Targeting the ICB2 site of the topoisomerase IIalpha promoter with a formamido-pyrrole-imidazole-pyrrole H-pin polyamide.
The synthesis, DNA binding characteristics and biological activity of an N-formamido pyrrole- and imidazole-containing H-pin polyamide (f-PIP H-pin, 2) designed to selectively target the ICB2 site on the topoIIalpha promoter, is reported herein. Thermal denaturation, circular dichroism, isothermal titration calorimetry, surface plasmon resonance and DNase I footprinting studies demonstrated that 2 maintained the selectivity of the unlinked parent monomer f-PIP (1) and with a slight enhancement in binding affinity (K(eq)=5 x 10(5)M(-1)) to the cognate site (5'-TACGAT-3'). H-pin 2 also exhibited comparable ability to inhibit NF-Y binding to 1, as demonstrated by gel shift studies. However, in stark contrast to monomer 1, the H-pin did not affect the up-regulation of topoisomerase IIalpha (topoIIalpha) in cells (Western blot), suggesting that the H-pin does not enter the nucleus. This study is the first to the authors' knowledge that reports such a markedly different cellular response between two compounds of almost identical binding characteristics.
Franks
Andrew
A
Division of Natural and Applied Sciences, Department of Chemistry, Hope College, Holland, MI 49423, USA.
Tronrud
Christopher
C
Kiakos
Konstantinos
K
Kluza
Jerome
J
Munde
Manoj
M
Brown
Toni
T
Mackay
Hilary
H
Wilson
W David
WD
Hochhauser
Daniel
D
Hartley
John A
JA
Lee
Moses
M
D000818:Animals; D000951:Antigens, Neoplasm / Q000235:genetics*; D001665:Binding Sites; D002151:Calorimetry; D002460:Cell Line; D002942:Circular Dichroism; D004250:DNA Topoisomerases, Type II / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics*; D005559:Formamides / Q000737:chemistry*; D007093:Imidazoles / Q000737:chemistry*; D051379:Mice; D009757:Nylons / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D011401:Promoter Regions, Genetic; D011489:Protein Denaturation; D011758:Pyrroles / Q000737:chemistry*; D020349:Surface Plasmon Resonance; D044366:Transition Temperature
D000951:Antigens, Neoplasm; D004268:DNA-Binding Proteins; D005559:Formamides; D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; C029899:imidazole; D004250:DNA Topoisomerases, Type II