PDGFR-β Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs

Abstract

Aberrant expression of PDGFR-β is associated with a number of diseases. The G-quadruplexes (G4s) formed in PDGFR-β gene promoter are transcriptional modulators and amenable to small molecule targeting. The major G4 formed in the PDGFR-β gene promoter was previously shown to have a broken G-strand. Herein, we report that the PDGFR-β gene promoter sequence forms a vacancy G-quadruplex (vG4) which can be filled in and stabilized by physiologically relevant guanine metabolites, such as dGMP, GMP, and cGMP, as well as guanine-derivative drugs. We determined the NMR structure of the dGMP-fill-in PDGFR-β vG4 in K+ solution. This is the first structure of a guanine-metabolite-fill-in vG4 based on a human gene promoter sequence. Our structure and systematic analysis elucidate the contributions of Hoogsten hydrogen bonds, sugar, and phosphate moieties to the specific G-vacancy fill-in. Intriguingly, an equilibrium of 3′- and 5′-end vG4s is present in the PDGFR-β promoter sequence, and dGMP favors the 5′-end fill-in. Guanine metabolites and drugs were tested and showed a conserved selectivity for the 5′-vacancy, except for cGMP. cGMP binds both the 3′- and 5′-end vG4s and forms two fill-in G4s with similar population. Significantly, guanine metabolites are involved in many physiological and pathological processes in human cells; thus, our results provide a structural basis to understand their potential regulatory functions by interaction with promoter vG4s. Moreover, the NMR structure can guide rational design of ligands that target the PDGFR-β vG4.

Highly Specific Recognition of Guanosine Using Engineered Base‐Excised Aptamers

“…To the best of our knowledge, SELEX‐derived guanosine DNA aptamers have not yet been reported. Recently, a few vacancy‐bearing G‐quadruplexes were found to bind guanosine and induce the formation of G‐quadruplexes [11c,d,f] . For example, a defect G‐quadruplex (named MYOG‐3332) was shown to have a parallel conformation by Tan and co‐workers (Figure 6 A), with the top layer bearing a guanosine binding pocket [11c] .…”

Quadruplex–Duplex Junction: A High‐Affinity Binding Site for Indoloquinoline Ligands

“…Intramolecular G‐quadruplexes with their four G‐columns connected by loops show highly diverse topologies. This polymorphism is reflected in different types of loops but may also include discontinuous G‐tracts [5–10] . In general, various G4 topologies in the genome may be specifically targeted by high‐affinity ligands for novel pharmaceutical approaches, but quadruplex topologies can also be rationally designed for use in an increasing number of technological applications, for example, as aptamers [11–14] …”

“…This polymorphism is reflected in different types of loops but may also include discontinuous G-tracts. [5][6][7][8][9][10] In general, various G4 topologies in the genome may be specificallyt argeted by high-affinity ligands for novel pharmaceutical approaches, but quadruplex topologies can also be rationally designedf or use in an increasingn umber of technological applications, for example, as aptamers. [11][12][13][14] DNA junctionsa re important elements in cellular maintenance processes.…”

Structural motifs and intramolecular interactions in non-canonical G-quadruplexes

“…67 Another example of a structurally characterized G-deficient quadruplex involves a modified human PDGFR-b gene promoter sequence d(AAG 3 AG 3 CG 2 CG 3 ACA) termed Pu19m2. 71 It was shown to adopt two stable G4 structures formed by the G 2 -tract shifted toward the 5 0 -or 3 0 -terminal quadruplex face with a corresponding vacancy in an outer plane adjacent to either the 3 0 -or 5 0 -terminus. The triad layer of the vG4 can again be complemented by the selective and strong external binding of physiologically relevant guanine metabolites such as dGMP, GMP,…”