DP3 aptamer

May 14, 2024 • Bo Fu, Jiali Wang

Timeline

Description

Since 2002, Michael Famulok et al. screened an RNA aptamer for neuropeptide Y (NPY) and not only investigated its binding specificity to the NPY C-terminus and specific arginine residues, but also found that the aptamer highly mimicked NPY binding to the Y2 receptor both structurally and functionally, which provided a new tool for probing the interaction between NPY and different receptor subtypes. A new tool to explore the interaction between NPY and different receptor subtypes. Then in 2005, Michael T Bowser et al. used capillary electrophoresis-exponential enrichment of systematically evolved ligands (CE-SELEX) to screen for aptamers that were highly selective for NPY and that specifically bound NPY even in the presence of ~50% homology to human tryptic polypeptide (hPP). By 2021, Rivera V, Cunci L et al. further developed an NPY measurement method based on aptamer-modified microelectrodes and electrochemical impedance spectroscopy (EIS), which took advantage of the high conductivity, chemical stability, and large surface area of carbon fiber or platinum microelectrodes to achieve highly specific detection and analysis of NPY. This series of studies demonstrates the important progress and application potential of aptamer technology in NPY research and detection^[1].

SELEX

Michael Famulok et al. used an RNA library with a complexity of 9 x 10¹⁴ different sequences, with all pyrimidine residues replaced by 2'-amino-2'-deoxy derivatives to enhance nuclease tolerance. NPY was immobilized on streptavidin-agarose by N-terminal biotinylation, to ensure maximum accessibility of its C-terminus for aptamer in vitro screening experiments. After 12 rounds of screening, 30 clones were cloned and sequenced, with 80% of the major sequence families, 7% of the minor sequence families, and the rest of the sequences occurring individually. Finally, the aptamer that specifically binds NPY, aptamer DP3, was obtained. The study used several methods to determine the affinity of the screened target aptamer and the target: calculation of the dissociation constant (Kd): the Kd value of the aptamer to NPY was calculated by a concentration-dependent binding assay. The Kd value of the aptamer DP3 to NPY was 370 nM^[1].
Detailed information are accessible on SELEX page.

Structure

The sequence and secondary prediction structure of the aptamer will be shown here, here we used ribodraw to complete the figure. The 2D structure of the figures is based on the prediction results of the RNA fold website by ribodraw tool to draw. We used the minimum free energy (MFE) structure. DP3 aptamer binding to Neuropeptide Y^[1].

5'-UCGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC-3'

Ligand information

SELEX ligand

Neuropeptide Y is a 36-amino acid peptide found in many organs and in many sympathetic noradrenergic neurons. It has vasoconstrictor and diuretic activity and regulates local blood flow, glandular secretion, and smooth muscle activity. The peptide also stimulates feeding and drinking behavior and influences pituitary hormone secretion.-----From ChEBI

Name	Molecular Formula	MW	CAS	Solubility	PubChem	MedChemExpress
Neuropeptide Y (NPY)	C190H287N55O57	4254 g/mol	82785-45-3	NA	16132350	DB11788

Similar compound

We used the PubChem database to screen compounds that were more similar to Substance P, and selected the most similar compounds for display. For those without CAS numbers, we will supplement them with Pubchem CID.

Named	CAS	Pubchem CID	Structure
Insulin	9004-10-8	70678557
Pramlintide	151126-32-8	70691388
Calcitonin Salmon	9007-12-9	16220016
Lepirudin	138068-37-8	118856773
Hirudin	8001-27-2	72941487
Voxzogo	NA	119058036

References

[1] A Y2 receptor mimetic aptamer directed against neuropeptide Y.
Proske D, Höfliger M, Söll RM, Beck-Sickinger AG, Famulok M
The Journal of biological chemistry. 2002 Mar 29;277(13):11416-22. (2002)
[2] In vitro selection of aptamers with affinity for neuropeptide Y using capillary electrophoresis.
Mendonsa SD, Bowser MT
Journal of the American Chemical Society. 2005 Jul 6;127(26):9382-3. (2005)
[3] Measurement of Neuropeptide Y Using Aptamer-Modified Microelectrodes by Electrochemical Impedance Spectroscopy.
López L, Hernández N, Reyes Morales J, Cruz J, Flores K, González-Amoretti J, Rivera V, Cunci L
Analytical chemistry. 2021 Jan 19;93(2):973-980. (2021)
[4] Development of an Electrochemical, Aptamer-Based Sensor for Dynamic Detection of Neuropeptide Y.
Seibold JM, Abeykoon SW, Ross AE, White RJ
ACS sensors. 2023 Dec 22;8(12):4504-4511. (2023)
[5] Development of a Neuropeptide Y-Sensitive Implantable Microelectrode for Continuous Measurements.
Fernández-Vega L, Meléndez-Rodríguez DE, Ospina-Alejandro M, Casanova K, Vázquez Y, Cunci L
ACS sensors. 2024 May 24;9(5):2645-2652. (2024)