DNA G-Quadruplex in Human Telomeres and Oncogene Promoters: Structures, Functions, and Small Molecule Targeting

Abstract

Metrics & MoreArticle RecommendationsCONSPECTUS: DNA G-quadruplex secondary structures formed in guanine-rich human telomeres and oncogene promoters are functionally important and have emerged as a promising new class of cancer-specific drug targets. These globular intramolecular structures are stabilized by K + or Na + and form readily under physiological solution conditions. Moreover, G-quadruplexes are epigenetic features and can alter chromatin structure and function together with interactive proteins. Here, we discuss our efforts over the last two decades to understand the structures and functions of DNA G-quadruplexes formed in key oncogene promoters and human telomeres and their interactions with small molecules. Using high-field NMR spectroscopy, we determined the high-resolution structures of physiologically relevant telomeric G-quadruplexes in K + solution with a major form (hybrid-2) and a minor form (hybrid-1), as well as a two-tetrad intermediate. The intrinsic structural polymorphism of telomeric DNA may be important for the biology of human telomeres, and we proposed a model for the interconversion. More recently, we have worked on G-quadruplexes of MYC, BCL2, PDGFR-β, VEGF, and k-RAS oncogene promoters. We determined the structure of the major G-quadruplex formed in the MYC promoter, a prototype for parallel G-quadruplexes. It is the first example of the parallel-stranded G 3 NG 3 structure motif with a 1-nt loop, which is prevalent in promoter sequences and likely evolutionarily selected to initiate folding. Remarkably, the parallel MYC promoter G-quadruplexes are highly stable. Additionally, we determined the molecular structures of G-quadruplexes formed in human BCL2, VEGF, and PDGFR-β promoters, each adopting a unique structure. For example, the BCL2 promoter contains distinct interchangeable G-quadruplexes in two adjacent regions, suggesting precise regulation by different proteins. The PDGFR-β promoter adopts unique "broken-strand" and vacancy G-quadruplexes, which can be recognized by cellular guanine metabolites for a potential regulatory role.Structural information on G-quadruplexes in complex with small-molecules is critical for understanding specific recognition and structure-based rational drug design. Our studies show that many G-quadruplexes contain unique structural features such as capping and loop structures, allowing specific recognition by drugs and protein. This represents a paradigm shift in understanding DNA as a drug target: Rather than a uniform, nonselective binding site in duplex DNA, the G-quadruplex is being pursued as a new class of selectively targetable drug receptors. We focus on targeting the biologically relevant MYC promoter G-quadruplex (MycG4) with small molecules and have determined its first and additional drug complex structures. Very recently, we have discovered clinically tested indenoisoquinolines as strong MycG4 binders and potent MYC inhibitors. We have also discovered drugs targeting the unique dGMP-bound-vG4 formed in the PDGFR-β promoter. Moreover, w...

Promoters vs. telomeres: AP-endonuclease 1 interactions with abasic sites in G-quadruplex folds depend on topology

“…The various G4 topologies differ in their grooves, exposure of the exterior G-tetrad faces for π stacking, capping base pairs, and steric effects associated with the loops that can cause the differences observed. 50 There exist many future opportunities that extend from these findings to understand the G4-topological aspects of APE1 recognition. This G4 topological feature may occur with other protein interactions, particularly those at the interface of DNA damage, DNA repair and gene regulation.…”

Template-Assembled Synthetic G-Quartets (TASQs): multiTASQing Molecular Tools for Investigating DNA and RNA G-Quadruplex Biology

“…15 Massive chemical biology efforts were thus needed to demonstrate that nature also tamed the unique supramolecular property of Gs by providing G-containing nucleic acid sequences with the ability to fold into G4s. 16 To make this possible, G-rich DNA sequences (e.g., those found at the telomeres 17 and in gene promoter regions) 18 must be freed from their duplex constraint: this occurs when DNA is at work, i.e., when being replicated or transcribed (see the schematic representation of a G loop 19 formed during the transcription of a G-rich region in Figure 2) or being repaired. This makes G4 formation not only tightly patrolled by the protein machinery in charge of DNA transactions but also transient in nature, explaining why their detection in fixed 20 then in living cells was challenging.…”

Development and Characterization of Benzoselenazole Derivatives as Potent and Selective c-MYC Transcription Inhibitors

“…With the release of single-stranded DNA, the c-MYC G-quadruplex formation will prevent RNA polymerase from binding to this region and thus lead to the transcriptional arrest. To ensure the uninterrupted transcription of c-MYC , several transcription factors and helicases may bind with the released guanine-rich region and resolve the c-MYC G-quadruplex to initiate transcription. , Stabilization of the c-MYC G-quadruplex structure is thus an effective strategy to inhibit c-MYC transcription. , Based on this, a large number of G-quadruplex-stabilizing compounds have been developed as c-MYC transcription inhibitors . However, few of these compounds have been shown to exhibit specificity for the c-MYC G-quadruplex.…”

“…22,23 Stabilization of the c-MYC G-quadruplex structure is thus an effective strategy to inhibit c-MYC transcription. 24,25 Based on this, a large number of G-quadruplex-stabilizing compounds have been developed as c-MYC transcription inhibitors. 26 However, few of these compounds have been shown to exhibit specificity for the c-MYC G-quadruplex.…”