c-MYC promoter G-quadruplex formed at the 5′-end of NHE III 1 element: insights into biological relevance and parallel-stranded G-quadruplex stability

Abstract

We studied the structures and stabilities of G-quadruplexes formed in Myc1234, the region containing the four consecutive 5′ runs of guanines of c-MYC promoter NHE III1, which have recently been shown to form in a supercoiled plasmid system in aqueous solution. We determined the NMR solution structure of the 1:2:1 parallel-stranded loop isomer, one of the two major loop isomers formed in Myc1234 in K+ solution. This major loop isomer, although sharing the same folding structure, appears to be markedly less stable than the major loop isomer formed in the single-stranded c-MYC NHE III1 oligonucleotide, the Myc2345 G-quadruplex. Our NMR structures indicated that the different thermostabilities of the two 1:2:1 parallel c-MYC G-quadruplexes are likely caused by the different base conformations of the single nucleotide loops. The observation of the formation of the Myc1234 G-quadruplex in the supercoiled plasmid thus points to the potential role of supercoiling in the G-quadruplex formation in promoter sequences. We also performed a systematic thermodynamic analysis of modified c-MYC NHE III1 sequences, which provided quantitative measure of the contributions of various loop sequences to the thermostabilities of parallel-stranded G-quadruplexes. This information is important for understanding the equilibrium of promoter G-quadruplex loop isomers and for their drug targeting.

Therapeutic Strategies to Inhibit MYC

“…Another noteworthy approach to targeting MYC transcription derives from a unique and well-characterized feature of the MYC locus, namely, a predisposition for formation of Gquadruplex DNA (Siddiqui-Jain et al 2002;Mathad et al 2011). Small-molecule stabilizers of G-quadruplex DNA have been developed as tool compounds, which establish an impediment to RNA Pol II transcription of MYC.…”

DNA quadruplex folding formalism – A tutorial on quadruplex topologies

“…[23] 9. Prevalence of loop type combinations [24], (b) 1XAV [25], (c) 2LEE [26], (d) 2LBY [27], (e) 2KYP [28], (f) 2LPW [29], (g) 2KZE [30] and (h) 2LXQ [31] with examples determined in crowded conditions (2LD8, [32]) and in dimeric form stacked 5 0 -5 0 (2LE6, [33] and 2LXV, [31]). It is noteworthy that all these examples are three-stacked quadruplexes.…”

Quinazoline derivative QPB-15e stabilizes the c-myc promoter G-quadruplex and inhibits tumor growth in vivo

“…Some targeted G-quadruplex telomerase inhibitors stabilize the c-myc promoter region G-rich sequence to form a G-quadruplex. Properly regulated c-myc expression is important for tumor prevention and treatment [15–16]. In the present study, the interaction of QPB-15e with a G-rich sequence located upstream of the c-myc NHE III1 region was investigated, and the effects of this interaction on c-myc function in vitro and in vivo were determined.…”

“…This sequence is located upstream (−142 to −115 bp) of the P1 promoter in the human c-myc oncogene and controls 85–90% of c-myc transcription [14]. This tract can form specific G-quadruplex structures enhanced by G-quadruplex-interactive ligands, leading to c-myc downregulation in human tumor cells [15–16]. Small molecules that can selectively bind to and stabilize the c-myc G-quadruplex are likely to be effective therapeutics for cancer treatment.…”