Nickel-guanine interactions in DNA: crystal structure of nickel-d[CGTGTACACG]2.
The aim of this study was to clarify whether Ni2+ ions could bind to guanine bases in a standard B-DNA duplex and eventually induce a B-->Z transition. We have determined by X-ray crystallography at 3.1 A resolution the structure of the alternating deoxynucleotide d(CGTGTACACG), which contains both internal and terminal guanines. The duplex is in the B form. It is shown that nickel ions bind selectively to the N7 atom of guanine 10, which is in an extra-helical position, and guanine 2, which is in the terminal position of the duplex. It does not bind to guanine 4, which lies within a standard B-DNA tract. This simple but unambiguous result proves that nickel ions select between different guanines via steric accessibility. Guanine-Ni2+-guanine bridges among symmetry-related duplexes have also been found. These bridges may explain why Ni2+ ions may act either as a precipitant or a renaturing agent for DNA under certain conditions. The biochemical interaction of nickel with DNA can thus be related to its capacity to specifically bind to B-DNA regions with exposed guanines. Also, from the structural point of view, we have found a terminal cytosine, which forms a C.G:C reverse-Hoogsteen triple structure with a base pair of a neighbor duplex. This type of triplet is seldom found and is here described for the first time for a DNA structure.
Abrescia
Nicola A
NA
Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain.
Huynh-Dinh
Tam
T
Subirana
Juan A
JA
D018360:Crystallography, X-Ray / Q000379:methods; D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006147:Guanine / Q000737:chemistry*; D008958:Models, Molecular; D009532:Nickel / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009695:Nucleic Acid Renaturation / Q000502:physiology; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*
D009838:Oligodeoxyribonucleotides; D006147:Guanine; D009532:Nickel; D003596:Cytosine; D004247:DNA