent with experiment, the polyG-polyC (GC) structures are found to be much more A-phillic than the polyA-polyT (AT) structures, the latter being quite A-pho- bic. The dominant energy components responsible for this difference comes from the internal and van der Waal energies. A perhaps less appreciated difference between the GC and AT rich sequences is suggested by the calculated salt dependence which demonstrates a significantly enhanced ability to drive GC rich sequences towards an A-form structure compared to AT rich sequences. In addition to being A-phobic, the AT structure also has a noticably larger helical repeat than GC and other mixed sequence duplexes, consistent with experiment. Analysis of the average solvent density from the trajectories shows hydration patterns in qualitative agreement with experiment and previous theoretical treatments.

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 P21 with a= 7.472(3)Å, b = 26.853(6) Å, c = 9.184(l)Å, b = 113.36(l)Å and Z= 4. 2′-AMP.Na and 2′-AMP.K crystallize in the trigonal space groups P31 and P3 121 with a= 8.762(l)Å, c = 34.630(5)Å, Z= 6 and a= 8.931(4), Åc = 34.852(9)Å and Z= 6 respectively while 2′-AMP.Ca and 2′-AMP.Mg belong to space groups P6522 and P21 with cell parameters a= 9.487(2), c = 74.622(13), Z = 12 and a = 4.973(1), b = 1 0.023(2), c = 16.506(2), β = 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 05′ -N3 intramolecular hydrogen bond as in free acid and ammonium complex reported earlier. In striking contrast, the adenine base is in the anti geometry(XCN = -156.4(2)°) 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. 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 1.99Å. 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 OWl, OW2 and 02 and their symmetry mates at distances 2.18 to 2.42Å forming an octahedron. A classic example of an exception to the existence of the 05′-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 2.11Å. 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. Manring, Am. Chern. 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.

Conformational analysis of the complete series of 2′ and 3′ monofluorinated dideoxyuridines

The solution conformations of a set of uridine 2′,3′-dideoxynucleosides, where each of the hydrogens at the 2′- and 3′-positions of the sugar ring were individually replaced with a fluorine atom, were studied by nuclear magnetic resonance spectroscopy and pseudorotational analysis. The distribution of the north/south (N/S) puckering equilibrium for each compound was calculated by coupling constant analysis aided by the program PSEUROT. The data confirmed that the pseudorotational equilibrium of the fluorinated glycones is governed by the position of the fluorine atom. The preferred rotamer populations about the C4′–C5′ ( γ) and C1′–N1′ ( χ) bonds calculated from coupling constant and NOE analysis, respectively, were also influenced by the presence of fluorine. Proton coupling to the fluorine atom was also used to qualitatively estimate the N/S equilibrium population. Through space, long range 1H– 19F coupling constants were observed in compounds where the fluorine atom was above the plane of the ring (`up'). The pseudorotational parameters of the compounds described were tempered by the anomeric effect which drives the pseudorotational equilibrium towards the 2′-exo/3′-endo (northern) pucker. Ab initio calculations using the 3–21 G * basis set yielded a measure of the energy differences between the N and S local minima in each compound. These results agree with previous conformational studies of other fluorinated nucleoside analogues and prove that the furanose ring pucker is governed by the highly electronegative fluorine atom. However, the competing anomeric effect plays a major role in determining the mole fraction of the minor conformer of these compounds in solution.

4-Amino-1-(2-deoxy-β-D-ribofuranosyl)-6,7-dihydro-1H,5H-cyclopentapyrimidine-2-one

The crystal structure of C12H17N304 has been determined. This modified base is in a syn conformation with respect to the deoxyribose sugar, which adopts a distorted C3'/04'-endo pucker.

The α-Pyridyl Nucleoside Analogue 2-Bromo-5-(2-deoxy-α-D-ribofuranosyl)pyridine

The structure of the title compound, C 10 H 12 BrNO 3 , is reported. The ribose sugar has a C3′-endo pucker and the exocyclic torsion angle O5′ - C5′ - C4′ - C3′ adopts a gauche + value of 61.0 (9)°.

Crystal structure of RNase T1 complexed with the product nucleotide 3'-GMP. Structural evidence for direct interaction of histidine 40 and glutamic acid 58 with the 2'-hydroxyl group of the ribose.

The crystal structure of RNase T1 complexed with 3'-GMP has been determined. The glycosyl conformation of 3'-GMP is in the syn conformation, and the ribose adopts the O4'-endo pucker. This observed pucker is different from that in any complex structures of RNase T1. In the present complex, this energetically unfavorable conformation is stabilized by the water molecule with the bridged hydrogen bonds between the O2' and the O3' atoms of the ribose. The guanine base is recognized in the same manner as observed in the complex of 2'-GMP. The 2'-hydroxyl group of the ribose shows a tight hydrogen bond to both His-40 and Glu-58 with the suitable geometry for the proton transfer. These hydrogen bonds suggest that the two residues can participate directly in the proton transfer. His-92 is hydrogen bonded to two the proton transfer. His-92 is hydrogen bonded to two oxygen atoms of the phosphate group. Based on the geometry in the active site, the O1P atom may correspond to the O5' atom of the leaving nucleotide in the phosphoryl transfer or a water molecule as a nucleophile in the hydrolysis reaction. In the present complex, the conformations of the 3'-GMP molecule and the side chains of the catalytic residues would be represented as the conformation before the phosphoryl transfer reaction and/or after the hydrolysis reaction.

O5′,6-Methanocytidine — Synthesis, Conformational Properties and Deamination by Cytidine Deaminase

Abstract The synthesis of O5′,6-methanocytidine (4), a pyrimidine nucleoside restricted to the anti conformation, is described. Molecular modeling studies suggest that 4 is more flexible than conventional cyclonucleosides because of its larger-than-usual bridging system and that it can exist in a number of low energy conformations where the glycosyl rotation angles (X) cover an ∼80° segment of the anti range. However, while both N-type (C2′-exo) and S-type (C3′-exo) sugar puckerings are possible, none of the low energy conformers adopt the C3′-endo or C2′-endo puckering modes generally seen for unconstrained nucleosides. The lowest energy conformer predicted for 4 (X = −152°, y = 73°, P = 206°) is similar to the X-ray structure of a related compound, namely 5-hydroxy-O5′,6 -methanouridine (12, X = −138°. Y = 63°, P = 200°). In solution, NMR evidence suggests an equilibrium between C2′-exo and C3′-exo puckerings for 4, and CD evidence suggests an average glycosyl rotation angle (X) of around −160°. O5′,6 -...

Molecular dynamics simulations of a r(GA12G).d(CT12C) hybrid duplex.

RNA.DNA hybrid duplexes are relevant in various biological mechanisms like transcription and replication. Enzymes like RNase H cleave specifically the RNA strand in RNA.DNA duplexes. In antisense technology the complexation of mRNA with "modified" oligo(deoxy)-nucleotides leads to new hybrid duplexes. The knowledge about structure and dynamical behavior on an atomic level is fundamental for the understanding of any process involving hybrid duplexes. Therefore, molecular dynamics studies (200 picoseconds of trajectory) on a hybrid duplex structure r(GA12G).d(CT12C) were performed. During the stimulations, the deoxyribose residues assumed a puckering state between C2'-endo and C3'-endo, with an average mode around O4'-endo-C1'-exo, whereas the riboses of the RNA strand remained in the C3'-endo puckering domain. The results are compared to those obtained for the DNA.DNA duplex d(GA12G).d(CT12C) under identical simulation conditions. The DNA strand in the hybrid duplex behaves similar to that in a standard B-type DNA duplex. The helical parameters of the hybrid duplex however are closer to A- than to B-type. These observations suggest that RNA.DNA hybrid double helices are neither clearly A-form nor B-form. The furanoses in both strands can assume different puckering modes without the appearance of major geometrical constraints. The simulation results are in excellent agreement with recent experimental data.

3-beta-D-ribofuranosyl-6,7-dihydro-9H-thiazolo[3,2-a]purin-9-one hydrate.

The title molecule, C12H14N4O5S.H2O (I), has a syn-XCN glycosyl torsion angle, which is stabilized by an intramolecular hydrogen bond between N3 of the tricylic base and O5' of the ribose (in a C2'-endo pucker). [The purine base, including atoms S and O6, of the molecule is planar to within 0.043 (2) A.] The tricyclic bases are stacked along a with an interplanar distance of 3.602 (3) A.

A Single 2′-Hydroxyl Group Converts B-DNA to A-DNA : Crystal Structure of the DNA-RNA Chimeric Decamer Duplex d(CCGGC)r(G)d(CCGG) with a Novel Intermolecular G·C Base-paired Quadruplet

We have found that the introduction of a single 2′-hydroxyl group on the sugar-phosphate backbone of the B-DNA decamer d(CCGGCGCCGG) transforms it to A-DNA. Thus, for the first time the X-ray structures of the same sequence have been observed in both the A and B-DNA conformations, permitting a comparison. Crystals of the DNA-RNA chimeric decamer d(CCGGC)r(G)d(CCGG) belong to the orthorhombic space group P 2 12 12 1 with unit cell dimensions a = 25·63 Å, b = 45·24 Å and c = 47·99 Å, and one decamer duplex in the asymmetric unit. The structure was solved by a rigid body search using the coordinates of the isomorphous structure d(CCCGGCCGGG) and refined to an R value of 0·136 using 2753 unique reflections at 1·9 Å resolution. The final model contains 406 nucleotide atoms and 61 water molecules. The chimeric duplex exhibits typical A-DNA geometry, with all the sugars in the C (3′)- endo puckering and the base-pairs inclined and displaced from the helix axis. The 2′-hydroxyl groups on rG6 and rG16 protrude into the minor groove surface and form different types of hydrogen bonds; that on strand 1 forms an intermolecular hydrogen bond with the furanose ring O (4′) of a symmetry-related C1 residue, while that on strand 2 is involved in two water bridges. Crystal packing forces the G4·C17 base-pair in the top half of the duplex to slide significantly into the minor groove compared to the corresponding C7·G14 base-pair in the bottom half, resulting in these base-pairs exhibiting different base stacking and intermolecular interactions. The base G4 of the G4·C17 base-pair forms an unorthodox base "triple", G4 *(G10·C11), hydrogen-bonding through its minor groove sites N (2) and N (3) to the minor groove atoms N (2) and O (2) of both bases of the G10·C11 base-pair of a symmetry-related molecule. The base G10 of this triple in turn forms a second similar unorthodox base triple, G10 *(G3 *C18), with the adjacent base-pair G3·C18 of the duplex, thus G10 is involved in a double triple. On the other hand, in the bottom half of the duplex, the C7·G14 base pair is involved only in a single similar unorthodox base triple with G20, (C7·G14) *G20, while the adjacent base-pair rG6·C15 is involved in a novel quadruple with C1·G20, (rG6·C15) * (C1·G20), where the latter base-pairs are hydrogen-bonded to each other via the minor groove sites G(N (2))…C(O (2)). The double base triple and quadruple are features observed for the first time.

Molecular Structure of Cyclic Diguanylic Acid at 1 Å Resolution of Two Crystal Forms: Self-association, Interactions with Metal Ion/Planar Dyes and Modeling Studies

Cyclic ribodiguanylic acid, c-(GpGp), is the endogenous effector regulator of cellulose synthase. Its three dimensional structure from two different crystal forms (tetragonal and trigonal) has been determined by x-ray diffraction analysis at 1 A resolution. Both structures were solved by direct methods and refined by block-matrix least squares refinement to R-factors of 0.112 (tetragonal) and 0.119 (trigonal). In both crystal forms, two independent c-(GpGp) molecules associate with each other to form a self-intercalated dimer. All four c-(GpGp) molecules have very similar backbone conformation. The riboses are in the C3'-endo pucker with pseudorotation angles ranging from -7.2 degrees to 16.5 degrees and the bases have anti glycosyl chi angles (-175.5 degrees to 179.7 degrees). In the tetragonal form, a hydrated cobalt ion is found to coordinate to two N7 atoms of adjacent guanines, forcing these two guanines to destack with a large dihedral angle (33 degrees). This metal coordination mechanism has been noted previously in other Pt- or Co-GMP complexes and may be relevant to the binding of the anticancer drug cisplatin to a GpG sequence in DNA. A model of the adduct between cisplatin and a d(CAATGGATTG) duplex has been constructed in which the induced bending of the DNA helix at the Pt crosslinking site is 33 degrees, consistent with earlier electrophoretic analyses. Moreover, c-(GpGp) exhibits unusual spectral properties not seen in other cyclic dinucleotides. It interacts with planar organic intercalator molecules in ways similar to double helical DNA. We propose a cage-like model consisting of a tetrameric c-(GpGp) aggregate in which a large cavity (host molecule) is generated to afford a binding site for certain planar intercalators (guests molecules). The aggregate likely uses a hydrogen bonding scheme the same as that found in the G-quartet molecules, e.g., telomere DNA. The conformation of c-(GpGp) also suggests that certain nearest-neighbor intercalators may be synthesized on the basis of its unique molecular framework. Modeling studies have been carried out to test this hypothesis.

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 Synthetased

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.

Crystal Structure of Sodium Deoxyinosine Monophosphate

Abstract The crystal and molecular structure of sodium deoxyinosine monophosphate (5′-dIMP) has been determined by x-ray crystallographic methods. The crystals belong to orthorhombic space group P212121, with a = 21.079(5) Å, b = 9.206(3) Å and c = 12.770(6) Å. This deoxynucleotide shows common nucleotide features namely anti conformation about the glycosyl bond, C2′ endo pucker for the deoxyribose sugar and gauche-gauche orientation for the phosphate group. The sodium ion is directly coordinated to the O3′ atom, a feature observed in many crystal structures of sodium salts of nucleotides.

Computer modeling studies on the subsite interactions of ribonuclease T1.

The modes of binding of pGp,ApG,CpG and UpG to the enzyme ribonuclease T1 were determined by computer modeling. Essentially two binding modes are possible for all the four ligands--one with the 3'-phosphate group occupying the phosphate binding site (substrate mode of binding) and the second with the 5'-phosphate group occupying the phosphate binding site (inhibitor mode of binding). The latter binding mode is energetically favoured over the former and in this mode the base (G) and the 5'-phosphate moieties occupy the same sites on the enzyme as 5'-GMP when bound to RNase T1. The ribose moiety of pGp adopts a C3'-endo pucker form when bound to the enzyme and the glycosyl torsion angle will be in -syn range as 5'-GMP in the RNase T1-5'-GMP complex. Based on these results, a mechanism for the release of the product subsequent to cleavage of the substrate by the enzyme has been proposed. The amino acid residues Asn98 and Tyr45 are shown to form the subsites for the phosphate and the base respectively on the 5'-side of the guanine occupying the primary binding site. These studies also provide a stereochemical explanation for the specificity of the 1N subsite for adenine.

Unusual conformational flexibility in N 1-substituted uncommon purine nucleosides Crystal structure of 1-allyl-isoguanosine and 1-allyl-xanthosine

Several new N 1-substituted uncommon purine nucleosides, including doridosine (1-methyl-isoguanosine; m-iG), 1-allyl-isoguanosine (a-iG) and 1-allyl-xanthosine (a-X), have been synthesized and tested as agonists for the adenosine receptors. Some have smooth muscle relaxant or negative chronotropic activities. The X-ray crystal structure of these compounds has been determined at atomic resolution in order to understand the structure-activity relationship. The structures were solved by direct methods and refined by full-matrix least-squares refinement procedure. The crystallographic parameters are: a-iG, space group P2 1, a=10.573 (1) Å, b=21.955 (2) Å, c=14.360 (1) Å, β=110.65 (1)°, no. of 3σ Fo's=4585, R=0.047; a-X, space group P2 12 12 1, a=16.015 (2) Å, b=16.239 (1) Å, c=5.3723 (5) Å, no. of 3σ Fo's= 1169, R=0.031. In the a-iG crystal, there are 4 independent molecules (with different conformation) per asymmetric unit. While all 4 molecules adopt anti χCN glycosyl torsion angle, their riboses have 3 distinct puckers (C 2′-exo, C 2′-endo and C 1′-exo). In contrast, the a-X structure adopts a syn χCN glycosyl torsion angle, which is stabilized by an intramolecular hydrogen bond between the N 3 or purine base and the O 5′ of the ribose (in C 2′-endo pucker). Both purine bases (a-iG and a-X) are mainly in the keto tautomer form. For the isoguanine base, the averaged N 1C 2 bond distance (1.42 Å) is significantly longer than that (1.375 Å) of the guanine base. For the xanthine base, N 3 nitrogen has an imino proton attached which is unambiguously located in the electron density map. The surprising flexibility in the ribose ring of these N 1-substituted uncommon purine nucleosides suggests flat the ribose moiety may not participate in the binding of nucleoside to the adenosine receptors.

Molecular structures of two new anti-HIV nucleoside analogs: 9-(2,3-dideoxy-2-fluore-β-D-threopentofuranosyl)adenine and 9-(2,3-dideoxy-2-fluoro-β-D-threo-pentofurancsyl)hypoxanthine

The x-ray crystal structures off two new anfi-HIV compounds, 9-(2,3-dideoxy-2-fluoro-β-D- threo -pento-furanosyl,adenine (2'-F-dd-araA) and 9-(2,3-dideoxy-2-fluoro-β-D- threo -pentofuranosyl)hypoxanthine (2'-F-dd-aral), have been determined aft two temperatures. Both crystals are in the space group P2 1 2 1 2 1 , and their structures were solved by direct methods. Least-squares refinement produced kintal R-factors of 0.027 for the 2'-F-dd-araA structure and of 0.044 for the 2'-F-dd-aral structure, respectively. The latter structure contains a two-fold disordered conformation of the sugar moiety. All three conformmers (one for 2'-F-dd-araA and two for 2'-F-dd-aral) adopt an anti xCN glycosyl torsion angle. The sugar in the 2'-F-dd-araA structure has a C2' -endo pucker conformatioin), whereas the sugar in the 2'-F-dd-araO structure has a mixture of C2' -endo and C3' -endo pucker conformations. When the sugar adopts the C2' -endo conformation, the torsion angle about the C4'-G5' bond is in a transgauche + -conformation. On contrast, when the sugar adopts the C3'-endo conformation, the torsion angle about the C4'-C5' bond is in a gauche + -gauche − conformation. The C2'-F bond distance is 1.403(3) A, similar to that found in other aliphatic C-F bonds. The results suggest that the 2'-fluoro-2', 3'-dideoxyarabino-syl nucleosides do not have a strong preference for either C2' -endo or C3 -endo sugar pucker.

Investigations on the dynamic structures of adenine- and thymine-containing DNA

The structures of poly(dA-dT), poly(dA-dBr 5U) and of poly(dA) · poly(dT) have been investigated in solution and in fibers, by Raman spectroscopy. Both the alternating poly(dA-dT), poly(dA-dBr 5U) and non-alternating poly(dA) · poly(dT) exhibit, in the region of sugar phosphate backbone vibrations, two bands of almost equal intensity at about 841 cm −1 and 817 cm −1. The analysis of the characteristic bands of thymine residues that are sensitive to sugar puckers gives indication of a significant displacement from the C (2′)- endo conformer suggesting the adoption of alternative conformers such as O (4′)- endo. In contrast, the diagnostic Raman bands for the sugar pucker of adenine residues suggest, instead, predominant adoption of C (2′)- endo conformations. These Raman results are compatible with rapid dynamic changes of sugar puckers between C (2′)- endo and O (4′)- endo for the thymine (and uridine) residues, whereas in adenine residues the sugar puckers fluctuate around the C (2′)- endo pucker in all synthetic DNA molecules studied. Molecular dynamics simulations, performed on six different starting models using two distance-dependent dielectric functions ε( r) = 4 r and a sigmoidal dependence), all gave similar dynamic behavior in agreement with these Raman data and their interpretation. The mean calculated pseudorotation phases of the adenine residues are systematically higher (around C (2′)- endo) than those of the thymine residues (close to O (4′)- endo-C (1′)- exo). Besides, the mean lifetimes of the thymine residues are 1.5 to 2.0-fold higher in the O (4′)- endo than in the C (2′)- endo domain, while those of the adenine residues are two to threefold higher in the C (2′)- endo than in the O (4′)- endo domain. In the Raman spectra of the alternating poly(dA-dBr 5U), the splitting of a band into two components arising from the two contributions of ApBr 5U and Br 5UpA provides strong evidence for a repeating dinucleotide structure in solution. The calculated twist values averaged over the simulation runs are also systematically higher in the 5′T-A3′ step (39 °) than in the 5′A-T3′ step (33 °). Simultaneously, the calculated roll values are positive in the 5′T-A3′ step (6 °) and negative in the 5′A-T3′ step (−9 °), while the propeller twist values are about the same (−11 ° to −16 °). On the other hand, in the homopolymer, the average twist value is close to 36 ° with the roll angle close to 0 ° and large propeller twist values (−20 °).

Unusual ribose conformation in a ternary copper(II) 2′deoxyribonucleotide complex

The ternary metal deoxyribonucleotide complex [Cu(bzim)(5′-dGMP)(H2O)3](bzim = benzimidazole, 5′-dGMP = 2′-deoxyguanosine 5′-monophosphate) has been prepared and the structure analysed by X-ray diffraction. The compound crystallizes in the space group P1 with a= 7.069(6), b= 13.959(10), c= 14.204(12)A, α= 75.12(6), β= 94.15(6), γ= 97.98(6)° and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least-squares procedures on the basis of 2813 observed [I 3σ(I)] reflections to final R and R′ values of 0.050 and 0.052 respectively. There are two independent molecules in the asymmetric unit and both copper(II) centres have square-pyramidal co-ordination geometry. An unusual feature of the structure is the co-ordination of the metal by N(7) of the base, in the presence of a π-aromatic amine, bzim. The structure is stabilized by intermolecular base–bzim stacking. The nucleotides of both the molecules have an anti conformation about the glycosyl bond, and a gauche-gauche conformation about the C(4′)–C(5′) bond. A feature of particular interest is the unusual sugar conformation. The base furanose rings of the two nucleotide molecules adopt C(3′)-exo/C(2′)-endo pucker and C(3′)-exo pucker respectively.

An isotope edited classical Raman difference spectroscopic study of the interactions of guanine nucleotides with elongation factor Tu and H-ras p21

We have measured the Raman spectrum of GDP bound to the elongation factor protein, EF-Tu, and the c-Harvey-ras protein, p21, two proteins of the guanine nucleotide binding family. In order to separate the Raman spectrum of the nucleotide from the much more intense protein spectrum, we investigate the feasibility of "tagging" the normal modes of the nucleotide by isotopic substitution, here by incoporating deuterium-labeled guanine at the C8 position into the active site. A difference spectrum between the labeled and unlabeled protein-nucleotide complex shows the changes in the Raman spectrum of the bound nucleotide that arise from the isotopic exchange. We find that surprisingly good Raman spectra of bound ligands can be obtained with this method and that the method can be easily generalized to other systems. The data show that the guanine amino group of the nucleotide interacts differently with both EF-Tu and p21 than it does with water, showing a change in hydrogen-bonding properties upon binding. On the other hand, no change in hydrogen bonding is observed at guanine's N7. The data strongly suggest that the conformation of the nucleotide when bound to EF-Tu and that p21 is the C2' endo pucker of the ribose ring and anti about the glycosidic bond. These results are compared to previous structural and chemical studies.