Synthesis of oligonucleoside phosphorodithioates by the H-phosphonothioate method

The phosphorodithioate octamer [(TpS₂)₇T] was efficiently synthesized using bis(2,6-dimethylphenyl) phosphorochloridate as a coupling agent by application of the H-phosphonothioate method, where oxidation was facilitated using elemental sulfur following completion of oligonucleoside H-phosphonothioates assembly, as with the standard H-phosphonate method.     

Synthesis of oligonucleoside phosphorodithioates on a solid support by the H-phosphonothioate method

Phosphorodithioate-type short oligonucleotides were efficiently synthesized using bis(2,6-dimethylphenyl) phosphorochloridate as a coupling agent on a solid support by application of the H-phosphonothioate method, where oxidation was facilitated using elemental sulfur following completion of H-phosphonothioate oligomer assembly, as with the standard H-phosphonate method.     

Psoralen-Derivatized Oligothymidine Methylphosphonates form Triple Helices with DNA and Crosslink to a Specific Strand

Oligothymidine methylphosphonates derivatized at the 5′-end with 4′-aminoalkyl-4,5′,8-trimethylpsoralen (AMT) were prepared. The interaction of these oligonucleoside methylphosphonates with double-stranded DNA was studied. Oligothymidine tnethylphosphonates, T₇ and T₁₄, were found to form triple helix with an oligodeoxyribonucleotide 45-mer DNA duplex which contains an A₁₅-T₁₅ sequence. Upon irradiation with 365 nm (UV light, AMT crosslinked to accessible thymidine residues in the target DNA. Both AMT-derivatized T₇ and T₁₄ crosslink to the T₁₅ containing strand of the double-stranded DNA target, but they do not crosslink to the A₁₅ containing strand which also contains a potential thymidine crosslinking site. Methylphosphonate oligomer, T₇, was derivatized with AMT using either an ethyl-, butyl- or hexyl-linker. The efficiency of crosslinking is affected by the length of the aminoalkyl linker arm connecting the AMT to the methylphosphonate oligomer. The relative crosslinking efficiencies of the oligomers with these three types of linkers were different. Greatest crosslinking, 45%, was obtained using an oligomer having a butyl-or a hexyl-linker. The interaction of oligothymidine methylphosphonates with DNA can be enhanced by using two shorter AMT-oligomers instead of using one full-length AMT-derivatized oligomer. This strategy was demonstrated by the interaction of AMT-derivatized T₇ with duplex DNA 35-mer and 45-mer target. The extent of crosslinking to the 45-mer target, whose binding site can accommodate two molecules of AMT-derivatized T₇, is 45% whereas that with the 35-mer target, which can accommodate only one T₇ molecule, is only 3%. The results of our experiments suggest that AMT-derivatized oligothymidine methylphosphonates can form triple-stranded complex and psoralen photoadduct with DNA. The formation of such complexes may be useful in probing and controlling gene expression at the DNA level.     

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 17

The formation of cyclic duplexes (pairing) of known oxymethylene‐linked self‐complementary U*[o]A⁽*⁾ dinucleosides contrasts with the absence of pairing of the ethylene‐linked U*[c_a]A⁽*⁾ analogues. The origin of this difference, and the expected association of U*[x]A⁽*⁾ and A*[x]U⁽*⁾ dinucleosides with x=CH₂, O, or S was analysed. According to this analysis, pairing occurs via constitutionally isomeric Watson–Crick, reverse Watson–Crick, Hoogsteen, or reverse Hoogsteen H‐bonded linear duplexes. Each one of them may give rise to three diastereoisomeric cyclic duplexes, and each one of them can adopt three main conformations. The relative stability of all conformers with x=CH₂, O, or S were analysed. U*[x]A⁽*⁾ dinucleosides with x=CH₂ do not form stable cyclic duplexes, dinucleosides with x=O may form cyclic duplexes with a gg‐conformation about the C(4′)? C(5′) bond, and dinucleosides with x=S may form cyclic duplexes with a gt‐conformation about this bond. The temperature dependence of the chemical shift of H? N(3) of the self‐complementary, oxymethylene‐linked U*[o]A⁽*⁾ dinucleosides 1 – 6 in CDCl₃ in the concentration range of 0.4–50 mM evidences equilibria between the monoplex, mainly linear duplexes, and higher associates for 3 , between the monoplex and cyclic duplexes for 6 , and between the monoplex, linear, and cyclic duplexes as well as higher associates for 1, 2, 4 , and 5 . The self‐complementary, thiomethylene‐linked U*[s]A⁽*⁾ dinucleosides 27 – 32 and the sequence isomeric A*[s]U⁽*⁾ analogues 33 – 38 were prepared by S‐alkylation of the 6‐(mesyloxymethyl)uridine 12 and the 8‐(bromomethyl)adenosine 22 . The required thiolates were prepared in situ from the C(5′)‐acetylthio derivatives 9, 15, 19 , and 25 . The association in CHCl₃ of the thiomethylene‐linked dinucleoside analogues was studied by ¹H‐NMR and CD spectroscopy, and by vapour‐pressure osmometric determination of the apparent molecular mass. The U*[s]A⁽*⁾ alcohols 28, 30 , and 31 form cyclic duplexes connected by Watson–Crick H‐bonds, while the fully protected dimers 27 and 29 form mainly linear duplexes and higher associates. The diol 32 forms mainly cyclic duplexes in solution and corrugated ribbons in the solid state. The nucleobases of crystalline 32 form reverse Hoogsteen H‐bonds, and the resulting ribbons are cross‐linked by H‐bonds between HOCH₂? C(8/I) and N(3/I). Among the A*[s]U⁽*⁾ dimers, only the C(8/I)‐hydroxymethylated 37 forms (mainly) a cyclic duplex, characterized by reverse Hoogsteen base pairing. The dimers 34 – 36 form mainly linear duplexes and higher associates. Dimers 34 and particularly 38 gelate CHCl₃. Temperature‐dependent CD spectra of 28, 30, 31 , and 37 evidence π‐stacking in the cyclic duplexes. Base stacking in the particularly strongly associating diol 32 in CHCl₃ solution is evidenced by a melting temperature of ca. 2°.     

Nucleoside derived amino acids (NDA) in foldamer chemistry: synthesis and conformational studies of homooligomers of modified AZT

Homo short-oligomers of a novel trans-β-amino acid derived from AZT were synthesized and characterized. These adopt right-handed helical turns with their bases positioned systematically along the helix axis. These studies open up new possibilities for synthesizing nucleoside derived functional foldamers.