The scientific team at Base Pair brings more than 50 years of aptamer discovery and development experience to every project. We’ve developed proprietary techniques and technologies at every stage of the aptamer discovery and development process to improve aptamer performance in your specific application.


Proprietary Aptamer Libraries

Base Pair Bio selects from a menu of standard libraries and specialized libraries designed to increase hydrophobicity or optimize secondary and tertiary structural combinations to enhance aptamer binding. Highly-customized libraries for sensor-specific sequences and specific conformational structures are often designed for individual projects.

Multiplex Aptamer Selection

Through a patented application of nucleic acid barcoding, Base Pair aptamer scientists can simultaneously screen for up to 30 targets. Select aptamers to two potential drug targets or a whole family of related proteins within a single selection process. Simultaneous selection significantly reduces development time and reduces development cost.

VENNmultiplex Selex

Through patented multiplex aptamer selection and proprietary algorithms, Base Pair is able to select optimal aptamers to a family of targets and evaluate aptamer specificity in relation to a matrix control. A complex Venn diagram analysis identifies aptamers that are specific for individual targets, pan-binders to all members of a related family, and aptamers with binding to specific subsets of targets.

Small Molecule Expertise

Because of their small size, small molecules tend to be non-immunogenic and difficult to immobilize. Base Pair has a number of proprietary techniques for developing aptamers to small molecules and actively applies two novel methods for determining solution phase affinity of small molecule aptamers.

Advanced Aptamer Modification

Following initial selection, aptamers can be modified to further enhance affinity, stability, solubility, or detection. Aptamers can be “matured” by generating highly-focused, aptamer-specific libraries containing smaller randomized regions, truncations, nuclease-blocking technology, or conformational locking. Sequence modifications can be applied to specific aptamers to further improve performance.

Functional Aptamer Testing

Developing aptamers with high affinity for specific targets is a key aspect of aptamer development. Developing aptamers that perform in the desired detection method and the expected matrix is just as important. Base Pair scientists take method and matrix into account when designing aptamers. Assistance with functional assay testing and assay development is available.

Aptamer Pair Testing

Many applications require two aptamers with complementary binding sites. Base Pair utilizes proprietary methods for identifying matched aptamer pairs for use in ELASA (ELISA-like assays), lateral flow assays, and other applications. Where possible, aptamer pairs are made available as catalog products.