FMN aptamer

Mar 28, 2024 • Yuhang Luo, Zhizhong Lu

Timeline

Description

In 1994, Dr. Michael Famulok et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for Flavin mononucleotide (FMN). In 1996, Patel DJ. Molecular et al. elucidated the structure of the aptamer complexed with FMN using multidimensional nuclear magnetic resonance spectroscopy and molecular dynamics calculations^[1].

SELEX

Dr. Michael Famulok et al. performed the screening using an RNA 113-mer library containing 10¹⁵ different sequences, each consisting of 14 random nucleotides surrounded by two specific primer binding sites. Specifically bound RNAs (aptamers) were selected from the RNA pool by affinity chromatography with a given cofactor (FMN)-derivatized agarose. RNA sequences bound to agarose were subsequently eluted with a solution containing the appropriate ligand. After six rounds of screening, a large number of RNAs bound to FMN and NAD⁺ columns. From the pool of FMN-selected RNAs, the researchers cloned and sequenced 17 different clones that demonstrated the ability to specifically bind FMN. These FMN-binding RNAs contained two conserved regions with the sequences AGGNUAU and AGAAGG. 13 FMN-binding RNAs contained the two conserved regions described above, and these sequences were surrounded by variable nucleotides that were capable of pairing to form defined secondary structures. The dissociation constants of the FMN-2 aptamer/FMN complexes were determined by analytical affinity chromatography^[1].
Detailed information are accessible on SELEX page.

Structure

2D representation

Here we use ribodraw to complete the figure, through the 3D structure information^[2].

5'-GGCGUGUAGGAUAUGCUUCGGCAGAAGGACACGCC-3'

3D visualisation

Dinshaw J. Patel present the solution structure, as determined by multidimensional NMR spectroscopy and molecular dynamics calculations, of the complex of flavin mononucleotide (FMN) bound to the conserved internal loop segment of a 35 nucleotide RNA aptamer identified through in vitro selection. Their comprehensive study reveals the detailed interactions between FMN and the RNA aptamer, including base-pair mismatches, a base-triple formation, and the specific intercalation of FMN's isoalloxazine ring into the RNA helix, contributing to our understanding of RNA folding and molecular recognition principles. The PDB ID of this structure is 1FMN^[2].
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: 1FMN by NMR. Flavin mononucleotide (FMN) (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with FMN.

Ligand information

SELEX ligand

The dissociation constant Kd of the FMN-2 aptamer/FMN complex was determined using analytical affinity chromatography by Dr. Michael Famulok et al. The specificity of this RNA was quantified by elution with 7,8-dimethylisobeacodyl, Flavin adenine dinucleotide (FAD),Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP)^[1].

Structure ligand

Flavin mononucleotide is a form of vitamin B2 used to restore riboflavin in anemia, migraine, alcoholism, and hyperhomocysteinemia.-----From Drugbank

PubChem CID	Molecular Formula	MW	CAS	Solubility	Drugbank ID
643976	C17H21N4O9P	456.3 g/mol	146-17-8	92 mg/mL	DB03247

Similar compound

We screened the compounds with great similarity to Flavin mononucleotide (FMN) 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	Named	CAS	Pubchem CID	Structure
ZINC000003831428	Riboflavin Monophosphate	130-40-5	23666409
ZINC000030730210	Riboflavin Cyclic-4',5'-Phosphate	NA	11026517
ZINC000003869906	1,5-Dihydroriboflavin 5'-(dihydrogen phosphate)	5666-16-0	445395
ZINC000008551105	Riboflavin 5'-phosphate sodium	6184-17-4	23687712
ZINC000008551106	[(2S,3R,4S)-5-(7,8-dimethyl-2,4-dioxobenzo[g]pteridin-10-yl)-2,3,4-trihydroxypentyl] dihydrogen phosphate	NA	51435500
ZINC000003831427	[(2R,3R,4S)-5-(7,8-dimethyl-2,4-dioxobenzo[g]pteridin-10-yl)-2,3,4-trihydroxypentyl] dihydrogen phosphate	NA	7048781
ZINC000008551108	Lyxoflavin 5'-monophosphate	53860-75-6	51435503
ZINC000027414762	[(2S,3R,4R)-5-(7,8-dimethyl-2,4,6-trioxo-1H-benzo[g]pteridin-10-yl)-2,3,4-trihydroxypentyl] dihydrogen phosphate	NA	44354184

References

[1] Isolation of RNA Aptamers for Biological Cofactors by In Vitro Selection†.
Dipl.-Chem. Petra Burgstaller, Dr. Michael Famulok
Nature, 364(6437), 550–553 (1994)
[2] Molecular recognition in the FMN-RNA aptamer complex.
Fan P, Suri AK, Fiala R, Live D, Patel DJ.
J Mol Biol. 1996 May 10;258(3):480-500. (1996)
[3] Flavin-Dependent Photocleavage of RNA at G·U Base Pairs.
Petra Burgstaller, Michael Famulok.
Journal of the American Chemical Society 1997 119 (5), 1137-1138 (1997)
[4] A molecular dynamics simulation of the flavin mononucleotide-RNA aptamer complex.
Schneider C, Sühnel J.
Biopolymers. 1999 Sep;50(3):287-302. (1999)
[5] Specific labeling approaches to guanine and adenine imino and amino proton assignments in the AMP-RNA aptamer complex.
Jiang, F., Patel, D. J., Zhang, X., Zhao, H., & Jones, R. A
Journal of biomolecular NMR, 9(1), 55–62. (2000)
[6] Expression mechanism of the allosteric interactions in a ribozyme catalysis.
Araki M, Okuno Y, Sugiura Y.
Nucleic Acids Symp Ser. 2000;(44):205-6. (2001)
[7] Electrochromatographic retention studies on a flavin-binding RNA aptamer sorbent.
Clark SL, Remcho VT.
Anal Chem. 2003 Nov 1;75(21):5692-6. (2003)
[8] Identification of a 14mer RNA that recognizes and binds flavin mononucleotide with high affinity.
Anderson PC, Mecozzi S
Nucleic Acids Res. 2005 Dec 23;33(22):6992-9 (2005)
[9] Competitive regulation of modular allosteric aptazymes by a small molecule and oligonucleotide effector.
Najafi-Shoushtari SH, Famulok M.
RNA. 2005 Oct;11(10):1514-20. (2005)
[10] Computational selection of nucleic acid biosensors via a slip structure model.
Hall B, Hesselberth JR, Ellington AD.
Biosens Bioelectron. 2007 Apr 15;22(9-10):1939-47. (2007)
[11] Role of Mg²⁺ ions in flavin recognition by RNA aptamer.
Sengupta A, Gavvala K, Koninti RK, Hazra P.
J Photochem Photobiol B. 2014 Nov;140:240-8. (2014)