DNA aptamers are functional molecular recognition sensors in protic ionic liquids

Area of Science:

• Biochemistry
• Molecular Biology
• Materials Science

Background:

• Aptamer beacons are crucial for molecular recognition.
• Ionic liquids offer unique solvent properties for biochemical applications.
• Understanding aptamer behavior in ionic liquids is key for novel biosensor development.

Purpose of the Study:

• To investigate the function and structural changes of an AMP aptamer beacon in ethylammonium nitrate (EAN).
• To assess the molecular recognition capacity and specificity of the aptamer for adenosine monophosphate (AMP) in EAN.
• To explore the impact of EAN on DNA hybridization kinetics and thermal stability.

Main Methods:

• Systematic exploration of aptamer beacon function in solution using protic ionic liquid (EAN).
• Assessment of molecular recognition capacity using adenosine monophosphate (AMP) as the target.
• Specificity testing using guanosine monophosphate (GMP) as a control target.
• Analysis of double-stranded DNA formation, thermal stability, and hybridization rates in varying EAN concentrations.

Main Results:

• The AMP aptamer beacon successfully recognized AMP with maintained specificity up to 2 M EAN in TBS buffer.
• Specificity was confirmed as guanosine monophosphate (GMP) was not recognized.
• While double-stranded DNA formation and thermal stability decreased with higher EAN concentrations, single-stranded DNA hybridization rate (kh) significantly accelerated.
• This acceleration of hybridization in EAN has potential implications for DNA technology.

Conclusions:

• AMP aptamer beacons retain their recognition capabilities and specificity in protic ionic liquids like EAN.
• Ethylammonium nitrate (EAN) significantly accelerates DNA hybridization rates, despite reducing DNA duplex stability.
• These findings are important for designing DNA-based biosensing and nanodevices in nonconventional solvents like ionic liquids.