1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Molecular docking study of the quenching mechanisms of luminol through interaction with ssDNA aptamer
Paper ID : 1351-ICB10
Authors:
Raheleh Torabi *, هدایت الله قورچیان
آزمایشگاه بیوآنالیز-مرکز تحقیقات بیوشیمی و بیوفیزیک- دانشگاه تهران- تهران- ایران
Abstract:
Generally, luminol as a signal producing element in chemiluminescent aptasensor is used for recognition of biomarkers [1]. However, in some cases it was observed that luminol emission intensity is quenched when it came close to single stranded DNA (ssDNA) aptamer. It was hypothesized that this phenomenon could be happened due to the interaction between luminol and nucleobases in ssDNA. To realize this idea, luminol was superimposed with nucleobases by LS-align [2] and then, luminol structure was docked with ssDNA structure by HADDOCK [3]. The obtained models were analyzed by Discovery Studio Visualizer and Ligplot for detection of intermolecular interactions. The results revealed that due to the high structural similarity between luminol and double-ring nucleobases, luminol tends to form hydrogen bonds with pyrimidines (cytosine and thymine) rather than purines (adenine and guanine). Formation of hydrogen bonding prevents the excitation of luminol by inhibiting the reversible generation of HOO• and O2•− radicals, and finally, less L•− were oxidized to 3-AP2−*, which led to the static quenching [4]. Moreover, docking results showed that at excited state π-π stacking are formed between π-orbitals of excited luminol and nucleotides. π-π stacking beside hydrogen-bonding could lead to Förster resonance energy transfer in which nucleotides as acceptor of energy absorb the emitted fluorescence of the excited luminol and consequently the fluorescence intensity of excited-state is quenched [5-7]. Therefore, it seems that ssDNA is able to quench the luminol emission via static and/or dynamic quenching mechanism.
Keywords:
Aptamer, Docking, Luminol, Quenching
Status : Paper Accepted (Poster Presentation)