Description

In 2005, Verdine, G. L. et al. used SELEX to identify RNA aptamers that specifically bind to the tFKBP3R-2G complex. After seven rounds of selection, they identified two key aptamers, s23 and T1, which showed high affinity with Kd values below 50 nM. Aptamer s23 exhibited exceptional specificity for both the guanine base and the tether length in the small molecule. It also demonstrated strong binding to tFKBP3R but not to the wild-type tFKBP*, confirming its specificity for the engineered protein-small molecule interface. This study highlighted the potential of SELEX for developing RNA aptamers targeting specific composite surfaces.^[1].

SELEX

In 2005, Verdine, G. L. et al. designed an in vitro RNA selection process to identify aptamers that specifically bind to the TFKBP3R-2G complex. Starting with a DNA template containing a 60-nucleotide random region, they performed seven rounds of SELEX. Among the selected aptamers, s23 and T1 showed the highest affinity, binding to TFKBP3R-2G with Kd values below 50 nM. The RNA library was denatured at 94°C for 2 minutes, then cooled to room temperature in phosphate-buffered saline (PBS). The RNA pool was mixed with TFKBP*3R-2G and incubated in PBS. After incubation, the mixture was passed through a 0.45 μm nitrocellulose filter (Millipore) and washed with PBS. The bound RNAs were eluted with 7 M urea at 90°C for 5 minutes, ethanol precipitated, and reverse transcribed using AMV reverse transcriptase at 42°C for 1 hour.^[1].

Structure

2D representation

The 2D structure of the figure is based on the article by ribodraw tool to draw. The s23 aptamer was named by Verdine, G. L. et al. in the article.^[1].

5'-GGGUUCGAAUGCAAGUCUGGUGAGUGUUGGGAGGGCAGUGACUUGCUUCGUAGUGUAAACUGACGUGGCGGUGUUACUUUACUGUUACGCUAGGUUACGGG-3'

Ligand information

SELEX ligand

The FKBPs, or FK506 binding proteins, constitute a family of proteins that have prolyl isomerase activity and are related to the cyclophilins in function, though not in amino acid sequence. FKBPs have been identified in many eukaryotes, ranging from yeast to humans, and function as protein folding chaperones for proteins containing proline residues. Along with cyclophilin, FKBPs belong to the immunophilin family. ------From Wiki

Aptamer bind to the affinity of the protein.

Similar compound

We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.

Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).

Z-score: a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious.

RMSD: (Root Mean Square Deviation) is used to measure the degree to which atoms deviate from the alignment position.

PDB: PDB ID+ chain name.

References