Structural polymorphism of the four-repeat Oxytricha nova telomeric DNA sequences.
G-quadruplexes are four-stranded nucleic acid complexes that exhibit a great deal of polymorphism. Recently a group described the polymorphism exhibited by the four-repeat of the Oxytricha nova telomeric sequences (Lee, J.Y., Yoon, J., Kihm, H.W., Kim, D.S., Biochemistry 2008, 47, 3389-3396). In this study we evaluated the effects of G-tract and loop lengths on this behaviour using circular dichroism (CD) and gel electrophoresis. The largest changes were detected for oligonucleotides with different numbers of consecutive G residues. Furthermore, decreasing the number of residues between the G runs, the loops, from four to three only results in minor alteration in the polymorphism. However, the shortening of the G-tract from four to three guanine residues led to characteristically anti-parallel G-quadruplex CD spectra. Finally, we show that adenine bases in the loop sequences are less likely to form G-quadruplexes in the presence of Na(+) cations than those comprised of thymine residues. The results presented here are an addition to the modest information available for predicting the type of G-quadruplex to be formed from G-rich sequences in aqueous solutions containing sodium or potassium ions.
Abu-Ghazalah
Rashid M
RM
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Canada.
Macgregor
Robert B
RB
D000225:Adenine / Q000737:chemistry; D000818:Animals; D001345:Autoradiography; D002942:Circular Dichroism; D016054:DNA, Protozoan / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D016813:Oxytricha / Q000737:chemistry*; D010761:Phosphorus Radioisotopes; D012964:Sodium / Q000737:chemistry; D013941:Thymine / Q000737:chemistry
D016054:DNA, Protozoan; D009838:Oligodeoxyribonucleotides; D010761:Phosphorus Radioisotopes; D006147:Guanine; D012964:Sodium; D000225:Adenine; D013941:Thymine