@article { ISI:000247546800008, title = {Structure-editing of nucleic acids for selective targeting of RNA}, journal = {Current Topics in Medicinal Chemistry}, volume = {7}, number = {7}, year = {2007}, month = {JAN}, pages = {715-726}, publisher = {BENTHAM SCIENCE PUBL LTD}, type = {Article}, address = {EXECUTIVE STE Y26, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES}, abstract = {

The synthesis of backbone-modified nucleic acids has been an area of very intense research over the last two decades. The main reason for this research activity is the instability of nucleic acid based drugs in the intracellular conditions. Changes in the sugar-phosphate backbone invariably bring about the changes in the complementation properties of the nucleic acids. The naturally occurring deoxyribose- (DNA) and ribose (RNA) sugar-phosphate backbones are endowed with considerable differences in their binding affinities towards themselves. This occurs because of the different sugar conformations prevalent in DNA and RNA and the subtle structural changes accruing from these in hydrogen bonding, base-stacking interactions and hydration of major/minor grooves. The six-atom phosphodiester linkages and pentose-sugars give immense opportunities for chemical modifications that lead to several backbone-modified nucleic acid structures. This article is focused on such modifications that impart RNA-selective binding properties to the modified nucleic acid mimics and the rationale behind the said selectivity. It is found that the six-atom sugar-phosphate backbone could be replaced by either one-atom extended or one-atom edited repeating units, leading to the folded or extended geometries to maintain the internucleoside distance-complementarity. Other important contributions come from electronegativity of the substituent groups, hydration in the major/minor groove, base stacking etc.

}, issn = {1568-0266}, doi = {10.2174/156802607780487722}, author = {Kumar, Vaijayanti A. and Ganesh, Krishna N.} } @article { ISI:000321231700008, title = {Synthesis and properties of 2 {\textquoteleft}-O-[R- and S-(2-amino-3-methoxy)propyl] (R-AMP and S-AMP) nucleic acids}, journal = {Tetrahedron}, volume = {69}, number = {31}, year = {2013}, month = {AUG}, pages = {6404-6408}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

Substitution at 2{\textquoteright}-position by either amino- or methoxy-pendant groups of the antisense oligonucleotides (AONs) is known to enhance their therapeutic value. A simple modification is described here in which we introduce both these groups in the form of enantiospecific tethers at 2{\textquoteright}-position. Practical synthesis of modified nucleosides using natural L-serine, en route to R-AMP- and S-AMP-AONs is presented. Such tethered ONs formed stable DNA:RNA duplexes and the stability was found to be marginally better than the methoxyethyl/methoxypropyl-substituted MOE/MOP-AONs. The stereochemistry of the tether effectively differentiated the hydrolytic cleavage of AONs and the R-AMP-AON was three times more stable than the S-AMP-AONs after 4 h. In comparison, the MOE- or MOP-AONs were almost completely digested by SVPD after 1 h. (C) 2013 Elsevier Ltd. All rights reserved.

}, keywords = {Antisense therapeutics, MOE-AONs, Positively charged ON analogues}, issn = {0040-4020}, doi = {10.1016/j.tet.2013.05.104}, author = {Kotikam, Venubabu and Kumar, Vaijayanti A.} } @article { ISI:000312946200007, title = {Synthesis and structural studies of S-type/N-type-locked/frozen nucleoside analogues and their incorporation in RNA-selective, nuclease resistant 2 {\textquoteleft}-5 {\textquoteleft} linked oligonucleotides}, journal = {Organic \& Biomolecular Chemistry}, volume = {11}, number = {5}, year = {2013}, month = {NOV}, pages = {746-757}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

2{\textquoteright}-endo locked or frozen (S-type)/3{\textquoteright}-endo locked or frozen (N-type) nucleoside analogues were synthesized. Conformational analysis based on (3)J(HH) and NOE measurements is presented which is further confirmed by X-ray crystal structural studies. 2{\textquoteright}-5{\textquoteright} isoDNA oligonucleotides (ON) were synthesized using these modified nucleoside analogues and UV-T-m studies of the resultant 2{\textquoteright}-5{\textquoteright} isoDNA : RNA duplexes reflect the site-and sequence-dependent effects and confirm that the S-type sugar conformations were preferred over the N-type sugar geometry in such duplexes.

}, issn = {1477-0520}, doi = {10.1039/c2ob26762d}, author = {Erande, Namrata D. and Gunjal, Anita D. and Fernandes, Moneesha and Gonnade, Rajesh G. and Kumar, Vaijayanti A.} } @article { ISI:000315060600030, title = {Synthesis of all four nucleoside-based beta-amino acids as protected precursors for the synthesis of polyamide-DNA with alternating alpha-amino acid and nucleoside-beta-amino acids}, journal = {Tetrahedron}, volume = {69}, number = {3}, year = {2013}, month = {JAN}, pages = {1210-1216}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

A simple approach is described for the synthesis of all four orthogonally protected nucleoside-beta-amino acids from commercially available starting materials. Synthesis of a model tetrameric DNA sequence in 5{\textquoteright}-3{\textquoteright}direction employing trityl strategy and glycine as alpha-amino acid alternating with nucleoside-beta amino acids is described. (C) 2012 Elsevier Ltd. All rights reserved.

}, keywords = {Antisense therapeutics, Neutral DNA analogues, Nucleoside-beta amino acids}, issn = {0040-4020}, doi = {10.1016/j.tet.2012.11.028}, author = {Seema Bagmare and Varada, Manojkumar and Banerjee, Anjan and Kumar, Vaijayanti A.} } @article { ISI:000341339300024, title = {Second generation, arginine-rich (R-X {\textquoteleft}-R)(4)-type cell-penetrating alpha-omega-alpha-peptides with constrained, chiral omega-amino acids (X {\textquoteleft}) for enhanced cargo delivery into cells}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {24}, number = {17}, year = {2014}, month = {SEP}, pages = {4198-4202}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

The syntheses of novel N-aminoalkyl proline-derived spacers (X{\textquoteright}) in polycationic (R-X{\textquoteright}-R)-motif cell-penetrating alpha-omega-alpha-peptides are described as improved molecular transporters and their structural features studied by CD. FACS analysis shows enhanced cellular uptake and confocal microscopy indicates predominantly cytoplasmic localization. The oligomers are efficient at transporting pDNA into cells. The chirality together with the hydrophobicity and flexibility derived from the spacer chain are found to have marked influence on the cell-penetrating and cargo delivery properties of the cell-penetrating peptides (CPPs). The peptides containing N-(3-aminopropyl)-D-proline spacers are found to be the best at cell penetration and cargo delivery in the present study. (C) 2014 Elsevier Ltd. All rights reserved.

}, keywords = {(R-X-R)-motif, alpha-omega-alpha-Peptide, Cell-penetrating peptide, Constrained chiral amino acid, Peptidomimetics}, issn = {0960-894X}, doi = {10.1016/j.bmcl.2014.07.040}, author = {Patil, Kiran M. and Naik, Rangeetha J. and Vij, Manika and Yadav, Amit K. and Kumar, Vaijayanti A. and Ganguli, Munia and Fernandes, Moneesha} } @article { ISI:000344471800052, title = {Simple molecular engineering of glycol nucleic acid: progression from self-pairing to cross-pairing with cDNA and RNA}, journal = {Bioorganic \& Medicinal Chemistry}, volume = {22}, number = {21}, year = {2014}, month = {NOV}, pages = {6227-6232}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

The acyclic chiral nucleic acid analogue, Glycol Nucleic Acid (GNA), displayed exceptional structural simplicity and atom economy while forming self-paired duplexes, using canonical Watson-Crick base pairing. We disclose here that the replacement of phosphodiester linker in GNA with somewhat rigid and shorter carbamate linker in Glycol Carbamate Nucleic Acid (GCNA) backbone allows unprecedented stability to the antiparallel self-paired duplexes. The R-GCNA oligomers were further found to form cross-paired antiparallel duplexes with cDNA and RNA following Watson-Crick base pairing. The stability of cross-paired GCNA: DNA and GCNA: RNA duplexes was higher than the corresponding DNA: DNA and DNA: RNA duplexes. The chiral (R) and (S) precursors were easily accessible from naturally occurring L-serine. (C) 2014 Elsevier Ltd. All rights reserved.

}, keywords = {Acyclic chiral nucleic acid, Cross-pairing, GCNA, GNA, Self-pairing}, issn = {0968-0896}, doi = {10.1016/j.bmc.2014.08.022}, author = {Bose, Tanaya and Kumar, Vaijayanti A.} }