Corpus ID: 13891850

Studies on the Non-covalent Interactions (Stereoelectronics, Stacking and Hydrogen Bonding) in the Self-assembly of DNA and RNA

  title={Studies on the Non-covalent Interactions (Stereoelectronics, Stacking and Hydrogen Bonding) in the Self-assembly of DNA and RNA},
  author={P. Acharya},
To understand why the RNA-RNA duplexes in general has a higher thermodynamic stability over the corresponding DNA-DNA duplexes, we have measured the pK(a) values of both nucleoside 3',5'-bis-ethyl phosphates [Etp(d/rN)pEt] and nucleoside 3'-ethyl phosphates [(d/rN)pEt] (N = A, G, C, or T/U), modeling as donors and acceptors of base pairs in duplexes. While the 3',5'-bis-phosphates, Etp(d/rN)pEt, mimic the internucleotidic monomeric units of DNA and RNA, in which the stacking contribution is… Expand
3 Citations
Structural and Biophysical Studies of Nucleic Acids
This thesis is based on six research publications concerned with (i) study of the molecular structures and dynamics of modified nucleosides; (ii) investigation of the effect of incorporation ofExpand
Molecular dynamics simulation of the preferred conformations of 2-thiouridine in aqueous solution
Transfer RNA (tRNA) molecules display a large diversity of posttranscriptionally modified nucleosides at the anticodon wobble at position 34 and 3′ to the anticodon triplet at position 37. Some ofExpand


The RNA molecular wire: the pH-dependent change of the electronic character of adenin-9-yl is transmitted to drive the sugar and phosphate torsions in adenosine 3 ',5 '-bisphosphate
This thesis is based on ten publications (Papers I-X). The phosphodiester backbone makes DNA or RNA to behave as polyelectrolyte, the pentose sugar gives the flexibility, and the aglycones promoteExpand
Cross-modulation of the pKa of nucleobases in a single-stranded hexameric-RNA due to tandem electrostatic nearest-neighbor interactions.
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. Expand
The hydrogen bonding and hydration of 2'-OH in adenosine and adenosine 3'-ethyl phosphate.
The 2'-OH group has major structural implications in the recognition, processing, and catalytic properties of RNA. We report here intra- and intermolecular H-bonding of 2'-OH in adenosine 3'-ethylExpand
Tandem electrostatic effect from the first to the third aglycon in the trimeric RNA owing to the nearest-neighbor interaction.
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. Expand
Cross-modulation of physicochemical character of aglycones in dinucleoside (3'-->5') monophosphates by the nearest neighbor interaction in the stacked state.
The net result of this cross-talk between two neighboring aglycones is a unique set of agly Cones in an oligo- or polynucleotide, whose physicochemical property and the pseudoaromatic character are completely dependent both upon the sequence makeup, and whether they are stacked or unstacked. Expand
Stereoelectronic effects in nucleosides and nucleotides
This thesis is based on 12 original publications from 1994-98. Intramolecular stereoelectronicforces (anomeric and gauche effects), beside intermolecular forces such as hydrogen bonding,baseExpand
The Transmission of the Electronic Character of Guanin-9-yl Drives the Sugar-Phosphate Backbone Torsions in Guanosine 3',5'-Bisphosphate.
The intrinsic flexibility of the pentoses in RNA allows dynamic transmission of information on the electronic character of the nucleobase to modulate the sugar conformation by an interplay of gaucheExpand
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
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 beenExpand
A repertoire of pyridinium-phenyl-methyl cross-talk through a cascade of intramolecular electrostatic interactions.
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. Expand
A straightforward correlation of our experimental NMR findings on 3′-substituted thymidine derivatives with that of the ab initio calculations shows that (i) the ΔG of N ← S equilibrium in nucleosideExpand