2LBY

G-quadruplex structure formed at the 5'-end of NHEIII_1 element in human c-MYC promoter

Summary for 2LBY

• Entry DOI: 10.2210/pdb2lby/pdb
• Related: 1XAV 2F8U 2L7V 2M27
• NMR Information: BMRB: 17580
• Descriptor: DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3') (1 entity in total)
• Functional Keywords: dna, g-quadruplex, c-myc
• Total number of polymer chains: 1
• Total formula weight: 6070.92

Authors

Mathad, R.,Hatzakis, E.,Yang, D. (deposition date: 2011-04-07, release date: 2012-02-22, Last modification date: 2024-05-15)

Primary citation

Mathad, R.I.,Hatzakis, E.,Dai, J.,Yang, D.
c-MYC promoter G-quadruplex formed at the 5'-end of NHE III1 element: insights into biological relevance and parallel-stranded G-quadruplex stability.
Nucleic Acids Res., 39:9023-9033, 2011

PubMed 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 III(1,) 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 III(1) 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 III(1) 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.

PubMed: 21795379
DOI: 10.1093/nar/gkr612

Experimental method

SOLUTION NMR