Figure 1
From: From sequence to structure and back again: approaches for predicting protein-DNA binding
Characteristics of C-G and T-A base pairs Intermolecular H-bonds (dotted lines) in the C-G and T-A bp, stabilize the DNA double helix. The bp edges form a pattern of H-bond acceptors and donors that can be recognized by amino acid side chains of proteins. This pattern is unique for each bp (C-G, G-C, T-A, and A-T) in the major groove (up), whereas it is only possible to distinguish a C-G bp (top) form an T-A bp (bottom) in the minor groove (down) [9]. H-bond acceptors and donors are indicated by outward and inward pointing arrows respectively. The letter M is the methyl group of the base T and H R is a ring hydrogen donor. The chemical composition of the DNA sugar-phosphate backbone (not shown) is constant and independent of the bp sequence.