Molecular docking study of the quenching mechanisms of luminol through interaction with ssDNA aptamer

Generally, luminol as a signal producing element in chemiluminescent aptasensor is used for recognition ofbiomarkers. However, in some cases it was observed that luminol emission intensity is quenched when itcame close to single stranded DNA (ssDNA) aptamer. It was hypothesized that this phenomenon could behappened due to the interaction between luminol and nucleobases in ssDNA. To realize this idea, luminolwas superimposed with nucleobases by LS-align and then, luminol structure was docked with ssDNAstructure by HADDOCK. The obtained models were analyzed by Discovery Studio Visualizer and Ligplotfor detection of intermolecular interactions. The results revealed that due to the high structural similaritybetween 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 preventsthe excitation of luminol by inhibiting the reversible generation of HOO• and O۲•− radicals, and finally, lessL•− were oxidized to ۳-AP۲−*, which led to the static quenching. Moreover, docking results showed that atexcited state π-π stacking are formed between π-orbitals of excited luminol and nucleotides. π-π stackingbeside hydrogen-bonding could lead to Förster resonance energy transfer in which nucleotides as acceptor ofenergy absorb the emitted fluorescence of the excited luminol and consequently the fluorescence intensity ofexcited-state is quenched. Therefore, it seems that ssDNA is able to quench the luminol emission via staticand/or dynamic quenching mechanism.

کلیدواژه ها:

Aptamer ، Docking ، Luminol ، Quenching