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...

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...

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...

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...

Coralyne is an alkaloid drug that binds homo-adenine DNA (and RNA) oligonucleotides more tightly than it does Watson-Crick DNA. Hud's laboratory has shown that poly(dA) in the presence of coralyne forms an anti-parallel duplex, however attempts to determine the structure by NMR spectroscopy and X-ray crystallography have been unsuccessful. Assuming adenine-adenine hydrogen bonding between the t...

UV-light-induced cyclobutane pyrimidine dimers (CPDs) present a severe block to synthesis by replicative DNA polymerases (Pols), whereas Poleta promotes proficient and error-free replication through CPDs. Although the archael Dpo4, which, like Poleta, belongs to the Y family of DNA Pols, can also replicate through a CPD, it is much less efficient than Poleta. The x-ray crystal structure of Dpo4...

Thermodynamic measurements are reported for 51 DNA duplexes with A.A, C.C, G.G, and T.T single mismatches in all possible Watson-Crick contexts. These measurements were used to test the applicability of the nearest-neighbor model and to calculate the 16 unique nearest-neighbor parameters for the 4 single like with like base mismatches next to a Watson-Crick pair. The observed trend in stabiliti...