Non‐Canonical DNA in the c‐Myc Hotspot Region

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G‐quadruplexes and H‐DNA are non‐canonical or non‐B form DNA structures. G‐quadruplexes are three dimensional structures formed by planar stacking of guanine quartets in the DNA. H‐DNA structures form at inverted repeats consisting of poly(purine)•poly(pyrimidine) sequences, in which the poly(purine) portion of one half of the repeat forms a Pu•Py‐Pu triplex by binding to the duplex form of the other half. Genetic “hotspots” are regions of DNA that are especially susceptible to double strand breaks. It has been shown that the structural conformation of DNA could be the cause for some of these breaks in “hotspot” regions. In particular, the well‐known transpositions involving the c‐Myc oncogene in Burkitt Lymphoma involves a “hotspot” region of the gene that is proposed to form two non‐canonical structures, a G‐quadruplex and H‐DNA structure, which are in competition which each other.Surface plasmon resonance (SPR) was used to detect H‐DNA or G‐quadruplex DNA formation in c‐MYC. An immobilized single‐stranded DNA construct encompassing the c‐MYC hotspot region was probed with short oligonucleotides complementary to different regions of the putative H‐DNA and G‐quadruplex DNA structures. These studies demonstrated that both the duplex portion of the putative H‐DNA as well as the poly(purine) track displayed limited hydridization to complement probes, commensurate with formation of an H‐DNA structure.Spectroscopic methods such as UV/vis melting, Förster resonance energy transfer (FRET), and circular dichroism (CD) have been used in previous studies to detect and characterize G‐quaduplexes. Using these spectroscopic methods, we were able to characterize the formation of non‐canonical DNA structure from an oligonucleotide comprised of the entire poly(purine) tract from the c‐MYC hotspot. These studies demonstrate that this poly(purine) sequence adopts a stable intermolecular G‐quadruplex in preference to the intramolecular G‐qaudruplex predicted earlier. This means that the H‐DNA in c‐MYC is likely not in competition for formation with the intramolecular G‐quadruplex suspected to form from this same region.Support or Funding InformationCancer Prevention and Research Institute of TexasThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.