Mm. Harding et al., DNA-BINDING STUDIES OF XSPTSPSZ, DERIVATIVES OF THE INTERCALATING HEPTAD REPEAT OF RNA-POLYMERASE-II, Biopolymers, 42(4), 1997, pp. 387-398
The synthesis, solution conformation, and interaction with DNA of thre
e 8-residue peptides structurally related to the heptad repent unit fo
und at the C-terminus of RNA polymerase II are reported. Peptides QQ,
XQ, and Pe are derived from the parent sequence YSPTSPSY (peptide YY),
which was reported to bind to DNA by bisintercalation [M. Suzuki (199
0) Nature, Vol. 344, pp. 562-565], and contain either a 2-quinolyl (Q)
, 2-quinoxolyl (X), or 5-phenanthrolyl (P) group in place of the aroma
tic side chains of the N- and C-terminal tyrosine residues present in
the parent sequence. The combined results of linear dichroism and indu
ced CD measurements of peptides QQ, Xe, and Pe with calf thymus DNA ar
e consistent with weak binding of the peptides to DNA in a preferred o
rientation in which the chromophores are intercalated. Small increases
in the melting temperatures of poly[d(A-T)(2)] are also consistent wi
th the peptides interacting with DNA. While enzymatic footprinting wit
h DNase I showed no protection from cleavage by the enzyme, chemical f
ootprinting with fotemustine showed that the peptides modify the react
ivity of the major groove, presumably via minor groove binding. Peptid
e QQ inhibited fotemustine alkylation significantly more than either X
e or Pe, and slightly more than YY. In aqueous solution, nmr experimen
ts on QQ, XQ, and PQ show a significant population of conformation in
which Ser2-Pro3-Thr4-Ser5 form both type I and type II beta-turn confo
rmations in equilibrium with open chain conformations. Nuclear magneti
c resonance titration experiments of PQ with (GCGTACGC)(2) showed smal
l changes in chemical shifts, consistent with the formation of a weak
nonspecific complex. Analogous experiments, using peptides QQ and XQ w
ith (GCGTACGC)(2), and peptide YY with (CGTACG)(2), showed no evidence
for the interaction of the peptides with these oligonucleotides. Thes
e results show that peptides of general structure XSPTSPSZ are weak no
nspecific DNA binders that differ significantly from previously charac
terized S(T)PXX DNA-binding motifs that are generally AT-selective min
or groove binders. (C) 1997 John Wiley & Sons, Inc.