A sensor is a molecule or device that exhibits a change in a detectable signal upon interaction with a specific analyte. Aptamers can be used to create many novel types of in vivo and in vitro sensors. Base Pair can design an aptamer sensor that is customized for use with any sensor platform. Some of the most common sensor formats are described below.

Optical Sensors

Optical sensors can be fluorogenic, colorimetric, or use other modes for optical detection.  They generally fall into two major categories: Labeled Optical Sensors and Label-free Optical Sensors.

Labeled Optical Sensors.

Many aptamers undergo a large conformational change upon binding their targets.  This property can be used to create optical sensors.  Quencher/fluorophore pairs can be used as dual aptamer labels to generate fluorogenic aptamers – aptamers that exhibit a large increase in fluorescence upon binding.  A quencher at one terminus of the molecule or at the base of a stem-loop structure can absorb energy from a fluorophore that is directly adjacent only when the original stem loop structure is present, preventing fluorescence.  When binding occurs in the loop region, for example, the fluorophore and quencher are separated from one another physically, generating fluorescent signal. Fluorophores can be organic dye molecules, quantum dot nanocrystals, or any light-emitting moiety.  Quenchers can be any type of molecule, particle or moiety that can absorb that light or associated energy, whether through true fluorescence resonance energy transfer (FRET), plasmonic interactions (e.g. with gold particle-gold particle interactions), bioluminescence resonance energy transfer (BRET), time-resolved fluorescence resonance energy transfer (TR-FRET) or other interactions.  The fluorophore or other light-emitting entity becomes unquenched, giving rise to a fluorescent or similar signal. These types of aptamers can be used to develop easy-to-use, add-and-read, homogenous solution-based assays for use with fluorescence microplate readers, fluorometers, minifluorometers, luminometers and other fluorescence or light detection instruments.  Base Pair can screen or select for aptamers that have fluorogenic properties, and which bind your analyte of choice.  Another type of plasmonic interaction between nanogold particles can give rise to colorimetric signal changes in which the visible color of the solution changes when two particles are brought into close proximity.

Label-free Optical Sensors.

Yet another type of optical sensor utilizes an aptamer that contains an analyte binding site as well as a second site for binding to a chromophore.  When chromophore binding takes place, the aptamer complex becomes fluorescent.  If designed correctly, the chromophore binding site is generated only when the target analyte is also bound.  This type of sensor can be expressed and used in vivo to choose the best cell lines for expressing particular analytes, to monitor expression during bioproduction or to study gene expression or stability in vivo.  Base Pair has a new technology that can be used to create in vivo sensors and would be glad to design such sensors for you.

  1. Song, S. et al. Aptamer-based biosensors. Trends in Analytical Chemistry. 2008. 27(2):108-117. doi:10.1016/j.trac.2007.12.004.
  2. Wang, R. E, et al. Aptamer-based fluorescent biosensors. Curr. Med. Chem. 2011. Sep 1; 18(27): 4175–4184.


Plasmon Resonance Sensors

Surface-Enhanced Ramen Scattering (SERS) is frequently used with aptamers to detect analyte binding, particularly for small molecule analytes. Raman signal stems from photon scattering caused by a molecule’s electric cloud. The signal is unique for each analyte. While Raman scattering signal was originally too low for sensitive detection, the addition of colloidal nanoparticles offers enhanced signal generation and improved sensitivity. Raman scattering involving nanoparticles, though more sensitive, originally lacked specificity and reproducibility. This has been overcome with the addition of highly-selective aptamers. In a recent study, apatamer conjugated to nanoparticles showed target affinity that was comparable to free aptamer. SERS and BPA-specific aptamer were used to detect BPA (bisphenol A released from plastics) in human blood at levels as low as 600fM. This technique can be used to detect a wide range of targets in complex samples.

  1. Fu, C., et al. Aptamer-based surface-enhanced Raman scattering-microfluidic sensor for sensitive and selective polychlorinated biphenyls detection. Anal. Chem. 2015. 87 (19):9555-9558. doi: 10.1021/acs.analchem.5b02508.
  2. Marks, H.L., et. al. Rational design of a bisphenol A aptamer-selective surface-enhanced Raman scattering nanoprobe. Anal. Chem. 2014. 86:11614-11619. dx.doi.org/10.1021/ac502541v.


Electrochemical Sensors

The same conformational change that is used to create fluorogenic sensors can also be used to create electrochemical sensors.  In most cases, one end of the aptamer is covalently attached to an electrically conductive surface, such as a gold-coated electrode.  The other end is attached to a moiety that can contribute free electrons, such as ferrocene or methylene blue.  When the aptamer binds to the target analyte, the free electron donor comes into close proximity with the surface or can be pushed further away from the surface, giving rise to a change in current.  Surfaces can be nanowires, nanotubes, graphene constructs, and many other types of materials.  Giant magnetoresistance sensors (GMR sensors) provide a unique method for detecting binding by detecting a change in electrical resistance as a result of binding.  Many Base Pair aptamers have been used in combination with electrochemical sensors.  Please contact us if you would like Base Pair to design such aptamers for you.

  1. Akhtar Hayat and Jean L. Marty, Aptamer based electrochemical sensors for emerging environmental pollutants. Front. Chem. 2014. 2:41. doi:  10.3389/fchem.2014.00041.
  2. Cheng, A.K., et al. Design and testing of aptamer-based electrochemical biosensors for proteins and small molecules. Bioelectrochemistry. 2009 Nov. 77(1):1-12. doi: 10.1016/j.bioelechem.2009.04.007.
  3. Schoukroun-Barnes L.R., et al. Reagentless, structure-switching, electrochemical aptamer-based sensors. Annu. Rev. Anal. Chem. (Palo Alto Calif). 2016 Jun 12;9(1):163-81. doi: 10.1146/annurev-anchem-071015-041446.
  4. Schoukroun-Barnes L.R., et al. Heterogeneous electrochemical aptamer-based sensor surfaces for controlled sensor response. Langmuir. 2015 Jun 16;31(23):6563-9. doi: 10.1021/acs.langmuir.5b01418.

Ongoing Aptamer-Based Biosensor Development

Courtesy of Nanomedical Diagnostics, Inc.

Base Pair Biotechnologies is currently developing several aptamer-based biosensors using the Nanomedical Diagnostics Agile R100 assay system.  The biosensor chip is built with proprietary Field Effect Biosensing (FEB) technology. FEB, an electrical technique, measures the current across a field effect graphene biosensor to which targets are immobilized. Any interaction or binding that occurs on the surface causes a change in conductance that is monitored in real-time, enabling accurate kinetic, affinity, and concentration measurements. For more information on the Agile R100 biosensing technology, visit Nanomedical Diagnostics, Inc.

Contact us today to learn more about developing aptamer-based sensors with Base Pair.