Aptamer Selection, Characterization, 3D Structure Simulation And Target Identification
We combine methods of computer simulation such as molecular dynamics (MD) simulations and quantum chemical calculations with the small-angle X-ray scattering (SAXS) experiment to reveal the structure of the aptamer in the solution. The developed approach allows us to choose the most probable secondary structure of the aptamer from the variety of options offered by the folding servers and obtain the aptamer conformation taking into account solution temperature, ions presence and other conditions. We use computer simulations to determine which nucleotides are responsible for the stability of the aptamer conformation.
Computer molecular design is widely used to visualize the complex spatial structure by three-dimensional (3D) molecular models. Aptamer 3D models are applied for directed design of aptamers in order to enhance their specificity and affinity, prediction of the binding sites and explaining the mechanisms of interaction with a target.
We determine the most probable spatial structure of the aptamer in a buffer solution using the small-angle X-ray scattering (SAXS) method.
We process the data of the SAXS experiment, calculate the structural parameters, estimate the molecular weight of the molecule in solution, and construct a three-dimensional electron density of the molecule from pseudoatoms.
Based on the aptamer sequence we perform computer molecular design aimed at obtaining the secondary structure options and respective three-dimensional models.
We carry out molecular dynamics (MD) simulation of the spatial structures to predict the native aptamer conformation in the solution. We compare the MD and SAXS data to find out which model fits the experimental results better.