Mapping a specific binding sequence of an aptamer oligonucleotide to decrease the molecule size for many practical applications such as drug molecules
- Identification of key positions of a consensus sequence for enhancing binding affinity (possibly by modifying those positions) for an aptamer drug candidate.
- Through this strategy, we can map a small but highly specific binding aptamer oligonucleotide.
- Macugen (pegaptanib sodium) is an ophthalmic aptamer drug being developed by Pfizer/Eyetech for the treatment of the ‘wet’ forms of age-related macular degeneration (AMD).
- The consensus sequence is CGGAAUCAGTGAATGCTTATACATCCGt, an RNA 28 mer where all pyrimidines are modified with a 2′-F and the all the purines (except 2 As) are modified with a 2′-’OMe group.
- Our aptamer chip is a powerful tool for further refining the consensus sequences identified from the in vitro evolution (SELEX), by finding the minimal length of oligonucleotide required for specific
binding (core sequence) and systematic modification of the core sequence. The above example shows a strategy for searching the region of core sequence, which will show highest binding signals.
Sequence Design Example
- 3′ End Truncation
- 5′ End Truncation
- 3′ & 5′ End Truncation
- 14 mer Frame Walking
We can start by truncating the sequence at the 3′ end, removing one base at a time.
Next, truncate the sequence at the 5′ end, removing one base at a time.
Next remove two bases at a time, one from either end.
Last, we set the sequence length at 14 mer starting from the 5′ end and move the frame down the sequence (toward 3′ end) as far as we can.