Targeting genomic DNAs and oligonucleotide on base specificity: A comparative spectroscopic, computational and in vitro study

Drug discovery in targeted nucleic acid therapeutics encompass several stages and rigorous challenges owing to less specificity of the DNA binders and high failure rate in different stages of clinical trials. In this perspective, we report newly synthesized ethyl 4-(pyrrolo[1,2-a]quinolin-4-yl)benzoate (PQN) with minor groove A-T base pair binding selectivity and encouraging in cell results. This pyrrolo quinolin derivative has shown excellent groove binding ability with three of our inspected genomic DNAs (cpDNA 73 % AT, ctDNA58% AT and mlDNA 28 % AT) with varying A-T and G-C content. Notably in spite of similar binding patterns PQN have strong binding pref-erence with A-T rich groove of genomic cpDNA over the ctDNA and mlDNA. Spectroscopic experiments like steady state absorption and emission results have established the relative binding strengths (Kabs = 6.3 x 105 M-1, 5.6 x 104 M-1, 4.3 x 104 M-1 and Kemiss = 6.1 x 105 M-1, 5.7 x 104 M-1 and 3.5 x 104 M-1 for PQN-cpDNA, PQN-ctDNA and PQN-mlDNA respectively) whereas circular dichroism and thermal melting studies have unveiled the groove binding mechanism. Specific A-T base pair attachment with van der Waals interaction and quantitative hydrogen bonding assessment were characterized by computational modeling. In addition to genomic DNAs, preferential A-T base pair binding in minor groove was also observed with our designed and synthesized deca-nucleotide (primer sequences 5/-GCGAATTCGC-3/ and 3/-CGCTTAAGCG-5/). Cell viability assays (86.13 % in 6.58 & mu;M and 84.01 % in 9.88 & mu;M concentrations) and confocal microscopy revealed low cytotoxicity (IC50 25.86 & mu;M) and efficient perinuclear localization of PQN. We propose PQN with excellent DNA-minor groove binding capacity and intracellular permeation properties, as a lead for further studies encom-passing nucleic acid therapeutics.

Automated summary

In this study, a newly synthesized compound called ethyl 4-(pyrrolo[1,2-a]quinolin-4-yl)benzoate (PQN) showed selectivity in binding to the minor groove A-T base pair of genomic DNAs. The compound demonstrated strong binding preference for A-T rich groove over other sequences. Spectroscopic experiments confirmed the binding strength, while computational modeling revealed the binding mechanism. PQN also exhibited low cytotoxicity and efficient intracellular localization, suggesting its potential as a lead compound for nucleic acid therapeutics.