Search results for "phosphodiester bond"
showing 10 items of 12 documents
Molecular Mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a Twister Ribozyme
2017
Published as part of the special collection of articles derived from the 10th Congress on Electronic Structure: Principles and Applications (ESPA-2016). The catalytic activity of some classes of natural RNA, named as ribozymes, has been discovered just in the past decades. In this paper, the cleavage of the RNA phosphodiester backbone has been studied in aqueous solution and in a twister ribozyme from Oryza sativa. The free energy profiles associated with a baseline substrate-assisted mechanism for the reaction in the enzyme and in solution were computed by means of free energy perturbation methods within hybrid QM/MM potentials, describing the chemical system by the M06-2× functional and t…
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…
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 .
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…
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. …
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 …
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…
The interaction of S,N-coordinated dimethyltin(IV) derivatives with deoxyribonucleic acid: structure and dynamics by119Sn Mössbauer spectroscopy
1999
Complexes Me2SnCl(SPy) and Me2SnCl(SPym) (HSPy = 2-mercaptopyridine; HSPym = 2-mercaptopyrimidine), from ethanol solutions, interact with aqueous calf-thymus DNA yielding condensed phases with probable Me2Sn(SPy,SPym) (DNA monomer) stoichiometries of 1:1; the condensation of DNA is inferred originated from electrostatic bonding between complex cations Me2Sn(SPy,SPym)+ and the phosphate oxygen of the phosphodiester groups. Octahedral-or trigonal-bipyramidal tin environments are inferred from the point-charge model treatment of the 119Sn Mossbauer parameter nuclear quadrupole splitting, considering the bonding by S and N, or only S donor atoms from the ligand, as well as possible coordination…
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…