DO THE 16 MER, 5′-GUGGUCUGAUGAGGCC-3′ AND THE 25 MER, 5′-GGCCGAAACUCGUAAGAGUCACCAC-3′, FORM A HAMMERHEAD RIBOZYME STRUCTURE IN PHYSIOLOGICAL CONDITIONS? AN NMR AND UV THERMODYNAMIC STUDY
- Edouard Zamaratski, Anna Trifonova, P. Acharya, Johan Isaksson, T. Maltseva, Jyoti Chattopadhayaya
- ChemistryNucleosides, Nucleotides & Nucleic Acids
- 31 March 2001
Both the 16 mer and the 25 mer RNA both take up very stable hairpin structures, and when mixed together there is no major change of conformation in neither oligo-RNA.
Computational and NMR study of quaternary ammonium ion conformations in solution
- V. Luzhkov, F. Österberg, P. Acharya, J. Chattopadhyaya, J. Åqvist
- Chemistry
- 19 September 2002
Conformations around C–N bonds at the quaternary centre in tetraalkylammonium ions in water solution are investigated. Structures of Me4N+, Et4N+, n-Pr4N+, n-Bu4N+, and n-Pe4N+ are calculated using…
Measurement of nucleobase pKa values in model mononucleotides shows RNA-RNA duplexes to be more stable than DNA-DNA duplexes.
- P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya, J. Chattopadhyaya
- Chemistry, BiologyJournal of the American Chemical Society
- 13 February 2004
It is found that the relative contribution of base-pairing strength and nucleobase stacking in RNA-RNA over DNA-DNA is mutually compensating as the % A-T/U content increases or decreases.
Synthesis, physicochemical and biochemical studies of 1',2'-oxetane constrained adenosine and guanosine modified oligonucleotides, and their comparison with those of the corresponding cytidine and…
- P. Pradeepkumar, P. Cheruku, O. Plashkevych, P. Acharya, S. Gohil, J. Chattopadhyaya
- Biology, ChemistryJournal of the American Chemical Society
- 27 August 2004
We have earlier reported the synthesis and antisense properties of the conformationally constrained oxetane-C and -T containing oligonucleotides, which have shown effective down-regulation of the…
A repertoire of pyridinium-phenyl-methyl cross-talk through a cascade of intramolecular electrostatic interactions.
- P. Acharya, O. Plashkevych, C. Morita, S. Yamada, J. Chattopadhyaya
- ChemistryJournal of Organic Chemistry
- 28 January 2003
The whole pyridine-phenyl-methyl system in 1a(+) is electronically coupled at the ground state, cross-modulating the physicochemical property of the next neighbor by using the electrostatics as the engine, and the origin of this Electrostatics is a far away point in the molecule-the pyridinyl-nitrogen.
Significant pKa perturbation of nucleobases is an intrinsic property of the sequence context in DNA and RNA.
- S. Acharya, J. Barman, J. Chattopadhyaya
- Chemistry, BiologyJournal of the American Chemical Society
- 22 June 2004
The sequence-dependent variation of pKa of the central G and the modulation of its pKa transmission through the nearest-neighbors by variable electrostatic interaction is owing to the electronically coupled nature of the constituent nucleobases across the single strand, which demonstrates the unique chemical basis of the sequence context specificity of DNA or RNA in dictating the biological interaction, recognition, and function with any specific ligand.
Cross-modulation of the pKa of nucleobases in a single-stranded hexameric-RNA due to tandem electrostatic nearest-neighbor interactions.
- P. Acharya, S. Acharya, P. Cheruku, N. Amirkhanov, A. Földesi, J. Chattopadhyaya
- Chemistry, BiologyJournal of the American Chemical Society
- 24 July 2003
The studies have demonstrated that the electrostatically repulsive anion(G(-))-pi/dipole(Im(delta)(-)) interaction propagates from the first to the third nucleobase quite strongly in the oligo-RNAs 6-8, causing destacking of the helix, and then its effect is gradually reduced, although it is clearly NMR detectable along the RNA chain.
Tandem electrostatic effect from the first to the third aglycon in the trimeric RNA owing to the nearest-neighbor interaction.
- P. Acharya, S. Acharya, A. Földesi, J. Chattopadhyaya
- Chemistry, BiologyJournal of the American Chemical Society
- 30 January 2003
This intramolecular nearest neighbor electrostatic interaction in the single-stranded RNA modulates the pseudoaromaticity of the nearest neighbors by almost total transmission of because they constitute an extended array of offset-stacked coupled aromatic heterocycles within a polyanionic sugar-phosphate backbone at the ground state.
2′/3′‐O‐peptidyl Adenosine as a General Base Catalyst of its Own External Peptidyl Transfer: Implications for the Ribosome Catalytic Mechanism
- Mohamed M. Changalov, G. Ivanova, D. Petkov
- Chemistry, BiologyChemBioChem
- 6 June 2005
2'/3'-O-peptidyl Adenosine as a General Base Catalyst of its Own External Peptidyl Transfer: Implications for the Ribosome Catalytic Mechanism.
The strength of the 3′-gauche effect dictates the structure of 3′-O-anthraniloyladenosine and its 5′-phosphate, two analogues of the 3′-end of aminoacyl-tRNA
- P. Acharya, B. Nawrot, M. Sprinzl, C. Thibaudeau, J. Chattopadhyaya
- Chemistry
- 1999
Anthranilic acid charged yeast tRNAPhe or E. coli tRNAVal are able to form a stable complex with EF-Tu*GTP, hence the 2′- and 3′-O-anthraniloyladenosines and their 5′-phosphate counterparts have been…
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