02740nas a2200217 4500008004100000022001400041245015100055210006900206260007100275300001400346490000800360520189600368100001802264700001602282700001402298700001602312700002202328700002602350700001802376856012802394 2009 eng d a1520-610600aEffects for the incorporation of five-atom thioacetamido nucleic acid (TANA) backbone on hybridization thermodynamics and kinetics of DNA duplexes0 aEffects for the incorporation of fiveatom thioacetamido nucleic  a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcMAR a2944-29510 v1133 a

Thermodynamic studies of nucleic acids serve not only to widen our understanding on the nature and strength of forces that stabilize nucleic acids in a myriad of structural states they assume but also to facilitate the development of databases that could be used to predict the stability and selectivity of probe/primer-sets required in a broad range of nucleic acid-based diagnostic and therapeutic protocols. In the current study, we investigated the effect of a novel, backbone-modified ``thioacetamido linkage'' (TANA) on thermodynamics of hybridization, binding kinetics, and conformation of a DNA duplex. The modification comprises of an extended five-atom amide (N3'-CO-CH(2)-S-CH(2)) linker, as opposed to four-atom phosphodiester linker backbone present in DNA. One to three TANA-substitutions have been introduced in the linker backbone of two thymidine residues of one of the strand of the DNA duplex. Using spectroscopic and calorimetric techniques, we observed that TANA destabilizes the DNA helix by lowering the favorable enthalpy parameter of duplex formation. TANA center dot DNA duplexes were found to adopt a conformation toward an A-type duplex as shown by circular dichroism spectroscopy studies. Analysis of differential scanning calorimetry data indicated a nonzero heat capacity change, Delta C(p), accompanying the duplex formation. The average Delta C(p) change per duplex was found to be 832.5 cal mol(-1) K(-1), giving an average base-pair change of 59.5 cal (mol of base pairs)(-1) K(-1). Hybridization kinetic measurements using surface plasmon resonance indicated a decrease in binding affinity parameter (K(A)) that originates from higher dissociation rate constants (k(d)). Furthermore, optical melting studies showed that increasing the number of modifications results in a modest change in the number of counterions taken up during duplex formation.

1 aKaur, Harleen1 aArora, Amit1 aGogoi, K.1 aSolanke, P.1 aGunjal, Anita, D.1 aKumar, Vaijayanti, A.1 aMaiti, Souvik uhttps://library.ncl.res.in/content/effects-incorporation-five-atom-thioacetamido-nucleic-acid-tana-backbone-hybridization-002646nas a2200217 4500008004100000022001400041245010800055210006900163260010300232300001400335490000700349520178900356653001002145653003602155653002402191653002802215653001902243100001902262700001802281856012902299 2013 eng d a0300-908400aEffect of different arginine methylations on the thermodynamics of tat peptide binding to HIV-1 TAR RNA0 aEffect of different arginine methylations on the thermodynamics  a23 RUE LINOIS, 75724 PARIS, FRANCEbELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIERcJUL a1422-14310 v953 a

RNA-binding proteins are an important class of mediators that regulate cell function and differentiation. Methylation of arginine, a post-translational modification (PTM) found in these proteins, can modulate their function. Arginine can be monomethylated or dimethylated, depending on the type of methyl transferases involved. This paper describes a comparative study of the thermodynamics of unmodified and modified Tat peptide interaction with TAR RNA, where the peptide is methylated at epsilon (epsilon) and eta (eta) nitrogen atoms of guanidinium group of arginine side chain at position 52 or 53. The results indicate that monomethylation of arginine at epsilon (epsilon) nitrogen atom enhances binding affinity, owing to a more favourable enthalpy component which overrides the less favourable entropy change. In contrast, monomethylation of arginine residue at eta nitrogen results in reduced binding affinity originating exclusively from a less favourable enthalpy change leaving entropic component unaffected. However, in case of simultaneous methylation at epsilon and eta positions, the binding parameters remain almost unaffected, when compared to the unmodified peptide. In case of symmetric dimethylation at eta position the observed enthalpy change of the binding was found to be smaller than the values obtained for the unmodified peptide. Asymmetric dimethylation at eta position showed the most reduced binding affinities owing to less favourable enthalpy changes. These results provide insights that enable elucidation of the biological outcome of arginine methylation as PTMs that regulate protein function, and will contribute to our understanding of how these PTMs are established in vitro and in vivo. (C) 2013 Elsevier Masson SAS. All rights reserved.

10aHIV-110aPost-translational modification10aProtein methylation10aRNA-protein interaction10aThermodynamics1 aKumar, Santosh1 aMaiti, Souvik uhttps://library.ncl.res.in/content/effect-different-arginine-methylations-thermodynamics-tat-peptide-binding-hiv-1-tar-rna-001862nas a2200169 4500008004100000022001400041245007400055210006900129260007100198300001400269490000800283520123900291100002501530700002101555700001801576856009801594 2013 eng d a1520-610600aEffect of loops and G-quartets on the stability of RNA G-quadruplexes0 aEffect of loops and Gquartets on the stability of RNA Gquadruple a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcJUN a6896-69050 v1173 a

The loop length, loop composition, salt concentration, and number of G-quartets are major determinants of G-quadruplex stability. We examined the effect of each of these factors on the thermal stability and folding topology of a library of RNA quadruplexes. The thermal stability of G2 and G3 RNA quadruplexes was investigated upon varying the loop length (from 1-1-1 to 15-15-15) and salt concentration (from sequence 1 to 100 mM KCl), while the effect of loop composition was explored using 18 naturally occurring potential RNA quadruplexes predicted in untranslated regions (UTRs). We found loop length and quadruplex stability to be inversely related for G2 RNA quadruplexes and G3 RNA quadruplexes with shorter loops. However, melting temperature saturates for G3 RNA quadruplexes with longer loops. RNA G-quadruplexes with longer loops (G3 15-15-15) displayed T-m values significantly higher than the physiological temperature. This study thus highlights the need to modify the consensus motif presently used by quadruplex prediction tools. An increase in the loop size from 7 bases to IS bases in the consensus motif will add to its predictive value for the discovery of potential RNA quadruplexes across transcriptomes.

1 aPandey, Satyaprakash1 aAgarwala, Prachi1 aMaiti, Souvik uhttps://library.ncl.res.in/content/effect-loops-and-g-quartets-stability-rna-g-quadruplexes-002428nas a2200157 4500008004100000022001400041245011700055210006900172260009100241300001600332490000600348520175000354100001902104700001802123856012902141 2013 eng d a1932-620300aEffect of N-acetylation and N-methylation of lysine residue of tat peptide on its interaction with HIV-1 TAR RNA0 aEffect of Nacetylation and Nmethylation of lysine residue of tat a1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USAbPUBLIC LIBRARY SCIENCEcOCT aUNSP e775950 v83 a

Post-translational modification (PTM) of RNA binding proteins (RBPs) play a very important role in determining their binding to cognate RNAs and therefore regulate the downstream effects. Lysine can undergo various PTMs and thereby contribute to the regulation of different cellular processes. It can be reversibly acetylated and methylated using a pool of respective enzymes, to act as a switch for controlling the binding efficiency of RBPs. Here we have delineated the thermodynamic and kinetic effects of N-acetylation and N-monomethylation of lysine on interaction between HIV-1 TAR RNA and its cognate binder Tat peptide (a model system). Our results indicate that acetylation of lysine 50 (K50), leads to eight-fold reduction in binding affinity, originating exclusively from entropy changes whereas, lysine 51 (K51) acetylation resulted only in three fold decrease with large enthalpy-entropy compensation. The measurement of kinetic parameters indicated major change (4.5 fold) in dissociation rate in case of K50 acetylation however, K51 acetylation showed similar effect on both association and dissociation rates. In contrast, lysine methylation did not affect the binding affinity of Tat peptide to TAR RNA at K50, nonetheless three fold enhancement in binding affinity was observed at K51 position. In spite of large enthalpy-entropy compensation, lysine methylation seems to have more pronounced position specific effect on the kinetic parameters. In case of K50 methylation, simultaneous increase was observed in the rate of association and dissociation leaving binding affinity unaffected. The increased binding affinity for methylated Tat at K51 stems from faster association rate with slightly slower dissociation rate.

1 aKumar, Santosh1 aMaiti, Souvik uhttps://library.ncl.res.in/content/effect-n-acetylation-and-n-methylation-lysine-residue-tat-peptide-its-interaction-hiv-1-0