Watson-Crick (WK) finite automata are working on a tape, that is, DNA molecule. A double stranded molecule contains two strands, each having 5' and 3' end, these strands together form the with following properties. The have same length, their to directions opposite, in position, nucleotides complement of other (by complementary relation). Consequently, WK reading heads, one for strand. In tradi...

DNA computers provide new paradigms of computing (Păun et al., 1998). They appeared at the end of the last century. In contrast, the theory of finite automata is well developed and intensively used in both theory and practice. The Watson-Crick automata, introduced in (Freund et al., 1997), relate to both fields. They are important in the field of (DNA) computing and have important relation to f...

Nucleic acid duplexes containing non-Watson–Crick base pairs are of interest to several fields including structural biology, supramolecular chemistry, origin of life, and synthetic biology. An early observation of a natural non-Watson–Crick base pair was the tRNA–mRNA adenine–inosine wobble pair, and it is now known that purine–purine pairs occur frequently in natural RNAs, including ribosomes ...

The natural bases of nucleic acids have a strong preference for one tautomer form, guaranteeing fidelity in their hydrogen bonding potential. However, base pairs observed in recent crystal structures of polymerases and ribosomes are best explained by an alternative base tautomer, leading to the formation of base pairs with Watson-Crick-like geometries. These observations set limits to geometric...

Several crystal structures of RNA fragments, alone or in complex with a specific protein, have been recently solved. In addition, the structures of an artificial ribozyme, the leadzyme, and the cleavage product of a human pathogen ribozyme, have extended the structural diversity of ribozyme architectures. The attained set of folding rules and motifs expand the repertoire seen previously in tRNA...

The decoding of mRNA on the ribosome is the least accurate process during genetic information transfer. Here we propose a unified decoding mechanism based on 11 high-resolution X-ray structures of the 70S ribosome that explains the occurrence of missense errors during translation. We determined ribosome structures in rare states where incorrect tRNAs were incorporated into the peptidyl-tRNA-bin...

Watson-Crick complementarity can be viewed as a language-theoretic operation: \bad" words obtained through a generative process are replaced by their complementary ones. This idea seems particularly suitable for Lindenmayer systems. D0L systems augmented with a speci c complementarity transition, Watson-Crick D0L systems, have turned out to be a most interesting model and have already been exte...

Addition of 3' and 5' terminal phosphates to dApdA causes a decrease in conformational flexibility. pdApdAp has much fewer conformers with energies below 2.5 kcal./mole than dApdA. THE A, B and Watson-Crick (34) helices are the most preferred forms. Other important conformations are in the trans domain of psi. Thus, flexibility in psi as well as in omega and omega, and in the sugar pucker is in...