Propargyl groups are attractive functional groups for labeling purposes, as they allow CuAAC-mediated bioconjugation. Their size minimally exceeds that of a methyl group, the latter being frequent in natural nucleotide modifications. To understand under which circumstances propargyl-containing oligodeoxynucleotides preserve base pairing, we focused on the exocyclic amine of cytidine. Residues a...

This paper is a theoretical study of notions in combinatorics of words motivated by information being encoded as DNA strands in DNA computing. We generalize the classical notions of conjugacy and commutativity of words to incorporate the notion of an involution function, a formalization of the Watson-Crick complementarity of DNA single-strands. We define and study properties of Watson-Crick con...

Thermodynamic stabilities of 2 x 2 nucleotide tandem AG internal loops in RNA range from -1.3 to +3.4 kcal/mol at 37 degrees C and are not predicted well with a hydrogen-bonding model. To provide structural information to facilitate development of more sophisticated models for the sequence dependence of stability, we report the NMR solution structures of five RNA duplexes: (rGACGAGCGUCA)(2), (r...

Watson-Crick automata are finite state automata working on doublestranded tapes, introduced to investigate the potential of DNA molecules for computing. In this paper we introduce the concept of parallel communicating Watson-Crick automata systems. It consists of several Watson-Crick finite automata parsing independently the same input and exchanging information on request, by communicating sta...

Watson-Crick D0L systems, introduced in 1997 by V. Mihalache and A. Salomaa, arise from two major principles: the Lindenmayer rewriting and the Watson-Crick complementarity principle. Complementarity can be viewed as a purely language-theoretic operation. Majority of a certain type of symbols in a string (purines vs. pyrimidines) triggers a transition to the complementary string. The paper deal...

one-way quantum finite automata are reversible in nature, which greatly reduces its accepting property. In fact, the set of languages accepted by one-way quantum finite automata is a proper subset of regular languages. In this paper, we replace the tape head of one-way quantum finite automata with DNA double strand and name the model Watson-Crick quantum finite automata. The noninjective comple...

In describing the DNA double helix, Watson and Crick suggested that "spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms." Indeed, among many mispairing possibilities, either tautomerization or ionization of bases might allow a DNA polymerase to insert a mismatch with correct Watson-Crick geometry. However, despite substantial progress in ...