A. Nyilas

A Convergent Regiospecific Synthesis of the Lariat-Trinucleotides and A2′p 5′G and A2′p 5′G 3′p 5′C from A O4-2-Nitrophenyl) -Uridine Building Block

Abstract Total synthesis of title compounds 1_ and 2_ from a common intermediate 7 is reported using the phosphotriester-phosphiteamidite approach. Appropriate NMR evidence has been presented in support of the regiospecific synthesis of target molecules in addition to enzymatic analysis. Present work clearly shows that the NMR evidence is mandatory to establish the isomeric purity of branched RNA molecules; enzymatic or/and electrophoretic analysis alone as tools for confirmation of branched RNA structures can be misleading.

Regiospecific synthesis of branched tetranucleotides: U3'p5'A3'p5'U2'p5'G, U3'p5'A3'p5'C2'p5'G, A3'p5'A3'p5'U2'p5'G & A3'p5'A3'p5'C2'p5'G.

Abstract An efficient general strategy for the synthesis of branched tetranucleotides 14 , 15 , 24 and 25 is described using key intermediates 9 and 20 to give protected tetranucleotides 13 and 23 which could be specifically deprotected to give either 14 or 24 and 15 or 25 in good yields.

Conformation of Lariat Structures Formed in the Splicing of Pre-mRNA by NMR Spectroscopy

Abstract Temperature dependent 1H- and 31p-NMR studies have shown that lariat (branched) trimers show a preferential 2′ → 5′ stacking, while the branched tetramers resemble 3′ → 5′ linked linear trimers, reminiscent of a single stranded A-RNA helix.

Arenesulfonylethoxycarbonyl- a Set of Amino Protecting Groups for DNA and RNA Synthesis

Abstract Phenyl-, 4-chlorophenyl- and 4-nitrophenylsufonylethoxycarbonyl groups have been reported for the first time as the exocyclic amino protecting groups in nucleoside chemistry. They are all stable under the standard conditions of manipulations in phosphotriester and phosphiteamidite chemistry, they are removable both under the alkaline hydrolytic conditions and also under the influence of non-nucleophilic tertiary bases. N3-Phenyl- and 4-toluenesulfonylethoxycarbonyl derivatives of uridine have been also prepared and characterized by 15N-NMR spectroscopy, their stabilities under different conditions have been tested.

Temperature-dependent 31P n.m.r. shifts to assess the conformations of branched tri- and tetra-nucleotides which are formed as lariats in the splicing reactions

Temperature-dependent changes of 31P n.m.r. chemical shifts (Δδ) have been used to estimate the secondary structure of branched tri- and tetra-nucleotides formed in the splicing reaction; these studies have provided independent evidence, confirming our earlier 1H n.m.r. studies, that the 2′→ 5′ stacking is the predominant structural feature that dictates the secondary structure of the branched trinucleotides while the branched tetranucleotides exist in the form of a distorted A-RNA helix without any 2′→ 5′ stacking.

AN IMPROVED SYNTHESIS OF 1-BETA -D-ARABINOFURANOSYLCYTOSINE 5'-PHOSPHATE-L-1,2-DIACYLGLYCEROLS

Abstract 5′-O-MMTr-cytosine arabinoside was prepared on a large scale from 5′-O-MMTr-cytidine with diphenyl carbonate via 5′-protected cytidine-2′,3′-carbonate-aracytidine-2′,2-anhydro derivative at a 67 % yield. The synthesis of 1,2-L-dipalmitoyl-snglycerol, 1,2-L-distearoyl-sn-glycerol and 1,2-L-dioleoyl-sn-glycerol described here using 9-fluorenylmethoxycarbonyl (FMOC) group for protection of 3-position of glycerol which can be selectively removed by Et3N treatment on the overall 60–70 % yield based on 1.2,-isopropilidene-sn-glycerol. These glycerols were phosphorylated first with 2-chlorophenyl-phosphoro-bis-triazolide quantitatively1 in order to avoid acyl migration, then the glycerophosphate intermediates were condensed with 2′,3′,N4-trileulinyl-l-β-D-arabinofuranosylcytosine in the presence of 2-mesytilenesulphonyl chloride (MsCl) and 1 -methylimidazole (Melm)-which was used in the coupling of nucleotides2-− in an 85–95 % yield compared with the low yielding diester method of Ryu3. Deblocking was c...

A new protecting group: 9-fluorenylmethoxycarbonyl (FMOC) in the synthesis of 1,2-diacylglycerols

Abstract The synthesis of 1,2- l -dipalmitoyl-sn-glycerol, 1,2- l -distearoyl-sn-glycerol and 1,2- l -dioleoyl-sn-glycerol are described here using 9-fluorenylmethoxycarbonyl (FMOC) group for protection of the 3-position of glycerol which can be selectively removed by Et3N treatment on the overall 60–70% yield based on 1,2-isopropylidene-sn-glycerol. Little or no acyl migration occured during deprotection and purification.

Synthesis of 1-β-d-arabinofuranosyl-cytosine 5′-phosphate-l-1,2-diacylglycerols

Abstract 5′-O-MMTr-cytosine arabinoside was prepared on a large scale from 5′-O-MMTr-cytidine with diphenyl carbonate via 5′-protected cytidine-2′,3′-carbonate-ara-cytidine-2′,2-anhydro derivative at a 67% yield. 1,2-Dipalmitoyl-sn-glycerol, 1,2-distearoyl-sn-glycerol and 1,2-dioleoyl-sn-glycerol were phosphorylated first with 2-chlorphenyl-phosphoro-bis-triazolide quantitatively (Welch and Chattopadhyaya, 1985. Acta Chem. Scand. B39, 47–57). This method was used in order to avoid acyl migration, then the glycerophosphate intermediates were condensed with 2′,3′,N4-trileulinyl-1-β- d -arabinofuranosylcytosine in the presence of 2-mesytilensulphonyl chloride (MSCl) and 1-methylimidazole (MeIm)—which was used in the coupling of nucleotides (Nyilas et al., 1986. Acta Chem. Scand. B40, 678–684)—in an 85–88% yield compared with the low yielding diester method of Ryu et al., 1982. J. Med. Chem. 25, 1322–1329. Deblocking was carried out in two steps with tetrabutylammonium fluoride (TBAF) and hydrazine hydrate, producing target compounds (9a, 9b, 9c) at a 50% yield.

Synthesis of Branched Oligoribonucleotides (“Lariat”)

Abstract Four different strategies for the synthesis of branched oligoribonucleotides, from trimers to heptamer, are described.

Synthesis of Cytidylyl(3′→5′)cytidylyl(3′→5′)-(2′)3′-O-[Lα-alanyl]adenosine

Abstract A new synthesis of protected C-C-A-[Lα-Ala] 14 is reported using a new set of complementary groups such as 2-phenylsulfonylethoxycarbonyl (PSEC) for the protection of exocyclic amino functions, o-chlorophenyl (o-CIPh) for the internucleotide phosphotriester, 3-methoxy-1,5-dicarbomethoxypentan-3-yl (MDMP) and the 4-monomethoxytrityl (MMTr) for the protection of the a-amino fuction of the amino acid. 14 could be deprotected in two steps by treatments with 1,1,3,3-tetramethylguanidinium oximate under a dry condition and then by neat trifluoroacetic acid. Treatment with neat trifluoroacetic acid produced a stable salt: [C-C-A-Ala-NaH3+ CF3CO2-] and did not promote any internucleotide phosphate migration or degradation of the oligomeric molecule. This salt was considerably more stable than C-C-A-Ala conjugate with a free a-amino group, and, therefore, it could be easily purified on a silica gel column and was isolated in 82 % yield. This strategy should be useful for the synthesis of longer oligonucle...