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J Ninio

Publications and source records attributed to J Ninio.

51 records · Page 3Linked to original sources
PubMed1979

Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs.

Previously published models for predicting pairing schemes in RNA molecules, when applied to tRNA, give the clover leaf structure in only half the cases. We made a systematic investigation of the predictability of the clover leaf structure under various assumptions concerning the energetic contributions of single and double-stranded regions. We tested 21 different models and variants on a set of 100 tRNA sequences and many other variants on a smaller set of sequences. In our models we allowed not only G.C, A.U and G.U pairing, but also every other pair. Under conditions which are much less restrictive than those of previous attempts, we can nevertheless reach 90 per cent predictability for the clover leaf structure of tRNA. A most surprising and far-reaching result is that we can assign to C.G and C.C pairs binding energies quite close to the energies of G.U pairs, and still predict the clover leaf. The following ranking for non-complementary pairs was obtained : G.U, G.G and C.C, U.U, C.A, A.A and G.A, U.C. The main practical innovation which made possible the improvements in predictability are: i) not counting the stacking of base pairs separated by a bulge loop; ii) making the terminal C.C's in stems more stable than the terminal A.U's by merely -- 0.7 kcal; iii) replacing the distinction between G.C and A.U-closed loops by a distinction based on the presence of loop-favoring residues; iv) carefully adjusting the energetic balance between the various kinds of loops; v) narrowing the gap between the GC/GC and the GC/AU contributions; vi) using observations on nearest-neighbours in tRNA sequences to refine the contributions of G.U pairs.

Base Composition↗
PubMed1978

Heteropolynucleotides as templates for non-enzymatic polymerizations.

We have studied a number of condensation reactions involving ImpU, ImpT, ImpC, ImpA, ImpG, ImpUgG and ImpCpA as activated nucleotide donors and a variety of homo- and hetero-polynucleotides as templates. We did not not obtain any evidence of a template effect with ImpU and ImpT, but observed some condensation of ImpC with GpG on appropriate templates. ImpA and ImpG take part in a number of more or less efficient template-directed reactions, as do ImpUpG and ImpCpA. Our results suggest that, on the primitive Earth, pyrimidine nucleotides could most easily have been incorporated into polymers as constituents of short oligomers, which contained one or more purine nucleotide. The linkage of the product depends strongly on the nature of the substrates; the percentage of the natural 3'-5'-linkage was, in some cases, less than 10% and, in others, as high as 70%. Wobble-pairing was often very effective in promoting condensations, suggesting that transition mutations would have been very frequent in prebiotic polynucleotide replication.

Chemical Phenomena↗
PubMed1977

The geometry of the correspondence between two retinal projections.

Since each retinal projection of an object has some definite geometric relation to it, the two projections of a same object are related to each other. The correspondences between points, linear segments, and orientations on the two retinas are discussed thoroughly in three-dimensional geometry, and the constraints that tie the projections (the 'projective invariants') are presented. Some widely held conceptions on disparity or the ambiguity problem in binocular stereopsis appear to be based upon representation that are correct in particular situations, but are misleading in the general case. I suggest that in order to achieve binocular stereopsis, the brain does not proceed by complete trial and error, but may guide its search for correspondences by taking advantage of the geometric constraints. There are at least four major possible strategies: (i) a metric strategy, as initially proposed by Julesz; (ii) a projective strategy based on the law of invariance of the anharmonic ratio and Desargue's theorem; (iii) a perspective strategy discussed in relation to the homology relationships between vanishing points and in relation to physiological studies on cells of visual cortex; and (iv) a more dynamic strategy based upon the geometric properties of the Zöllner illusion.

Animals↗
PubMed1975

Kinetic amplification of enzyme discrimination.

The dependence of the accuracy of enzymatic systems on the mechanism of the catalyzed reaction is investigated, using a probabilistic approach. Certain mechanisms of reaction, involving a delay in one of the steps act as kinetic amplifiers of molecular discriminations. The relationship between our scheme for a delayed reaction [1] and Hopfield's scheme [i] is discussed.

DNA Nucleotidyltransferases↗