A nuclease hypersensitive element in the human c-myc promoter adopts several distinct i-tetraplex structures

Nucleic acid structure-function correlations are pivotal to major biologica l events like transcription, replication, and recombination. Depending on i ntracellular conditions in vivo and buffer composition in vitro, DNA appear s capable of inexhaustible structure variation. At moderately acidic, or ev en neutral pH, DNA strands that are rich in cytosine bases can associate bo th inter- and intramolecularly to form i-tetraplexes. The hemiprotonated cy tosine(+)-cytosine base pair constitutes the building block for the formati on of i-tetraplexes, and motifs for their formation are frequent in vertebr ate genomes. A major control element upstream of the human c-myc gene, whic h has been shown to interact sequence specifically with several transcripti on factors, becomes hypersensitive to nucleases upon c-myc expression. The control element is asymmetric inasmuch as that one strand is uncommonly ric h in cytosines and exhibits multiple motifs for the formation of i-tetraple xes. To investigate the propensity for their formation we employ circular d ichroism (CD) in combination with ultra violet (UV) spectroscopy and native gel electrophoresis. Our results demonstrate the cooperative formation of well-defined i-tetraplex structures. We conclude that i-tetraplex formation occurs in the promoter region of the human c-myc gene in vitro, and discus s implications of possible biological roles for i-tetraplex structures in v ivo. Hypothetical formation of intramolecular fold-back i-tetraplexes is im portant to c-myc transcription, whereas chromosomal translocation events mi ght involve the formation of bimolecular i-tetraplex structures. (C) 2000 A cademic Press.