Solution structures of unimolecular quadruplexes formed by oligonucleotides containing Oxytricha telomere repeats.
BACKGROUND
Oligonucleotides containing the guanine-rich telomeric sequence of Oxytricha chromosomes (dT4G4) have previously been shown to form DNA quadruplexes comprising guanine quartets stabilized by cations. Two different structures have been reported for both d(G4T4G4) (Oxy1.5) and d(G4T4G4T4G4T4G4) (Oxy3.5).


RESULTS
Here we present the solution structure of a uracil- and inosine-containing derivative of Oxy3.5, d(G4TUTUG4T4G4UUTTG3I) (Oxy3.5-U4128), determined using two-dimensional 1H and 31P NMR techniques. This oligonucleotide forms a unimolecular quadruplex that is very similar to the dimeric Oxy1.5 solution structure, in that it contains a loop spanning the diagonal of an end quartet. The groove widths, strand polarities, and positions of the syn bases along the G4 tracts and within the quartets are all as reported for Oxy1.5. The first and third pyrimidine tracts form parallel loops spanning a wide groove and a narrow groove respectively.


CONCLUSIONS
Both Oxy3.5 and Oxy3.5-U(4)128 form unimolecular quadruplexes in solution with a diagonal central T4 loop. These results conflict with those reported for d(G4TUTUG4TTUUG4UUTTG4) in solution, in which the central loop spans a wide groove.
Smith
F W
FW
Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.
Schultze
P
P
Feigon
J
J
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D006151:Guanosine / Q000737:chemistry; D007288:Inosine / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry* / Q000235:genetics; D016813:Oxytricha / Q000235:genetics*; D011188:Potassium / Q000737:chemistry; D011522:Protons; D012091:Repetitive Sequences, Nucleic Acid; D012984:Software; D016615:Telomere / Q000737:chemistry* / Q000235:genetics
D009841:Oligonucleotides; D011522:Protons; D006151:Guanosine; D007288:Inosine; D011188:Potassium