A model for the solution structure of a branched, three-strand DNA complex.
The solution structure of a DNA three-way junction (TWJ) containing two unpaired thymidines was elucidated using two- and three-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. TWJs with unpaired nucleotides are ubiquitous structural motifs of complex single-stranded nucleic acids. In the presence of Mg2+, the TWJ complex adopts a unique conformation in which the bases of one of the oligonucleotides ("strand 1") are continuously stacked across the junction. Guanosine 8 of strand 3 (S3-G8), which pairs with S1-C5, stacks on S2-G5, which is paired to S1-C6. The unpaired thymidine bases (S3-T6 and S3-T7) are exposed to the solvent, whereas the sugar of S3-G8 is largely buried. S3-T6 also interacts with the sugar residue of S3-G11. All three stems conform to B-type DNA.
Leontis
N B
NB
Department of Chemistry, Bowling Green State University, Ohio 43403.
Hills
M T
MT
Piotto
M
M
Malhotra
A
A
Nussbaum
J
J
Gorenstein
D G
DG
D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D006151:Guanosine / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015345:Oligonucleotide Probes; D013936:Thymidine / Q000737:chemistry
D015345:Oligonucleotide Probes; C051802:triplex DNA; D006151:Guanosine; D004247:DNA; D008274:Magnesium; D013936:Thymidine