To guide the design of alternative genetic systems, we measured melting temperatures of DNA duplexes containing matched and mismatched nucleobase pairs from natural and unnatural structures. The pairs were analyzed in terms of structural features, including nucleobase size, number of hydrogen bonds formed, the presence of uncompensated hydrogen bonding functional groups, the nature of the bond ...

Watson-Crick finite automata were inspired by formal language theory, finite states machines and some ingredients from DNA computing such as working with molecules as double stranded complementary strings. Here, we define different kinds of regular reversibility in this model. Mainly, we will explore regular reversibility in the upper (lower) strand and in the double strand.

5′ → 3′ WK-automata are Watson-Crick automata whose two heads start on opposite ends of the input word and always run in opposite directions. One full reading in both directions is called a run. We prove that the automatas’ power increases with every run more they can make. This defines an infinite hierarchy of language classes between the regular and the context-sensitive languages. This hiera...

Tricyclo-DNA belongs to the family of conformationally restricted oligodeoxynucleotide analogues. It differs structurally from DNA by an additional ethylene bridge between the centers C(3') and C(5') of the nucleosides, to which a cyclopropane unit is fused for further enhancement of structural rigidity. The synthesis of the hitherto unknown tricyclodeoxynucleosides containing the bases cytosin...

Watson-Crick (WK) finite automata are working on a Watson-Crick tape, that is, on a DNA molecule. Therefore, it has two reading heads. While in traditional WK automata both heads read the whole input in the same physical direction, in 5′→ 3′ WK automata the heads start from the two extremes and read the input in opposite direction. In sensing 5′ → 3′ WK automata the process on the input is fini...

Zinc, a component of a large number of enzymes and an abundant and essential trace metal, alters the structure of AGCT sites in negatively supercoiled DNA. Related sequences show little or no effect. Cobalt and cadmium show reactivities similar to zinc. The conformational change in DNA was fine mapped with haloacetaldehydes using chemical cleavage or primer extension methods. Since a many fold ...

Watson-Crick complementarity is one of the very central components of DNA computing, the other central component being the massive parallelism of DNA strands. While the latter component drastically reduces time complexity, the former component is the cause behind the Turing universality of models of DNA computing. This paper makes this cause explicit and also discusses it in terms of some speci...