Stacking interaction of guanine with netropsin in the minor groove of d(CGTATATACG)2.
We present the structure of the decanucleotide d(CGTATATACG) determined by single crystal X-ray diffraction at 1.58 A resolution. A netropsin drug is found in the minor groove with guanine stacked on a pyrrole ring of the drug, a feature described here for the first time. The stacked guanine is an extra-helical base coming from the end of a neighbour oligonucleotide. This observation may open the way to the development of minor groove binding drugs with a higher sequence selectivity. The oligonucleotide is in the B-conformation, but the terminal base-pairs are disrupted: the cytosine residues are disordered while the guanine residues penetrate into the minor groove of neighbouring duplexes. Four hydrated Ni ions with octahedral co-ordination are found associated with the N7 atoms of each guanine. The high affinity of these ions with guanine suggests that they may be used as probes for specific guanine residues.
Abrescia
N G
NG
Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona, E-08028, Spain.
Malinina
L
L
Subirana
J A
JA
D018360:Crystallography, X-Ray; D006147:Guanine / Q000378:metabolism*; D008958:Models, Molecular; D009429:Netropsin / Q000378:metabolism*; D009532:Nickel / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000378:metabolism*; D013329:Structure-Activity Relationship
D009841:Oligonucleotides; D006147:Guanine; D009429:Netropsin; D009532:Nickel