Thermodynamic stability and folding kinetics of the major G-quadruplex and its loop isomers formed in the nuclease hypersensitive element in the human c-Myc promoter: effect of loops and flanking segments on the stability of parallel-stranded intramolecular G-quadruplexes.
Overexpression of the c-Myc proto-oncogene is associated with a broad spectrum of human cancers. Nuclease hypersensitivity element III(1) (NHE III(1)) of the c-Myc promoter can form transcriptionally active and silenced forms, and the formation of DNA G-quadruplex structures has been shown to be critical for c-Myc transcriptional silencing. The major G-quadruplex formed in c-Myc NHE III(1) is a mixture of four loop isomers, which have all been shown to be biologically relevant to c-Myc transcriptional control. In this study, we performed a thorough thermodynamic and kinetic study of the four c-Myc loop isomers in a K(+) solution. The four loop isomers all form parallel-stranded G-quadruplexes with short loop lengths. While the parallel-stranded G-quadruplex has been known to favor short loop lengths, our results show that the difference in thermodynamic and kinetic properties of the four loop isomers, and hence between the parallel G-quadruplexes with similar loop lengths, is more significant than previously recognized. At 20 mM K(+), the average difference in the T(m) values between the most stable loop isomer 14/23 and the least stable loop isomer 11/20 is more than 10 °C. In addition, the capping structures formed by the extended flanking segments are shown to contribute to a stabilization of 2-3 °C in T(m) for the c-Myc promoter G-quadruplex. Understanding the intrinsic thermodynamic stability and kinetic properties of the c-Myc G-quadruplex loop isomers can aid in our understanding of their biological roles and drug targeting.
Hatzakis
Emmanuel
E
College of Pharmacy, The University of Arizona, 1703 East Mabel Street, Tucson, AZ 85721, USA.
Okamoto
Keika
K
Yang
Danzhou
D
D004720:Endonucleases / Q000235:genetics*; D054856:G-Quadruplexes; D006801:Humans; D007700:Kinetics; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D000090063:Proto-Oncogene Mas; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid; D013816:Thermodynamics; D044366:Transition Temperature
C000715470:MAS1 protein, human; D000090063:Proto-Oncogene Mas; D016271:Proto-Oncogene Proteins c-myc; D004720:Endonucleases