The Next Generation in Molecular Recognition Technology: High Performance Aptamers (HPAs)
Find out how HPAs may help you in diagnostics, research, or therapeutics
Velocity scientists have invented an expanded set of RNA nucleotides, which are modified with side chains possessing hydrophobic, aromatic, H-bond donor/acceptor, and other chemical properties. 1,2
Modified nucleotides imbue RNA with increased shape diversity and a broader spectrum of intermolecular interactions compared to native RNA and DNA.
Proprietary in vitro selection schemes isolate modified RNA aptamers for target molecules with higher affinities and specificities than any other molecular recognition technology.
Expanding the Genetic Code: Velocity's RNA Aptamers Incorporate Function-Enhancing Uridine Modifications
Native RNA Nucleotides (AGCU)
An Expanded Set of RNA Nucleotides (AGC + N, I, B...)
• RNA with protein-like side chains
• Provide increased RNA structural and chemical diversity
• Results in a higher target hit rate, affinity, and specificity vs. native RNA
Comparison of antibodies and Velocity’s high-performance aptamer affinity reagents.
|Antibodies||Velocity High-Performance Aptamers with Modified Nucleotides|
|Target Hit Rate (%)||51%3||80%4|
|Production||Cellular production||Solid-phase synthesis or enzymatic|
|Advantages in Therapeutics|
|Tissue Penetration||Larger size slows tissue penetration||Diameters <10-fold smaller than antibodies yield faster tissue penetration and longer retention5|
|Cell Targeting||Low efficiency of endosomal escape limits targets to outer cell membrane||Able to address targets in the cytosol and nucleus 6|
|Ease of Functionalization||Difficult to modify||HPA-drug conjugates with RNA and small-molecule drugs are prepared reproducibly using automated chemical synthesis|
|Advantages in Diagnostics|
|Assay Multiplex Capacity||Low plex only due to crosstalk||Assays from low to high plex (1,000s)|
|Ease of Functionalization||Difficult to modify||Easily modified with oligonucleotide bar codes, amplification primers, fluors, etc.|
|Stability||Sensitive to elevated temperature and undergo irreversible denaturation||Can be transported at ambient temperature and refolded if denatured|
Antibodies evolved to fight pathogens; HPAs are designed as diverse tools for many applications
Comparison of native oligo aptamers and Velocity HPAs
|Traditional Aptamers with Native Nucleotides||Velocity HPAs with Modified Nucleotides|
|Discovery Method||In vitro||In vitro|
|Target hit rate (%)||30% 7||>80%4|
|Assay Multiplex Capacity||Low plex only due to crosstalk||Easy to build assays from low to high plex (1,000s)|
Velocity Sciences has Produced a Libraray of Existing HPAs which is Expanding Rapidly. Here is a sampling.
HPAs that have been validated with Kds at or less than 10 < 10 nmolar
Cell Regulation (4)
Immune Response (24)
- Theodore M. Tarasow, Sandra L. Tarasow & Bruce E. Eaton, RNA-catalysed carbon – carbon bond formation, NATURE, VOL 389, 1997.
- Theodore M. Tarasow, Bruce E. Eaton, Dressed for Success: Realizing the Catalytic Potential of RNA, Biopolymers (Nucleic Acid Sciences), Vol. 48, 29–37 1998.
- Based upon a validation study of 9,000 antibodies. L. Berglund, et al., A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies, Molecular & Cellular Proteomics 7:2019 –2027, 2008.
- Kd < 50 nM.
- Dongxi Xiang, Conglong Zheng, Sarah Shigdar, Wei Duan et al., Superior Performance of Aptamer in Tumor Penetration over Antibody: Implication of Aptamer-Based Theranostics in Solid Tumors, Theranostics 2015, 5, 10.
- Jonathan W. Kotula, Elizabeth D. Pratico, Xin Ming, Osamu Nakagawa, Rudolph L. Juliano, and Bruce A. Sullenger, Aptamer-Mediated Delivery of Splice-Switching Oligonucleotides to the Nuclei of Cancer Cells, NUCLEIC ACID THERAPEUTICS, 22, 3, 2012.
- L. Gold, Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery, PLoS ONE 5(12): e15004. doi:10.1371/journal.pone.0015004