Jharna Barman

High-quality oligo-RNA synthesis using the new 2′-O-TEM protecting group by selectively quenching the addition of p-tolyl vinyl sulphone to exocyclic amino functions

During the F--promoted deprotection of the oligo-RNA, synthesized using our 2′-O-(4-tolylsulfonyl)ethoxymethyl (2′-O-TEM) group [Org. Biomol. Chem. 5, 333 (2007)], p-tolyl vinyl sulphone (TVS) is f ...

Targeting cancer cells using aptamers: cell-SELEX approach and recent advancements

Aptamers are short single stranded nucleic acid molecules, isolated from a pool of nucleic acid molecules by the method called SELEX (Systematic Evolution of Ligands by EXponential Enrichment) that can bind to the target with high affinity and specificity. A modified SELEX method where the targets are living whole cells is referred as cell-SELEX, and is of great interest because it opens up a simple and effective method for disease diagnostics and therapeutics. The cell-SELEX based approach and recent developments of the technique for identifying aptamers as well as their application in cancer diagnostics and therapeutics are summarized here.

2′-N-Guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligonucleotide exhibits triplex formation with excellent enzymatic stability

Here we present the synthesis and characterization of a new 2′-N-Guanidino,4′-C-ethylene bridged thymidine (GENA-T) modified oligonucleotide possessing North-locked sugar conformation. Incorporation of GENA-T nucleotide though did not change the thermal stability of the oligonucleotides toward the complementary RNA; it significantly increased the stability of the parallel triplex at pH 7. The melting temperature of the triplex was increased by +9.5 °C as compared to that of the isosequential unmodified sequence. Moreover this modification imparted exceptional nuclease stability to the oligonucleotides for over 33 h. This study clearly demonstrates that GENA-T modified oligonucleotides could improve triplex formation with phenomenal enzymatic stability and could be used for various biomedical applications.

Oxetane Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions—An NMR Structure and Hydration Study

Abstract The introduction of a North-type sugar conformation constrained oxetane T block, 1-(1′,3′-O-anhydro-β-D-psicofuranosyl) thymine, at the T 7 position of the self-complementary Dickerson-Drew dodecamer, d[(5′-C1G2C3G4A5A6 T 7T8C9G10C11G12-3′)]2, considerably perturbs the conformation of the four central base pairs, reducing the stability of the structure. UV spectroscopy and ID NMR display a drop in melting temperature of ∼10 °C per modification for the T 7 oxetane modified duplex, where the T 7 block has been introduced in both strands, compared to the native Dickerson-Drew dodecamer. The three dimensional structure has been determined by NMR spectroscopy and has subsequently been compared with the results of 2.4 ns MD simulations of the native and the T 7 oxetane modified duplexes. The modified T 7 residue is found to maintain its constrained sugar- and the related glycosyl torsion conformations in the duplex, resulting in staggered and stretched T 7·A6 and A6·T 7 nonlinear base pairs. The stacking is less perturbed, but there is an increased roll between the two central residues compared to the native counterpart, which is compensated by tilts of the neighboring base steps. The one dimensional melting profile of base protons of the T 7 and T 8 residues reveals that the introduction of the North-type sugar constrained thymine destabilizes the core of the modified duplex, promoting melting to start simultaneously from the center as well as from the ends. Temperature dependent hydration studies by NMR demonstrate that the central T 7·A6/A6·T7 base pairs of the T 7 oxetane modified Dickerson-Drew dodecamer have at least one order of magnitude higher water exchange rates (correlated to the opening rate of the base pair) than the corresponding base pairs in the native duplex.