Figure 1.
Fig. 1. Site-specific recognition of nucleosomal DNA by
clamp PAs. (A) NCP146 structure (PDB ID code 1AOI [PDB]
, ref. 2) viewed with the superhelical axis along the z axis.
The particle pseudo-two-fold dyad axis ( ) is shown for
orientation. DNA (blue and white) and associated histone
proteins (H2A, yellow; H2B, red; H3, blue; H4, green) are shown
in sphere or surface representation. (B) Supergrooves in NCP146.
Shown is a different view of NCP146 with the superhelical axis
along the y axis. Color scheme is the same as in A. One of the
DNA supergrooves is indicated by two asterisks. (C) Chemical
structures of clamp PAs, PW12 to -14. (D) Hydrogen bonding model
of PW12 to its target DNA site. Circles with dots represent lone
pairs of N3 of purines and O2 of pyrimidines. Circles containing
H represent the N2 hydrogen of guanine. Putative hydrogen bonds
are illustrated by dotted lines.
) is shown for
orientation. DNA (blue and white) and associated histone
proteins (H2A, yellow; H2B, red; H3, blue; H4, green) are shown
in sphere or surface representation. (B) Supergrooves in NCP146.
Shown is a different view of NCP146 with the superhelical axis
along the y axis. Color scheme is the same as in A. One of the
DNA supergrooves is indicated by two asterisks. (C) Chemical
structures of clamp PAs, PW12 to -14. (D) Hydrogen bonding model
of PW12 to its target DNA site. Circles with dots represent lone
pairs of N3 of purines and O2 of pyrimidines. Circles containing
H represent the N2 hydrogen of guanine. Putative hydrogen bonds
are illustrated by dotted lines.