Solution Structure of a RNA Decamer Duplex,Containing 9‐[2‐O‐(β‐D‐ribofuranosyl)‐β‐D‐ribofuranosyl]adenine,a Special Residue in Lower Eukaryotic Initiator tRNAs

The solution structure of the self‐complementary deca‐ribonucleotide 5′‐r(GCGA*AUUCGC)‐3′ containing 9‐[2‐O‐(β‐D ‐ribofuranosyl)‐β‐D ‐ribofuranosyl]adenine (A*), a modified nucleotide that occurs in lower eukaryotic methionine initiator tRNAs (tRNAs_i^Met), was determined by NMR spectroscopy. Unexpectedly, the modification has no effect on the thermal stability of the duplex. However, the extra ribose moiety is in the C(3′)‐endo conformation and takes up a well‐defined position in the minor groove, which is in agreement with its position in tRNAs_i^Met as determined by X‐ray crystallography. Molecular‐dynamics simulations on the RNA duplex in H₂O show that the position of the extra ribofuranose moiety seems to be stabilized by bridged H‐bonds (mediated by two H₂O molecules) to the backbone of the complementary chain.     

Oligodeoxynucleotides Containing 2′‐Deoxy‐1‐methyladenosine and Dimroth Rearrangement

2′‐Deoxy‐1‐methyladenosine was incorporated into synthetic oligonucleotides by phosphoramidite chemistry. Chloroacetyl protecting group and controlled anhydrous deprotection conditions were used to avoid Dimroth rearrangement. Hybridization studies of intramolecular duplexes showed that introduction of a modified residue into the loop region of the oligonucleotide hairpin increases the melting temperature. It was shown that modified oligonucleotides may be easily transformed into oligonucleotides containing 2′‐deoxy‐N⁶‐methyladenosine.     

Disaccharide nucleosides: The crystal and molecular structure of 2′-<Emphasis Type="Italic">O</Emphasis>-β-<Emphasis Type="Italic">D</Emphasis>-ribopyranosylcytidine

The crystal structure of a disaccharide nucleoside, 2′-O-β-D-ribopyranosylcytidine, is studied using X-ray diffraction (space group P2₁, a = 6.827(2) Å, b = 12.813(3) Å, c = 9.532(2) Å, β = 92.934(5)°, V = 832.7(4) ų, Z = 2). The stereochemical features of the molecular structure of 2′-O-β-D-ribopyranosylcytidine are analyzed, and the structural data are compared with those obtained for the previously studied disaccharide nucleoside 2′-O-β-D-ribofuranosyluridine.     

Acyclic analogs of nucleosides. Synthesis of 1,5-dihydroxy-3-oxa-2-pentyl derivatives of nucleic bases

A convenient method for the synthesis of 1,5-dihydroxy-3-oxa-2-pentyl derivatives of nucleic bases, which consists in the condensation of trimethylsilyl derivatives of nucleic bases with 1,2,5-triacetoxy-3-oxapentane in the presence of SnCl₄, is proposed. Optically active derivatives — (R)- and (S)-1-(1,5-dihydroxy-3-oxa-2-pentyl)uracil, respectively — were obtained by periodate oxidation of -L- and -D-arabinopyranosyluracil.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 223–228, February, 1988.     

Oligonucleotides Containing Disaccharide Nucleosides

Disaccharide nucleosides with 2′‐O‐(D ‐arabinofuranosyl), 2′‐O‐(L ‐arabinofuranosyl), 2′‐O‐(D ‐ribopyranosyl), 2′‐O‐(D ‐erythrofuranosyl), and 2′‐O‐(5‐azido‐5‐deoxy‐D ‐ribofuranosyl) substituents were synthesized. These modified nucleosides were incorporated into oligonucleotides (see Table). Single substitution resulted in a ΔT_m of +0.5 to −1.4° for DNA/RNA and a ΔT_m of −0.8 to −4.7° for DNA/DNA duplexes. These disaccharide nucleosides can be well accommodated in RNA/DNA duplexes, and the presence of a NH₂−C(5″) group has a beneficial effect on duplex stability.     

Synthesis and Properties of O‐β‐D‐ribofuranosyl‐(1″→2′)‐guanosine‐5″‐ O‐phosphate and Its Derivatives

The efficient synthesis of O‐β‐D ‐ribofuranosyl‐(1″→2′)‐guanosine‐5″‐O‐phosphate and O‐β‐D ‐ribofuranosyl‐(1″→2′)‐adenosine‐5″‐O‐phosphate, minor tRNA components, have been developed, and their conformational properties were examined by NMR spectroscopy.     

Synthesis of enantiomers of 3′,4′-seco-2′-desoxythymidine

The glycosylation of 1,3,4-tri-O-benzoyl-2-desoxy--D-ribopyranose by bis-trimethylsilylthymine in the presence of SnCl₄ and F₃CS0₂OSiMe₃ was studied. It was shown that the stereo-selectivity and directivity of the reaction are dependent on the choice of catalyst. The 1-(2-desoxy-- and -D-ribopyranosyl)-thymines obtained were converted into 3,4-seco-2-desoxythymidines.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 947–951, July, 1988.The authors wish to express their gratitude to M. Ya. Karpeiskii, S. V. Meshkov, and M. I. Struchkov for their help in the investigation.