Biomedical subjects

Shirshendu K Deb

Publications and source records attributed to Shirshendu K Deb.

4 recordsLinked to original sources

PubMed2005

Improved synthesis of 2'-amino-2'-deoxyguanosine and its phosphoramidite.

2'-Amino-2'-deoxynucleosides and oligonucleotides containing them have proven highly effective for an array of biochemical applications. The guanosine analogue and its phosphoramidite derivatives have been accessed previously from 2'-amino-2'-deoxyuridine by transglycosylation, but with limited overall efficiency and convenience. Using simple modifications of known reaction types, we have developed useful protocols to obtain 2'-amino-2'-deoxyguanosine and two of its phosphoramidite derivatives with greater convenience, fewer steps, and higher yields than reported previously. These phosphoramidites provide effective synthons for the incorporation of 2'-amino-2'-deoxyguanosine into oligonucleotides.

Deoxyguanosine↗

PubMed2005

Isotope edited internal standard method for quantitative surface-enhanced Raman spectroscopy.

A new isotope edited internal standard (IEIS) method for quantitative surface-enhanced Raman spectroscopy (SERS) is demonstrated using rhodamine 6G (R6G-d0) and rhodamine 6G (R6G-d4) edited with deuterium. The reproducibility and accuracy of the IEIS method is investigated both under optical resonance (SERRS) and nonresonance (SERS) conditions. A batch-to-batch concentration measurement reproducibility of better than 3% is demonstrated over a concentration range of 200 pM-2 microM with up to a factor of 3 difference between the concentration of the analyte and its IEIS. The superior performance of the IEIS method is further illustrated by comparing results obtained using absolute SERS/SERRS intensity calibration (with no internal standard) or using adenine (rather than R6G-d4) as an internal standard for R6G concentration quantization. Potential biomedical gene expression and comparative proteomic applications of the IEIS method are discussed.

Adenine↗

PubMed2004

An atomic mutation cycle for exploring RNA's 2'-hydroxyl group.

The 2'-hydroxyl group fulfills numerous structural and functional roles in RNA, including those of hydrogen bond donor and acceptor. While loss of function upon 2'-deoxynucleotide substitution establishes the importance of specific 2'-hydroxyl groups within RNA, this approach provides no information about how these hydroxyl groups impart their functional contribution. We use an atomic mutation cycle to evaluate the functional importance of the 2'-hydroxyl group's hydrogen atom. Using the Tetrahymena ribozyme reaction, we challenge the cycle to expose the catalytic contribution of the cleavage site 2'-hydroxyl group and its associated hydrogen bond network. The results establish the viability of this cycle as an approach to reveal 2'-hydroxyl groups that donate functionally significant hydrogen bonds.

Hydrogen Bonding↗

PubMed2004

New strategies for exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis.

The 2'-hydroxyl group contributes inextricably to the functional behavior of many RNA molecules, fulfilling numerous essential chemical roles. To assess how hydroxyl groups impart functional behavior to RNA, we developed a series of experimental strategies using an array of nucleoside analogs. These strategies provide the means to investigate whether a hydroxyl group influences function directly (via hydrogen bonding or metal ion coordination), indirectly (via space-filling capacity, inductive effects, and sugar conformation), or through interactions with solvent. The nucleoside analogs span a broad range of chemical diversity, such that quantitative structure activity relationships (QSAR) now become possible in the exploration of RNA biology. We employed these strategies to investigate the spliced exons reopening (SER) reaction of the group II intron. Our results suggest that the cleavage site 2'-hydroxyl may mediate an interaction with a water molecule.

Catalysis↗