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PubMed1977

Inhibition of chloramphenicol binding to Escherichia coli 70S ribosomes by 2'(3')-O-aminoacyl-dinucleoside phosphates derived from the aminoacyl-tRNA acceptor terminus.

The effect of 2' and 3'-O-aminoacyl-dinucleoside phosphates cytidylyl(3'-5')-2'(3')-O-L-phenyl-alanyladenosine (I), cytidylyl(3'-5')-3'-deoxy-2'-O-L-phenylalanyladenosine (IIa), cytidylyl(3'-5')-2'-deoxy-3'-O-L-phenylalanyladenosine (IIIa), cytidylyl(3'-5')-3'-deoxy-2'-O-glycyladenosine (IIb), cytidylyl(3'-5')-2'-deoxy-3'-O-glycyladenosine (IIIb), cytidylyl(3'-5')-3'-deoxy-2'-O-L-leucyladenosine (IIc), cytidylyl(3'-5')-2'-deoxy-3'-O-L-leucyladenosine (IIIc), cytidylyl(3'-5')-3'-O-L-phenylalanyladenosine (IIId) as analogs of the 2'(3')-aminoacyl-tRNA termini, on chloramphenicol binding to 70S Excherichia coli ribosomes was investigated. The association constants (Kb) of the investigated compounds were determined by the equilibrium dialysis method. Based on the constancy of Kb over the range of inhibitor concentration, it was determined that the binding site of the 2' isomers IIa-IIc overlaps with the chloramphenicol site, whereas the variability of Kb for the 3' isomers IIIb, IIIc and especially IIIa seems to indicate that they do not achieve a complete fit. The consistently higher values of the Kb values for the 3' isomers IIIa-IIIc relative to that of the 2' isomers IIa-IIc also indicate a stabilization of the binding of the former due to a specific interaction between its amino acid portion and a ribosomal site.

Chloramphenicol↗
PubMed1977

Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction.

The crystal structure of a 3:2 complex of the frameshift mutagen proflavine with the dinucleoside phosphate cytidylyl-3'5'-guanosine has been determined. The complex has one drug molecule intercalated between Watson--Crick base pairs of the nucleotide duplex. The other two proflavine molecules are bound to the exterior of the miniature double helix. The orientation of the base pairs in this miniature double helix has aspects similar to that found in RNA 11.

Acridines↗
PubMed1978

Base stacking in the dinucleoside phosphate rapa.

The pH-induced unstacking of rRpA has been investigated by batch calorimetry and uv spectroscopy. Equilibrium uv melting curves confirmed that the adenine bases in rApA are stacked at pH7 but unstacked at pH 1.5. The enthalpy change accompanying this pH-induced unstacking is +2.65 kcal (mole of A-A stack)-1 as measured by batch calorimetry. This represents the first direct determination of this important parameter for a dinucleoside phosphate. It is noted that the calorimetrically determined value reported here is considerably lower than published van't Hoff enthalpies but is consistent with values that can be derived from calorimetric data on polymers.

Base Sequence↗
PubMed1982

Alternate g-g- conformation for dinucleoside phosphates in solution.

An alternative g-g- conformation (conformer I') for dinucleosides in solution has been deduced, based on potential energy calculations and nuclear magnetic resonance spectroscopy. This conformation is characterized by larger glycosidic torsional angles (chi = 94-111 degrees) than those of conformer I (chi = 8-35 degrees), although the other torsional angles are similar. There are thus four stable conformers (I, I', II and III) for dinucleosides in equilibrium with the open forms. The structure of conformer I' supports that of the 'vertical' double helix constructed by Olson (W.K. Olson, Proc. Natl. Acad. Sci. U.S.A. 74, (1977) 1775). Our data may suggest the possibility of interconversion between the vertical double helix and the regular double helix of A-form DNA, RNA or A'-form RNA.

Dinucleoside Phosphates↗
PubMed1995

A two-binding-site kinetic model for the ribonuclease-T1-catalysed transesterification of dinucleoside phosphate substrates.

Ribonucleases have been found to have subsites that confer large rate enhancements but do not contribute to substrate binding. In this study, we present a kinetic model that formally explains how subsite binding energy is converted into chemical activation energy. The proposed mechanism takes into account a primary specificity site and a subsite, both of which must be occupied for chemical turnover. An unstable reaction intermediate is formed upon binding of the polymeric substrate monomers at the corresponding subsites. The structure of this reaction intermediate resembles the transition state of the catalysed transphosphorylation reaction. Similar mechanisms may be used by other depolymerizing enzymes including nucleases, glycosidases, and proteases.

Binding Sites↗
PubMedDate not supplied

[Study of the conformational situation in an aqueous solution of dinucleoside phosphates using proton spin lattice relaxation].

With the use of experimentally measured spin-lattice relaxation rates of H(5), H(6), H(2), H(8) and H(1') the analysis of the conformational situation in aqueous solution of CpC, CpA, ApC and ApA has been carried out. In all cases, the close state is shown to be described by the equilibrium of right- and left-handed forms. The right-handed forms are favourable for all DNP studied and are related to the "canonical" Pba type. On the contrary, the possibility of realization of one or the other noncanonical forms (these are mainly left-handed conformers) is determined strictly by nucleotide sequences. The noncanonical conformers for CpC and CpA are Mbb forms, in which both monomeric units are characterized by anti-conformation, and the base of the 3'-end is turned 180 degrees around the glycosidic bond as compared to the canonical form. The forms of Mab type are possible for ApC. In this case, the purine monomer exists in syn-, but the pyrimidine monomer--in anti-conformation. Both bases are turned to 180 degrees. Finally, in the case of ApA, the forms of Mba type with high-anti-conformation of both monomers are realized. The conformational behaviour of oligonucleotides and the possible biological role of noncanonical conformations are discussed taking into consideration the results obtained.

Chemical Phenomena↗
PubMed1980

An NMR study of the interaction of daunomycin with dinucleotides and dinucleoside phosphates.

The mode of action of the widely used anticancer drug daunomycin was studied by 360 MHz and 100 MHz proton NMR. Information obtained from scalar coupling constants indicates that the conformation of the A ring of the aglycone moiety of daunomycin is maintained upon binding to dinucleotides but that the conformation of the daunosamine ring moiety is altered upon binding. Ring-current-induced chemical shifts of the drug protons were observed as the drug was titrated with deoxydinucleotides. The chemical shift results that daunomycin forms 1 : 1 complexes with deoxydinucleotides and that the strength of the drug-nucleotide interaction is dependent upon the base composition of the dinucleotide. On the basis of the NMR data, a model for the drug/deoxydinucleotide complex is presented featuring intercalation of the drug between the bases of the dinucleoside.

Chemical Phenomena↗