Krishan L. Sadana

Improved Methods for 3′-O-Succinylation of 2′-Deoxyribo- and Ribonucleosides and Their Covalent Anchoring on Polymer Supports for Oligonucleotide Synthesis

Abstract A more convenient and efficient method is described for the preparation of 3′-O-succinates of 2′-deoxyribo- and ribonucleosides, in a variety of solvents. Also, a new one-pot procedure has been developed for anchoring these succinates to polymer supports, suitable for solid phase synthesis of oligonucleotides.

Metastable ion studies with a secondary ion time-of-flight mass spectrometer. Enhanced distinction between isomers of O-alkylated thymidines

Abstract First-order rate constants and half-lives have been measured for the decomposition of several metastable ions in the secondary ion time-of-flight mass spectra of 4- and 2- O -alkylthymidines. Some of the factors which influence the accuracy of these measurements have been analyzed. Relative values of the kinetic parameters appear to be a more reliable indicator of isomeric form than the “normal” mass spectra, which are sensitive to the method of sample preparation. In particular, the [M + Na] + ions of 4- O -alkylthymidines are significantly more stable than those of 2- O -alkylthymidines, an effect attributed to chelation of Na + by the 2, 4′, and 5′ oxygens of the former isomers. An interesting rearrangement involving loss of an alkene from the [B + 2H] + ion (B = pyrimidine base) has also been confirmed. The rate of this decomposion is much greater for O -isopropyl- than for O -ethylthymidines, an effect which is rationalized in terms of conformational preferences of the O -alkyl group.

Study of rearrangement reactions occurring during gas chromatography of tert.-butyldimethylsilyl ether derivatives of uridine

The gas chromatography of partial O-tert.-butyldimethylsilyl (TBDMS) derivatives of uridine is complicated by the occurrence of a 2′ ↔ 3′ rearrangement of the TBDMS group when uridine derivatives having a 2′- or 3′-O-TBDMS group and an underivatized OH group in the 3′- or 2′-position are injected into a gas chromatograph. When a 5′-O-TBDMS group is also present these rearrangements are accompanied by a thermal decomposition thought to involve elimination of methane. Further derivatization by acetylation or trimethylsilylation (but not trifluoroacetylation), both of which prevent the rearrangement and decomposition reactions, together with gas chromatography-mass spectrometry selected ion recording techniques, is suggested as an analytical procedure for the synthetically useful partial TBDMS derivatives of ribonucleosides.

Time-of-flight secondary ion mass spectrometry of isomeric O-alkylthymidines

Abstract Positive ion mass spectra of the title compounds and their parent molecule, thymidine, show prominent [M + H]+ and [M + Na]∗ ions, as well as base fragment ions resulting from cleavage of the N-glycosyl bond. In the case of alkylated nucleosides the base fragments can undergo further elimination of an alkene. In the negative ion spectra the prominent ions for all nucleosides are B− and NCO−. Molecular mass can be verified for thymidine by a prominent [M - H]− ion, which is not, or barely, detectable for the alkylated molecules. In addition, the NCO− ion produces a prominent [M + 41]− adduct with a (dT - H)• radical, but not with the alkylated species. Trends in the relative abundances of the ions are discussed.

A simplified strategy for the synthesis of dideoxyribonucleotide blocks

Abstract The rapid synthesis of dideoxyribonucleotide blocks in 60–85% isolated yields has been achieved by combining the phosphorylation and condensation steps in a sequential reaction series which also allows the recovery of unreacted nucleotides.