title: KRAS promoter oligonucleotide with decoy activity dimerizes into a unique topology consisting of two G-quadruplex units.
abstract: Mutations of the KRAS proto-oncogene are associated with several tumor types, which is why it is being considered as a target for anti-cancer drug development. The human KRAS promoter contains a nuclease hypersensitive element (NHE), which can bind to nuclear proteins and is believed to form G-quadruplex structures. Previous studies showed that a 32-nt oligonucleotide (32R-3n) mimicking the KRAS NHE can reduce gene transcription by sequestering MAZ, a crucial transcription factor. Here we show that 32R-3n has to dimerize in order to fold into a G-quadruplex structure. Individual 5'- and 3'-end G-quadruplex units are formed and both feature a symmetric head-to-head topology with edge-type loops. The MAZ binding sequence is located within the 3'-end unit. Nuclear magnetic resonance data complemented by CD and UV spectra show that nucleotides of the MAZ binding G-rich motif are dynamic and could be available for sequence or structure based recognition. Both stable G-quadruplex structures could protect 5'- and 3'-ends of 32R-3n and enhance its anti-cancer activity. Single stranded genomic KRAS NHE including nucleotides flanking the 32R-3n sequence could favor a different monomeric fold, which remains unknown.
authors.affiliation: Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia.
authors.forename: Peter
authors.initials: P
authors.lastname: Podbevšek
authors.affiliation: Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia janez.plavec@ki.si.
authors.forename: Janez
authors.initials: J
authors.lastname: Plavec
mesh_terms: D020029:Base Pairing; D001665:Binding Sites; D002942:Circular Dichroism; D004268:DNA-Binding Proteins / Q000378:metabolism; D019281:Dimerization; D054856:G-Quadruplexes; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D000090063:Proto-Oncogene Mas; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics*; D013056:Spectrophotometry, Ultraviolet; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; C117307:KRAS protein, human; C000715470:MAS1 protein, human; D000090063:Proto-Oncogene Mas; D014157:Transcription Factors; C076035:c-MYC-associated zinc finger protein; D016283:Proto-Oncogene Proteins p21(ras)