Search results for "Phosphodiester bond"
showing 10 items of 12 documents
A Post-Labeling Approach for the Characterization and Quantification of RNA Modifications Based on Site-Directed Cleavage by DNAzymes
2011
Deoxyribozymes or DNAzymes are small DNA molecules with catalytic activity originating from in vitro selection experiments. Variants of the two most popular DNAzymes with RNase activity, the 10-23 DNAzyme and the 8-17 DNAzyme, promote efficient in vitro cleavage of the phosphodiester bond in at least 11 out of 16 possible dinucleotide permutations. Judicious choice of the sequences flanking the active core of the DNAzymes permits to direct cleavage activity with high sequence specificity. Here, the harnessing of these features for the analysis of RNA nucleotide modifications by a post-labeling approach is described in detail. DNAzymes are designed such that RNase cleavage is directed precis…
Promiscuity in alkaline phosphatase superfamily. Unraveling evolution through molecular simulations.
2011
We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents promiscuous activity as a diesterase. The analysis of our simulations, carried out by means of molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, shows that the reaction takes place through a D(N)A(N) or dissociative mechanism, the same mechanism employed by AP in the hydrolysis of monoesters. The promiscuous activity observed in this superfamily can be then explained on the basis of a conserved reaction mechanism. …
Organotin(IV) chloride complexes with phosphocholine and dimyristoyl-L-?-phosphatidylcholine
2000
Several complexes of R n SnCl 4-n (R = Me, Ph, n = 1-3; R = nBu, n = 2, 3) with phosphocholine and dimyristoyl-L-α-phosphatidylcholine (phospholipid) have been synthesized and characterized by means of Mossbauer spectroscopy and NMR. Triorganotin chlorides form complexes of (R 3 SnCl) 2 .L stoichiometry with a trigonal bipyramidal pentacoordinate tin environment, while the others form 1:1 complexes with an octahedral hexacoordinate tin environment, with the ligands coordinating through anionic phosphodiester moieties in all cases.
Novel O-antigen of Hafnia alvei PCM 1195 lipopolysaccharide with a teichoic acid-like structure
2009
Abstract The lipopolysaccharide (LPS) of Hafnia alvei strain PCM 1195 was obtained by the hot phenol/water method. The O-specific polysaccharide was released by mild acidic hydrolysis and isolated by gel filtration. The structure of the O-specific polysaccharide was investigated by 1 H, 13 C, and 31 P NMR spectroscopy, MALDI-TOF MS, and GC–MS, accompanied by monosaccharide and methylation analysis. It was concluded that the O-specific polysaccharide is composed of a hexasaccharide repeating units interlinked with a phosphate group: {→4-α- d -Glc p -(1→3)-α- l - Fuc p NAc-(1→3)-[α- d -Glc p -(1→4)]-α- d -Glc p NAc-(1→3)-α- l - Fuc p NAc-(1→4)-α- d -Glc p -(1→P} n .
Identification of the reaction products of (2'-5')oligoadenylate synthetase in the marine sponge.
1998
Previously we reported on the presence of a high (2'-5')oligoadenylate synthetase activity in the marine sponge Geodia cydonium [Kuusksalu, A., Pihlak, A., Muller, W. E. G. & Kelve, M. (1995) Eur. J. Biochem. 232, 351-357]. The presence of (2'-5')oligoadenylates [(2'-5')A] in crude sponge extract was shown by radioimmunoassay and by their HPLC comigration with authentic (2'-5')A oligomers. In addition, the sponge (2'-5')oligoadenylates displayed biological activity, as determined by inhibition studies of protein biosynthesis in rabbit reticulocyte lysate. In the present study individual (2'-5')oligoadenylates synthesized by sponge enzyme were separated by HPLC. The exact composition of ever…
The Hammerhead Ribozyme: A Long History for a Short RNA
2017
Small nucleolytic ribozymes are a family of naturally occurring RNA motifs that catalyse a self-transesterification reaction in a highly sequence-specific manner. The hammerhead ribozyme was the first reported and the most extensively studied member of this family. However, and despite intense biochemical and structural research for three decades since its discovery, the history of this model ribozyme seems to be far from finished. The hammerhead ribozyme has been regarded as a biological oddity typical of small circular RNA pathogens of plants. More recently, numerous and new variations of this ribozyme have been found to inhabit the genomes of organisms from all life kingdoms, although th…
The interaction of organotins with native DNA
1992
The compounds R2SnCl2 and R3SnCl (RMe, Et, nBu, nOct, Ph, in ethanol solution) as well as the aqueous species [Me2Sn(OH2)n]2+ and [Me3Sn(OH2)2]+, react with aqueous native DNA, yielding solid phases. According to the pointcharge model treatment of the 119Sn Mossbauer parameter nuclear quadrupole splitting, trans-octahedral R2Sn(O2PXY)2, and trigonalbipyramidal R3Sn(O2PXY), (RMe, Et, nBu), would occur in the pellets, the tin atoms being coordinated by phosphodiester groups of the nucleic acid. The precipitates from Ph2SnIV would consist of the DNA complex as well as of the Ph2SnIV distannoxane obtained by hydrolysis of the reactant, whilst nOct2SnCl2, nOct3SnCl and Ph3SnCl would mainly yield…
Joining Two Natural Motifs: Catechol-Containing Poly(phosphoester)s.
2017
Numerous catechol-containing polymers, including biodegradable polymers, are currently heavily discussed for modern biomaterials. However, there is no report combining poly(phosphoester)s (PPEs) with catechols. Adhesive PPEs have been prepared via acyclic diene metathesis polymerization. A novel acetal-protected catechol phosphate monomer was homo- and copolymerized with phosphoester comonomers with molecular weights up to 42000 g/mol. Quantitative release of the catechols was achieved by careful hydrolysis of the acetal groups without backbone degradation. Degradation of the PPEs under basic conditions revealed complete and statistical degradation of the phosphotri- to phosphodiesters. In …
Microstructure analysis of biocompatible phosphoester copolymers
2013
Copolymers with varying compositions of 2-ethoxy-2-oxo-1,3,2-dioxaphospholane (EEP) and 2-ethoxy-4-methyl-2-oxo-1,3,2-dioxaphospholane (EMEP) have been synthesized via 1,5,7-triazabicyclo[4.4.0]dec-5-ene-catalyzed anionic ring-opening polymerization. The molecular weights and comonomer ratios were well controlled and polymers with reasonable molecular weight distributions (<1.5) were obtained in all cases. The copolymers were investigated by 1H and 31P NMR spectroscopies to determine the underlying microstructure via detailed dyad analysis. The copolymers were found to be nontoxic to HeLa cells. Furthermore, the obtained copolymers of EEP and EMEP show thermoresponsive properties, i.e., exh…
Theoretical study of phosphodiester hydrolysis in nucleotide pyrophosphatase/phosphodiesterase. Environmental effects on the reaction mechanism.
2010
We here present a theoretical study of the alkaline hydrolysis of methyl p-nitrophenyl phosphate (MpNPP(-)) in aqueous solution and in the active site of nucleotide pyrophosphatase/phosphodiesterase (NPP). The analysis of our simulations, carried out by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods, shows that the reaction takes place through different reaction mechanisms depending on the environment. Thus, while in aqueous solution the reaction occurs by means of an A(N)D(N) mechanism, the enzymatic process takes place through a D(N)A(N) mechanism. In the first case, we found associative transition-state (TS) structures, while in the enzyme TS structures have dissoc…