Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations.
Nathalie Casanova-MoralesNataniel L FigueroaKarol AlfaroFelipe MontenegroNelson P BarreraJ R MazeChristian A M WilsonPablo ConejerosPublished in: PloS one (2019)
Optical tweezers have enabled the exploration of picoNewton forces and dynamics in single-molecule systems such as DNA and molecular motors. In this work, we used optical tweezers to study the folding/unfolding dynamics of the APTSTX1-aptamer, a single-stranded DNA molecule with high affinity for saxitoxin (STX), a lethal neurotoxin. By measuring the transition force during (un)folding processes, we were able to characterize and distinguish the conformational changes of this aptamer in the presence of magnesium ions and toxin. This work was supported by molecular dynamics (MD) simulations to propose an unfolding mechanism of the aptamer-Mg+2 complex. Our results are a step towards the development of new aptamer-based STX sensors that are potentially cheaper and more sensitive than current alternatives.
Keyphrases
- single molecule
- molecular dynamics
- gold nanoparticles
- molecular dynamics simulations
- sensitive detection
- magnetic nanoparticles
- living cells
- atomic force microscopy
- high resolution
- label free
- density functional theory
- high speed
- escherichia coli
- quantum dots
- molecular docking
- cancer therapy
- circulating tumor
- binding protein
- drug delivery
- nucleic acid
- monte carlo