N. Balgobin

Rapid and quantitative recovery of DNA fragments from gels by displacement electrophoresis (isotachophoresis)

The use of displacement electrophoresis (synonymous to isotachophoresis, steady-state stacking, and moving boundary electrophoresis) for recovery of DNA fragments from agarose and polyacrylamide gels is described. Complete recovery of DNA molecules ranging from oligonucleotides to 20 000-basepairs-long fragments was achieved. The DNA is recovered in a small volume (0.1-0.3 ml) and can be used directly in enzyme-mediated cleavage and ligation reactions. The recovered DNA contained no inhibitory contaminants as revealed by ligation or restriction enzyme cleavage.

2-(Trimethylsilyl)ethyl chloroformate: A convenient reagent for protection of hydroxyl function

Abstract 2-(Trimethylsilyl)ethyl chloroformate reacts with alcohols to give carbonates in high yield. n-Bu4NF in THF(0.2M) solution for 10 min or ZnBr2 or ZnCl2 in CH3NO2 for 10 min regenerate the alcohol at 20°C.

2-Phenylsulfonylethyl, a new phosphate protecting group: Its application in the synthesis of dodecathymidylic acid.

Abstract 2-Phenylsulphonylethyl group has been employed for the first time to protect 3′-terminal phosphodiester to the triester level in the synthesis of dodecathymidylic acid using the phosphotriester approach.

The 2-phenylsulfonylethylcarbonyl (PSEC) group for the protection of the hydroxyl function

Abstract The PSEC group may be used to protect the hydroxyl function in conjunction with a variety of acid and base labile protecting groups; the PSEC group may be removed by treatment of triethylamine (15 equiv.) in dry pyridine solution within 20 h at 20°C while other base labile protecting groups remained intact.

The application of 2-(4-chlorophenyl)-sulfonylethoxycarbonyl (CPSEC) group in the synthesis of a DNA segment using the phosphotriester approach

The new base labile CPSEC group has been successfully employed for the protection of the 5′-hydroxyl function to synthesize a “universal Stop codon” DNA sequence: 5′d(TCAATCAATCA)3′.

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.

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.

Bausteine für Oligonucleotid-Synthesen mit einheitlich fragmentierbaren β-halogenierten Schutzgruppen /Building Blocks for Oligonucleotide Syntheses with Uniformly Fragmentable β-Halogenated Protecting Groups

Abstract 5′-Dimethoxytrityl-3′-phosphite amides of deoxynucleosides are synthesized. Phosphite/phosphate is protected by the 2,2,2-trichloro-1,1-dimethyl-ethyl (TCB) group, heterocyclic bases by the 2,2,2-trichloro-2,2-dimethyl-ethoxycarbonyl (TCBOC) group. Deoxyguanosine is also block ed by 6-O-trichloroethyl thus avoiding the difficulties observed with monoprotected guanine residues.