Beyond Intra-Base-Pair Hydrogen Bonds in DNA Structures: A Comprehensive Analysis

Jürgen Sühnel 1), Klaus Lindauer 1)
Institut für Molekulare Biotechnologie, Postfach 100813, D-07708 Jena / Germany
1) E-Mail: jsuehnel@imb-jena.de; klaus@imb-jena.de

Table I

DNA structures from the Protein Data Bank searched for non-intra-base-pair hydrogen bonds 1)

A-DNA (14 structures):

X-ray: 115d, 137d, 160d, 172d, 197d, 1ana, 1d91, 1d92, 1dn6, 218d, 221d, 2ana, 2d47, 3ana

B-DNA (49 structures):

X-ray: 111d, 112d, 113d, 114d, 119d, 122d, 123d, 126d, 150d, 153d, 158d, 167d, 178d, 194d, 196d, 1bdn_AB, 1bdn_CD, 1bna, 1cgc, 1d23, 1d27, 1d28, 1d29, 1d49, 1d56, 1d57, 1d60, 1d65, 1d75, 1d77, 1d80, 1d81, 1d89, 1d97, 1d98, 1d99, 1da3, 1dn9, 1dnm, 1ndn_ABC, 1ndn_TUV, 2bna, 2d25, 3bna, 4bna, 4dnb, 7bna, 9bna

NMR: 175d

Z-DNA (23 structures):

X-ray: 131d, 133d, 145d_AB, 145d_CD, 180d, 181d, 1d24, 1d39, 1d40, 1d41, 1d48, 1d53, 1d76, 1da1, 1da2, 1dcg, 1dn4, 1dn5, 1dn8, 1dnf, 1zna, 223d, 2dcg

Other DNA structures (27 structures):

X-ray: 190d, 191d, 192d, 1d16, 1d31, 1d59, 200d, 208d, 241d

NMR: 103d, 105d, 106d, 134d, 136d, 139d, 143d, 149d, 156d, 177d, 179d, 186d, 1d18, 1d19, 1d20, 1d70, 1da4, 201d

DNA-drug complexes (49 structures):

X-ray: 101d, 102d, 109d, 121d, 127d, 128d, 129d, 130d, 144d, 154d, 166d, 182d, 195d, 198d, 1d21, 1d22, 1d30, 1d32, 1d43, 1d44, 1d45, 1d46, 1d63, 1d64, 1d86, 1dne, 1dnh, 1gpg, 1lex, 1ley, 1prp, 209d, 224d, 227d, 264d, 2d55, 2dbe, 2des, 2dnd, 5bna, 6bna, 8bna

NMR: 107d, 108d, 146d, 185d, 193d, 199d, 202d

DNA-protein complexes (40 structures):

X-ray: 1apl, 1brn, 1cgp, 1cma, 1d66, 1dct, 1dnk, 1glu, 1hdd, 1hcr, 1hut, 1kln, 1lli, 1lmb, 1mdy, 1oct, 1par, 1per, 1pdn, 1pvi, 1pyi, 1rpe, 1rva, 1rvb, 1rvc, 1tro, 1ysa, 1ytb, 1zaa, 2bpf, 2bpg, 2dnj, 2drp, 2or1, 2rve, 3cro

NMR: 1gat, 1gau, 1msf, 1mse

1) Structures for which non-intra-base-pair H-bonds were found are given in bold.