Binding studies on peptide–oligonucleotide complex: intercalation of tryptophan in GC-rich region of c- myc gene

• Published in: Biochimica et biophysica acta Vol. 1622; no. 2; pp. 73 - 81
• Main Authors: Aklank Jain, Akanchha, Rajeswari, Moganty R.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 23.07.2003
• Subjects: Binding studies; c- myc; Circular Dichroism; GC Rich Sequence; Genes, myc; Hot Temperature; Oligonucleotide; Oligonucleotides - chemistry; Oligopeptides - chemistry; Peptide; Spectrophotometry, Ultraviolet; Thermodynamics; Tryptophan - chemistry; Tryptophan intercalation; Tryptophan intercalation; Oligonucleotide; c- myc; Peptide; Binding studies
• ISSN: 0304-4165; 0006-3002; 1872-8006
• DOI: 10.1016/S0304-4165(03)00119-3

Transcriptional regulation of the c- myc gene is essential for normal cellular proliferation; differentiation and overexpression of c- myc is associated with several human cancers. C- myc gene, particularly exon 1, which contains the conserved P1 and P2 promoter regions, has been a potential target for the intercalating drugs in chemotherapy. We have chosen a 21-mer GC-rich oligonucleotide sequence starting from 2281 to 2302 of human c- myc gene located 26 base pair upstream of P1 promoter and partially overlapping with the TATA box of P1. In this paper, we have studied the interaction of a tetrapeptide, KWGK-otBut, with duplex of the above 21-mer sequence under low-salt conditions using UV–Vis absorption, UV melting, fluorescence and circular dichroic (CD) spectroscopy. From the fluorescence quenching data, we determined the two binding constants, K 1 (involving only electrostatic interactions) and K 2 (involving intercalation), for the formation of (PN) 1 and (PN) 2 of the two-step mechanism previously established by us. Significant changes were observed in the UV difference absorption spectra and CD spectra of both KWGK and 21-mer duplex upon complex formation even at a very low peptide to nucleotide (P/N) ratios. These spectral changes accompanied by a high value of K 2 (=5.13) suggest a strong binding of KWGK involving intercalation of the tryptophan in 21-mer duplex. Based on the above data along with changes observed in Δ H, Δ S and Δ G and increase in melting temperature (by about 8 °C) of the 21-mer duplex in presence of KWGK, we propose a model for intercalation of tryptophan of in GC-rich region of c- myc gene. Present observations may be explored in understanding the role of intercalation in protein–nucleic acid interactions in c- myc expression and these results could also help in designing oligopeptides or other low molecular weight ligands to modulate gene expression.