DNA G-quadruplexes are DNA secondary structures formed in specific G-rich sequences. DNA sequences that can form G-quadruplexes have been found in regions with biological significance, such as human telomeres and oncogene-promoter regions. DNA G-quadruplexes have recently emerged as a new class of novel molecular targets for anticancer drugs. Recent progress on structural studies of the biologically relevant G-quadruplexes formed in human telomeres and in the promoter regions of human oncogenes will be discussed, as well as recent advances in the design and development of G-quadruplex-interactive drugs. DNA G-quadruplexes can readily form in solution under physiological conditions and are globularly folded nucleic acid structures. The molecular structures of intramolecular G-quadruplexes appear to differ from one another and, therefore, in principle may be differentially regulated and targeted by different proteins and drugs.

Overexpression of the c-Myc proto-oncogene is associated with a broad spectrum of human cancers. The 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 the 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 K + solution. The four loopisomers all form parallel-stranded G-quadruplexes with short loop lengths. While the parallelstranded 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 of the T m values between the most stable loopisomer 14/23 and the least stable loop-isomer 11/20 is greater than 10 degrees. 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 help understand their biological roles and drug targeting. Keywordsc-Myc promoter G-quadruplex; loop-isomers; parallel-stranded G-quadruplex; thermodynamic stability; folding kinetics * To whom correspondence should be addressed Telephone: (520) 626-5969 Fax: (520) 626-6988 yang@pharmacy.arizona.edu.. Supporting Information Available.ΔG 25 values for the c-Myc G-quadruplex loop-isomers, hysteresis between CD melting and annealing curves of 11/20 with a temperature gradient of 0.5 °C/min, the imino regions of 1D 1 H NMR spectra of the completely truncated sequences for the four loop-isomers, hysteresis between CD melting and annealing curves of 11/20 and 11/23 loop-isomers with temperature gradients of 2 °C/min and 4 °C/min. This material is available free of charge via the Internet at http://pubs.acs.org. NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2011 November 2. NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptOverexpression of the c-Myc proto-oncogene is associated with a broad spectrum of human cancers, including colon, breast, prostate, cervical, and lung carcinomas, osteosarcomas, lymphomas, and leukemias (1-9). In addition, elevated levels of c-Myc expression are often associated with poor therapeutic prognosis. c-Myc overexpression can be caused by different mechanisms, including gene amplification (10,11), translocation (12-14), and simple upregulation of transcription (1,15). The transcriptional regulation of c-Myc expression is complex and involves multiple promoters...