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 III

Statistics of non-intra-base-pair hydrogen bonds in DNA structures

Total number of non-intra-base-pair H-bonds:                           82
Three center H-bonds with one or two non-intra-base-pair H-bonds:              36
Two-center H-bonds:                                            46
Base-backbone H-bonds:                                         24
Base-base H-bonds:                                             58
Number of H-bonds for residue types:
  
  donor        acceptor
  A    T               29
  G    G               11
  G    C                8
  G    T                6
  G    A                6
  C    T                5
  C    G                4
  A    G                3
  C    A                3
  T    A                2
  T    C                2
  T    G               1
  A    A               1
  T    T               1 

Donor atoms:                   Acceptor atoms:
  A:N6                 33        T:O4                  32
  G:N2                 24        G:O6                  10
  C:N4                 12        C:O2                  6
  G:N1                 7         T:O2                  6
  T:N3                 6         A:O2P                 5
                                 G:O2P                 4
  two-H donor atoms              A:O4*                 3
  (A.N6, C:N4, G:N2):  69        C:O4*                 3
                                 G:O3*                 3
  one-H donor atoms:   13        T:O4*                 2
  (G:N1, T:N3)                   A:N1                  2
                                 G:N3                  1
                                 C:O1P                 1
                                 A:O1P                 1
                                 A:N7                  1
                                 G:O4*                 1
                                 T:O1P                 1

Fraction of structures with non-intra-base-pair H-bonds:
  A-DNA                                14%
  B-DNA                                18%
  Z-DNA                                -
  unusual DNA                  26%
  DNA-drug complexes           18%
  DNA-protein complexes                42%