DNA-sequence specific recognition by a thiazole analogue of netropsin: a comparative footprinting study.
Four different footprinting techniques have been used to probe the DNA sequence selectivity of Thia-Net, a bis-cationic analogue of the minor groove binder netropsin in which the N-methylpyrrole moieties are replaced by thiazole groups. In Thia-Net the ring nitrogen atoms are directed into the minor groove where they could accept hydrogen bonds from the exocyclic 2-amino group of guanine. Three nucleases (DNAase I, DNAase II, and micrococcal nuclease) were employed to detect binding sites on the 160bp tyr T fragment obtained from plasmid pKM delta-98, and further experiments were performed with 117mer and 253mer fragments cut out of the plasmid pBS. MPE.Fe(II) was used to footprint binding sites on an EcoRI/HindIII fragment from pBR322. Thia-Net binds to sites in the minor groove containing 4 or 5 base pairs which are predominantly composed of alternating A and T residues, but with significant acceptance of intrusive GC base pairs. Unlike the parent antibiotic netropsin, Thia-Net discriminates against homooligomeric runs of A and T. The evident preference of Thia-Net for AT-rich sites, despite its containing thiazole nitrogens capable of accepting GC sites by hydrogen bonding, supports the view that the biscationic nature of the ligand imposes a bias due to the electrostatic potential differences in the receptor which favour the ligand reading alternating AT sequences.
Plouvier
B
B
Institut de Chimie Pharmaceutique, Faculté de Pharmacie, Lille, France.
Bailly
C
C
Houssin
R
R
Rao
K E
KE
Lown
W J
WJ
Hénichart
J P
JP
Waring
M J
MJ
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004269:DNA, Bacterial / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism; D004492:Edetic Acid / Q000031:analogs & derivatives; D004706:Endodeoxyribonucleases / Q000378:metabolism; D006147:Guanine / Q000737:chemistry; D006860:Hydrogen Bonding; D007502:Iron Chelating Agents; D008836:Micrococcal Nuclease / Q000378:metabolism; D008969:Molecular Sequence Data; D009429:Netropsin / Q000031:analogs & derivatives / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000235:genetics*; D013844:Thiazoles / Q000378:metabolism*
D004269:DNA, Bacterial; D007502:Iron Chelating Agents; C036483:T-DNA; D013844:Thiazoles; C038200:methidiumpropyl-EDTA-iron(II); C071601:Thia-Net; D006147:Guanine; D009429:Netropsin; D004492:Edetic Acid; D004706:Endodeoxyribonucleases; D003850:Deoxyribonuclease I; C019329:deoxyribonuclease II; D008836:Micrococcal Nuclease