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A Kanavarioti

Publications and source records attributed to A Kanavarioti.

6 recordsLinked to original sources
PubMed1992

Self-replication of chemical systems based on recognition within a double or a triple helix: a realistic hypothesis.

A scenario is proposed by which non-enzymatic self-replication of short RNA molecules could occur. The hypothesis is illustrated for the self-replication of an oligopyrimidine (Y) strand. The successful replication of Y requires a series of plausible steps. The first, experimentally feasible, step involves the template-directed polynucleotide synthesis, based on Watson-Crick base pairing, of an oligopurine (R) strand using Y as the template, and chemically activated mononucleotides as the building blocks. This step will result in the formation of an oligopyrimidine.oligopurine (YR) double helix. The second step requires the use of the double helix as the template for the synthesis of a second oligopyrimidine (Y') strand from activated pyrimidine monomers. This synthesis could be facilitated by the binding of the monopyrimidines in the major groove of the YR double helix, via Hoogsteen-type base pairing with the R strand, establishing in that sense triple helix recognition. This step, if successful, should result in the formation of a new strand, Y', that runs parallel to the oligopurine strand. Y' differs from Y in that all 3'-5' phosphodiester linkages in Y are replaced by 5'-3' linkages in Y'. The resulting triple helix (YRY') is in dynamic equilibrium with YR and free Y'. In subsequent steps, unassociated Y' directs the synthesis of the complementary oligopurine (R') strand forming a new double helix Y'R' that may direct the synthesis of an oligopyrimidine strand, Y, that is expected to be identical to the first strand that started the whole sequence. An attempt is made to generalize the above hypothesis to mixed oligonucleotides containing all four bases and identify the limitations of this hypothesis.

Models, Chemical↗
PubMed1990

Limiting concentrations of activated mononucleotides necessary for poly(C)-directed elongation of oligoguanylates.

Selected imidazolide-activated nucleotides have been subjected to hydrolysis under conditions similar to those that favor their template-directed oligomerization. Rate constants of hydrolysis of the P-N bond in guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) and in guanosine 5'-monophosphate imidazolide (ImpG), kh, have been determined in the presence/absence of magnesium ion as a function of temperature and polycytidylate [poly(C)] concentration. Using the rate constant of hydrolysis of 2-MeImpG and the rate constant of elongation, i.e., the reaction of an oligoguanylate with 2-MeImpG in the presence of poly(C) acting as template, the limiting concentration of 2-MeImpG necessary for oligonucleotide elongation to compete with hydrolysis can be calculated. The limiting concentration is defined as the initial concentration of monomer that results in its equal consumption by hydrolysis and by elongation. These limiting concentrations of 2-MeImpG are found to be 1.7 mM at 37 degrees C and 0.36 mM at 1 degrees C. Boundary conditions in the form of limiting concentration of activated nucleotide may be used to evaluate a prebiotic model for chemical synthesis of biopolymers. For instance, the limiting concentration of monomer can be used as a basis of comparison among catalytic, but nonenzymatic, RNA-type systems. We also determined the rate constant of dimerization of 2-MeImpG, k2 = 0.45 +/- 0.06 M-1 h-1 in the absence of poly(C), and 0.45 +/- 0.06 less than or equal to k2 less than or equal to 0.97 +/- 0.13 M-1 h-1 in its presence at 37 degrees C and pH 7.95.(ABSTRACT TRUNCATED AT 250 WORDS)

Guanosine Monophosphate↗
PubMed1990

Computer simulation in template-directed oligonucleotide synthesis.

A computer simulation (KINSIM) modeling up to 33 competing reactions was used in order to investigate the product distribution in a template-directed oligonucleotide synthesis as a function of time and concentration of the reactants. The study is focused on the poly(C)-directed elongation reaction of an oligoguanylate (a 7-mer is chosen) with guanosine 5'-monophosphate-2-methyl-imidazolide (2-MeImpG), the activated monomer. It is known that the elongation of oligoguanylates to form oligomeric products such as 8-mer, 9-mer, 10-mer, etc., is in competition with (1) the dimerization and further oligomerization reaction of 2-MeImpG that leads to the formation of dimers and short oligomers, and (2) the hydrolysis of 2-MeImpG that forms inactive guanosine 5'-monophosphate, 5'-GMP. Experimentally determined rate constants for the above three processes at 37 degrees C and pH 7.95 were used in the simulation; the initial concentrations of 2-MeImpG, [M]o, and of the oligoguanylate primer, [7-mer]o, were varied, and KINSIM calculated the distribution of products as a function of time until equilibration was reached, i.e., when all the activated monomer has been consumed. In order to sort out how strongly the elongation reaction may be affected by the competing hydrolysis and dimerization, we also simulated the idealized situation in which these competing reactions do not occur.(ABSTRACT TRUNCATED AT 250 WORDS)

Biopolymers↗
PubMed1987

Kinetic analysis of the template effect in ribooligoguanylate elongation.

We have undertaken a complete kinetic analysis of the template-directed oligoguanylate synthesis originated in Orgel's laboratory (Inoue and Orgel, 1982). The reaction of guanosine 5'-phospho-2-methylimidazolide, 2-MelmpG, with ribooligoguanylates all 3'-5' linked, designated n3 with n = 7-12, was studied in the presence/absence of the complementary template polycytidylic acid, poly(C). Conditions were chosen where poly(C) and 2-MelmpG are in large excess over the oligoguanylate. In the absence of the template at 37 degrees C the reaction leads to three isomeric oligomers that are elongated by one monomer unit. They are the 3'-5' linked, (n + 1)3, the 2'-5' linked, (n + 1)2, and the pyrophosphate product, (n + 1)p, formed in an approximate ratio 1:2:5. In the presence of the template the reaction is 20-fold faster and yields products n + 1, n + 2, n + 3 etc. as long as 2-MelmpG is available. Most importantly the formation of the natural, 3'-5' linked isomer, is enhanced selectively by 140-fold at 37 degrees C. Qualitative observations allow the conclusion that this enhancement is temperature dependent and increases with decreasing temperature. For example, at 1 degree C only the 3'-5' linked isomers were detected. Initial rates for the disappearance of the n3 oligoguanylate were determined at 1, 23, and 37 degrees C. It was found that the pseudo-first order rate constant for oligoguanylate elongation was linearly proportional to the 2-MelmpG concentration. This implies that the reaction complex poly(C).n3.2-MelmpG does not accumulate under the reaction conditions, a conclusion which is also supported by infrared data (Miles and Frazier, 1982). The implication of the above results with respect to chemical evolution is that lower temperatures, i.e., close to freezing, enhance the regioselectivity of these template-directed reactions and that one way to improve replication models may be sought in finding conditions that favor stable reaction complexes.

Adenine Nucleotides↗
PubMedDate not supplied

Nucleotides as nucleophiles: reactions of nucleotides with phosphoimidazolide activated guanosine.

An earlier study of the reaction of phosphoimidazolide activated nucleosides (ImpN) in aqueous phosphate buffers indicated two modes of reaction of the phosphate monoanion and dianion. The first mode is catalysis of the hydrolysis of the P-N bond in ImpN's which leads to imidazole and nucleoside 5'-monophosphate. The second represents a nucleophilic substitution of the imidazole to yield the nucleoside 5'-diphosphate. This earlier study thus served as a model for the reaction of ImpN with nucleoside monophosphates (pN) because the latter can be regarded as phosphate derivatives. In the present study we investigated the reaction of guanosine 5'-phosphate-2-methylimidazolide, 2-MeImpG, in the presence of pN (N = guanosine, adenosine and uridine) in the range 6.9 less than or equal to pH less than or equal to 7.7. We observed that pN's do act as nucleophiles to form NppG, and as general base to enhance the hydrolysis of the P-N bond in 2-MeImpG, i.e. pN show the same behavior as inorganic phosphate. The kinetic analysis yields the following rate constants for the dianion pN2-: knpN = 0.17 +/- 0.02 M-1 h-1 for nucleophilic attack and khpN = 0.11 +/- 0.07 M-1 h-1 for general base catalysis of the hydrolysis. These rate constants which are independent of the nucleobase compare with kp.2 = 0.415 M-1 h-1 and khp2. = 0.217 M-1 h-1 for the reactions of HPO4(2-). In addition, this study shows that under conditions where pN presumably form stacks, the reaction mechanism remains unchanged although in quantitative terms stacked pN are somewhat less reactive. Attack by the 2'-OH and 3'-OH groups of the ribose moiety in amounts greater than or equal to 1% is not observed; this is attributed to the large difference in nucleophilicity in the neutral pH range between the phosphate group and the ribose hydroxyls. This nucleophilicity rank is not altered by stacking.

Guanosine↗