Crystal structure of the major quadruplex formed in the promoter region of the human c-MYC oncogene

Stump, Sascha; Mou, Tung-Chung; Sprang, Stephen R.; Natale, Nicholas R.; Beall, Howard D.

doi:10.1371/journal.pone.0205584

Title: Crystal structure of the major quadruplex formed in the promoter region of the human c-MYC oncogene

Journal Article · 11 October 2018 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0205584 · OSTI ID:1627869

Stump, Sascha ^[1]; Mou, Tung-Chung ^[2]; Sprang, Stephen R. ^[2];

^[2];

^[2]

Univ. of Montana, Missoula, MT (United States); DOE/OSTI
Univ. of Montana, Missoula, MT (United States)

The c-MYC oncogene mediates multiple tumor cell survival pathways and is dysregulated or overexpressed in the majority of human cancers. The NHE III₁ region of the c-MYC promoter forms a DNA quadruplex. Stabilization of this structure with small molecules has been shown to reduce expression of c-MYC, and targeting the c-MYC quadruplex has become an emerging strategy for development of antitumor compounds. Previous solution NMR studies of the c-MYC quadruplex have assigned the major conformer and topology of this important target, however, regions outside the G-quartet core were not as well-defined. Here, we report a high-resolution crystal structure (2.35 Å) of the major quadruplex formed in the NHE III₁ region of the c-MYC promoter. The crystal structure is in general agreement with the solution NMR structure, however, key differences are observed in the position of nucleotides outside the G-quartet core. The crystal structure provides an alternative model that, along with comparisons to other reported quadruplex crystal structures, will be important to the rational design of selective compounds. This work will aid in development of ligands to target the c-MYC promoter quadruplex with the goal of creating novel anticancer therapies.

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Research Organization:: SLAC National Accelerator Lab., Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC02-76SF00515

OSTI ID:: 1627869

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 10 Vol. 13; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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MYC on the Path to Cancer Dang, Chi V. Cell, Vol. 149, Issue 1 https://doi.org/10.1016/j.cell.2012.03.003	journal	March 2012
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Solution Structure of the Biologically Relevant G-Quadruplex Element in the Human c-MYC Promoter. Implications for G-Quadruplex Stabilization ^† Ambrus, Attila; Chen, Ding; Dai, Jixun Biochemistry, Vol. 44, Issue 6 https://doi.org/10.1021/bi048242p	journal	February 2005
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A Conserved Quadruplex Motif Located in a Transcription Activation Site of the Human c-kit Oncogene Fernando, Himesh; Reszka, Anthony P.; Huppert, Julian Biochemistry, Vol. 45, Issue 25 https://doi.org/10.1021/bi0601510	journal	June 2006
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Structure of an Unprecedented G-Quadruplex Scaffold in the Human c-kit Promoter Phan, Anh Tuân; Kuryavyi, Vitaly; Burge, Sarah Journal of the American Chemical Society, Vol. 129, Issue 14 https://doi.org/10.1021/ja068739h	journal	April 2007
Human Telomeric DNA Forms Parallel-Stranded Intramolecular G-Quadruplex in K ⁺ Solution under Molecular Crowding Condition Xue, Yong; Kan, Zhong-yuan; Wang, Quan Journal of the American Chemical Society, Vol. 129, Issue 36 https://doi.org/10.1021/ja0730462	journal	September 2007
Structure of Human Telomeric DNA in Crowded Solution Heddi, Brahim; Phan, Anh Tuân Journal of the American Chemical Society, Vol. 133, Issue 25 https://doi.org/10.1021/ja200786q	journal	June 2011
Solution Structure of a 2:1 Quindoline–c-MYC G-Quadruplex: Insights into G-Quadruplex-Interactive Small Molecule Drug Design Dai, Jixun; Carver, Megan; Hurley, Laurence H. Journal of the American Chemical Society, Vol. 133, Issue 44 https://doi.org/10.1021/ja205646q	journal	November 2011
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The Importance of Negative Superhelicity in Inducing the Formation of G-Quadruplex and i-Motif Structures in the c-Myc Promoter: Implications for Drug Targeting and Control of Gene Expression Sun, Daekyu; Hurley, Laurence H. Journal of Medicinal Chemistry, Vol. 52, Issue 9 https://doi.org/10.1021/jm900055s	journal	May 2009
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
Crystal structure
Crystallization
Guanine
Nucleotides
Oligonucleotides
Oncogenes
Potassium
Small molecules

Title: Crystal structure of the major quadruplex formed in the promoter region of the human c-MYC oncogene

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