Stereochemistry of nucleic acids and their constituents. XXIII. Crystal and molecular structure of dihydrouridine "hemihydrate", a rare nucleoside with a saturated base occurring in the dihydrouridine loop of transfer ribonucleic acids

Abstract

The crystal structure of dihydrouridine, a unique rare nucleoside occurring in the dihydrouridine loop of transfer RNAs, has been determined by X-ray diffraction. Crystals of dihydrouridine are orthorhombic, space group P2]2t2i, a = 8.131, b = 11.766, and c = 23.016 A. There are eight molecules of the nucleoside and four molecules of water per unit cell. The structural solution was obtained by a combination of Patterson search

Sodium 5,6-dihydrouracil-6-sulfonate monohydrate

“…The non-hydrogen atoms were refined with anisotropic thermal parameters and the H atoms with isotropic thermal parameters. The final values of R, the weighted R { [Yw(F o --Fc) consistent with those observed in other dihydro-diketo pyrimidines [dihydrouracil (Rohrer & Sundaralingam, 1970); dihydrouridine (Sundaralingam, Rao & Abola, 1971);5,6-dihydro-2-thiouracil (Koji6-Prodi6, Ru~.i6-Toro~ & Coffou, 1976); 5,6-dihydro-2-thiouracil-6-sulfonate (Jain, Lee, Mertes & Pitman, 1978)]. As in 5,6-dihydro-2-thiouracil-6-sulfonate, the sulfonate group is attached axially to the puckered ring.…”

“…The best four-atom least-squares plane is through atoms C(2), N(3), C(4) and C(5). The r.m.s, deviation of these atoms from the plane is 0.007 A. N(1) and C(6) are displaced on the same side of this plane by 0.206 and 0.763 A, compared to 0.197 and 0.729 and 0.133 and 0.759 A for the two independent molecules of dihydrouridine (Sundaralingam et al, 1971). The ring pucker is significantly different from that observed in 5,6-dihydro-2-thiouracil-6-sulfonate (Jain et al, 1978).…”

The uridine in “U-turn”: Contributions to tRNA-ribosomal binding

“…Six ASLs were synthesized with various substitutions at the position of U 33 (Fig+ 2)+ Each substitution was designed to test the functional importance of one or more of the interactions contributed by U 33 to the U-turn structure (Table 1)+ Two of the ASLs were designed such that nucleoside-33 lacked the ability to donate a proton from the 29-OH: 29-O-methyluridine (ASL-Um 33 ) and 29-deoxyuridine (ASL-dU 33 )+ Others were designed to negate proton donation from the N 3 -H position: cytidine (ASL-C 33 ), N 3 -methyluridine (ASL-m 3 U 33 ), and 6-methyluridine (ASL-m 6 U 33 )+ The latter precludes proton donation from N 3 to the phosphate of A 36 because the N-glycosidic bond of m 6 U 33 takes the syn conformation both in the mononucleoside (Felczak et al+, 1996) and within the ASL+ The syn, C39-endo conformation of m 6 U 33 in the ASL was determined by NMR spectroscopy (R+ Cain and P+F+ Agris, pers+ comm+)+ Two ASLs were designed to force the dynamic U 33 sugar pucker (;50% C39 endo in solution) to either the C39-endo conformation by methylation (ASL-Um 33 ; Kawai et al+, 1992) or the C29-endo conformation by elimination (ASLdU 33 ; Basti et al+, 1996)+ An additional ASL containing dihydrouridine (ASL-D 33 ) was designed to have the C29-endo sugar pucker, but unlike ASL-dU 33 , would retain the ability to donate a proton from the 29-OH+ Dihydrouridine is known to be highly constrained to the C29-endo conformation as a mononucleoside (Sundaralingam et al+, 1971) and within tRNAs and oligomers (Dalluge et al+, 1996(Dalluge et al+, , 1997Stuart et al+, 1996)+ Particular nucleoside substitutions, such as m 6 U 33 and D 33 , were also designed to affect the stacking interactions that characterize position 33+ The syn conformation of m 6 U 33 and the nonplanar, nonaromatic character of D 33 would negatively affect stacking interactions+ Thus, nucleosides substituted for U 33 were chosen for their abilities to disrupt local noncanonical H-bonds in the loop or affect nucleoside conformation and stacking interactions+ These substitutions could, however, have affected structure beyond that of the anticodon loop and would, in turn, affect the assessment of ribosome binding+…”

“…C29 endo)+ Sugar puckers of b deoxyuridine (dU) in the anticodon loop (Basti et al+, 1996) and e Dihydrouridine (D) (Sundaralingam et al+, 1971) have the C29 endo conformation+ c Methylation of the 29-OH of uridines is known to strongly constrain sugar pucker to the C39 endo conformation (Kawai et al+, 1992)+ d Sugar pucker of m 6 U in ASL-m 6 U 33 was determined to be .50% C39 endo (data not shown)+ the pretransition as well as the major transition over a tenfold range of RNA concentrations indicated the T m for pretransitions and that for all the major transitions were temperature independent+ Thus, the pretransitions were not due to hairpin-duplex equilibrium, and within the concentration range used, a unimolecular denaturation was being observed+ We believe that the pretransition region of the thermal denaturation profile is indicative of the denaturation of loop interactions in the ASL+ Thus, except for D 33 , incorporation of modified uridines only caused changes in the structure and/or dynamics of the ASL loop+ Attempts to detect any thermodynamic differences in the major transition (stem denaturation) by curve-fitting the profile to a two-state model did not yield any significant differences among six of the seven ASLs (Table 2)+…”

Crystal and molecular structure of (−)-(5S)-5-hydroxy-5,6-dihydrothymidine

“…The C(2)-O(2) and C(4)-O(4) distances indicate a double-bond character which Prodi6, Kvick & Ru~.i6-Toro~, 1976) and 5,6-dihydrouridine (Sundaralingam, Rao & Abola, 1971;Suck, Saenger & Zechmeister, 1972). The conformation of the base ring is described by the torsion angle about the ring bonds.…”