FAD aptamer

Apr 30, 2024 • Yuhang Luo, Linfei Li

Description

In 2022, John S. Samuelian et al.employed an in vitro selection method to screen for the FAD aptamer and, subsequently, utilised NMR structure resolution techniques to determine the structure of its binding complex with FMN. In this study, they demonstrated the aptamer that selectively binds to the oxidized forms of flavin over its reduced counterparts, significantly altering the flavin reduction potential by -40 mV, a change comparable to that observed in oxidoreductase enzymes^[1].

SELEX

John S. Samuelian et al. enriched an RNA library, comprising N42 random sequences, through 12 rounds of in vitro selection, culminating in the identification of four RNA aptamers. Among these, aptamer 12.29 was optimised and truncated to yield X2B2, which was subsequently refined to X2B2-C14U. The binding affinity of X2B2-C14U for ligands, including flavin mononucleotide (FMN), was ascertained using isothermal titration calorimetry (ITC), revealing a dissociation constant as low as 243 nM^[1].

Detailed information are accessible on SELEX page.

Structure

2D representation

X2B2-C14U is a mutant of the X2B2 aptamer, and the X2B2 aptamer is derived from the truncation and elongation of the original aptamer 12.29. Here we use ribodraw to complete the figure, through the 3D structure information^[1].

5'-GGAUACACAAGAGUGAUUGAAACUAAGUCUGUGUAUCC-3'

3D visualisation

In 2022, John S. Samuelian et al. isolated the aptamer and elucidated the structure of its complex with FMN using NMR structure resolution techniques. The NMR-derived structure revealed that the aptamer engages with FMN through π-π stacking and donor-π interactions, creating a specific binding pocket that markedly influences the redox potential of FMN. The FMN binding site is nestled within a platform structure of the aptamer X2B2-C14U and is stabilised by a base triad. Certain bases within the binding pocket participate in π-π stacking with the isoalloxazine ring of FMN and donor-π interactions, leading to substantial alterations in the redox potential of FMN. The interactions between the aptamer and the cofactor are focused on the isoalloxazine ring, with the binding pockets for FMN and riboflavin being consistent. The PDB ID for this structure is 7RWR^[1].

Additional available structures that have been solved and detailed information are accessible on Structures page.

Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 7RWR by NMR. Flavin mononucleotide (FMN) (shown in sticks) is labeled in magenta. Right: The hydrogen bonds of binding sites of the aptamer bound with FMN^[1].

Ligand information

SELEX ligand

John S. Samuelian et al. used isothermal titration calorimetry (ITC) to determine the binding affinity and specificity between flavin adenine dinucleotide (FAD) and RNA aptamers. This method accurately measures the heat absorbed or released during the binding process, enabling the derivation of dissociation constants. The specificity of this RNA was quantified through elution with flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN), and riboflavin (Rb)^[1].

Structure ligand

FMN is a flavin mononucleotide that is riboflavin (vitamin B2) in which the primary hydroxy group has been converted to its dihydrogen phosphate ester. It has a role as a coenzyme, a bacterial metabolite, a human metabolite, a mouse metabolite and a cofactor. It is a vitamin B2 and a flavin mononucleotide. It is a conjugate acid of a FMN(3-).-----From PubChem

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

Drugbank: a comprehensive database with detailed information on drugs and drug targets.

Name	PubChem CID	Molecular Formula	Molecular Weight	CAS	Solubility	Drugbank ID
Flavin mononucleotide(FMN)	643976	C17H21N4O9P	456.3 g/mol	146-17-8	92 mg/mL	DB03247

Similar compound

We screened the compounds with great similarity to Flavin adenine dinucleotide(FAD) by using the ZINC database and showed some of the compounds' structure diagrams. For some CAS numbers not available,we will supplement them with Pubchem CID.

ZINC ID: a compound identifier used by the ZINC database, one of the largest repositories for virtual screening of drug-like molecules.

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

ZINC ID	Name	CAS	Pubchem CID	Structure
ZINC000001532585	Flavin adenine dinucleotide disodium	84366-81-4	2734019
ZINC000035653106	Roseoflavin	51093-55-1	170973
ZINC000004430517	7,8-Diethylflavin	5720-12-7	3081394
ZINC000004430766	7,8-dichloro-10-[(2R,3S,4R,5R)-2,3,4,5,6-pentahydroxyhexyl]benzo[g]pteridine-2,4-dione	NA	92220574
ZINC000005386869	8-methoxy-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]benzo[g]pteridine-2,4-dione	NA	92262495
ZINC000002558223	8-(dimethylamino)-7-methyl-10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]pyrimido[4,5-b]quinoline-2,4-dione	NA	2063313
ZINC000104866581	10-[(2R,3R,4S)-2,3,4,5-tetrahydroxypentyl]-1H-pyrimido[4,5-b]quinoline-2,4,8-trione	NA	11966226
ZINC000004878473	10-[(2S,3S,4R)-2,3,4,5-tetrahydroxypentyl]pyrimido[4,5-b]quinoline-2,4-dione	NA	92237780

References

[1] An RNA aptamer that shifts the reduction potential of metabolic cofactors.
Samuelian, J.S., Gremminger, T.J., Song, Z., Poudyal, R.R., Li, J., Zhou, Y., Staller, S.A., Carballo, J.A., Roychowdhury-Saha, M., Chen, S.J., Burke, D.H., Heng, X., Baum, D.A.
Nature Chemical Biology 18, 1263–1269. (2022)