G‐Triplex DNA Formation Determined by SPR and Native Agarose Gel Electrophoresis

G‐quadruplex DNA structures (G4 DNA), such as those found in human telomeres, may play important roles in cellular replication and gene regulation. Dysregulation of processes involving G4 DNA is associated with cancer and some neurodegenerative diseases. G4 DNA, composed of stacked G‐tetrads based on hydrogen bonding between guanine nucleotides, has been characterized by a number of techniques, including the gel electrophoresis and surface plasmon resonance (SPR) methods used in the current study. G‐triplex DNA structures (G3 DNA) are folding intermediates of some quadruplexes, but their role in vivo is less clear. To further characterize G3 DNA we adapted a native agarose gel electrophoresis method for separating small oligonucleotides and also used SPR to probe the extent of folded and unfolded structures. We have previously used SPR to calculate the extent of intramolecular folding in the human telomeric G4 sequence under varying buffer conditions. G3‐forming oligonucleotides from a truncated human telomeric sequence, truncated thrombin binding aptamer sequence, and other similar G‐rich sequences were subjected to the same SPR method. The extent of folding was determined by calculating % hybridization values for a C‐rich complementary duplex binding probe to the immobilized G3‐forming sequence. Under most buffer conditions, hybridization to the truncated thrombin binding aptamer was >50%, in agreement with the lower thermal stability of this G3‐folded structure. Differences in kinetic profiles for the hybridization of the probe in the presence of different cations (Li + , Na + , K + , Ca 2+ ) were apparent. In contrast, almost no hybridization was observed for a G 3 TG 3 TG 3 sequence under similar buffer conditions. Analysis by native agarose gel electrophoresis indicates the persistence of folded structures for the truncated human telomeric sequence (G3), similar truncated telomeric G‐rich (G3) sequences, and a G4‐forming sequence from c‐MYC , but not for the truncated thrombin binding aptamer sequence. Support or Funding Information Cancer Prevention and Research Institute of Texas This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .