Design of a protein-targeted DNA aptamer using atomistic simulation

Area of Science:

• Biochemistry and Molecular Biology
• Analytical Chemistry
• Biotechnology

Background:

• Nucleic acid aptamers enable quantification of macromolecular species through molecular recognition.
• Electrochemical detection coupled with aptamers offers sensitive analyte quantification.
• Osmium tetroxide adducts with DNA aptamers are used for detecting analytes like human alpha thrombin.

Purpose of the Study:

• To rationally modify a DNA aptamer to enhance its binding affinity for human alpha thrombin in the presence of conjugated osmium.
• To improve the sensitivity of electrochemical sensors for quantifying low concentrations of thrombin.
• To explore the general applicability of molecular simulation in re-engineering aptamers for macromolecular binding.

Main Methods:

• Utilized a 27-mer DNA aptamer specific for exosite II of human alpha thrombin.
• Introduced long hydrophobic thymine derivatives in place of guanine 21 in the aptamer sequence.
• Employed molecular simulation to guide aptamer redesign and predict binding affinity changes.

Main Results:

• Modified aptamers exhibited enhanced binding affinities for osmium-conjugated thrombin by 10 to 15 kcal/mol.
• This enhancement overcomes the binding weakening caused by osmium conjugation (4 to 12 kcal/mol).
• The modified aptamers show potential for highly sensitive electrochemical detection of thrombin.

Conclusions:

• Rational modification of DNA aptamers can significantly improve binding affinity for target analytes in electrochemical sensors.
• The developed aptamers are promising for sensitive quantification of low thrombin concentrations.
• The strategy of using molecular simulation for aptamer re-engineering is broadly applicable to optimize other binding interfaces.