LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

268 Satoshi Kobayashi, Takashi Yokomori, and Yasubumi Sakakibara
of the set X. For integers i, j such that 1 ≤ i ≤ j ≤|α|, byα[i, j] wedenote
the substring of α starting from the ith letter and ending at the jth letter of α.
In case of i = j, wesimplywriteα[i]. In case of i>j, α[i, j] represents a null
string.
2.1 Secondary Structure
We will mainly follow the terminologies and notations used in [17]. Let us introduce
the Watson-Crick complementarity function θ : Σ → Σ defined by
θ(A) = T, θ(T) = A, θ(C) = G, and θ(G) = C 4 . A hydrogen bond between the
ith base and jth base of α is denoted by (i, j), and called a base pair. A hydrogen
bond (i, j) can be formed only if θ(α[i]) = α[j]. Without loss of generality, we
may always assume that i