NeomycinB RNA aptamer

Apr 22, 2024 • Linfei Li, Yuhang Luo

Timeline

Description

In 1995, Wallis et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for NeomycinB. The majority of the RNA molecules selected to specifically bind neomycin share a region of nucleotide sequence homology. From chemical probing and covariations among different clones we show that in all sequences this region folds into a hairpin structure, which from footprinting and partial alkaline hydrolysis experiments is shown to be the neomycin-binding site. In 1999, Patel, D. J. used chemical, biochemical, spectroscopy, NMR and computational methods to study the specific characteristics of aminoglycoside antibiotic RNA recognition of natural RNA targets and RNA aptamers identified in vitro^[1,2].

SELEX

In vitro selection experiments, a pool of 74 nucleotide random sequences was selected and applied to neomycin-derived agarose affinity columns, washed to remove nonspecific or weakly bound RNAs, and progress of the screen was determined by neomycin enrichment, which was performed by increasing the number of buffer washes in the first three rounds, from 5 to 30 to 50 progressively, with 50 fixations in rounds 3 through 6, and a 13-fold increase in the number of enrichments, prior to the affinity wash. Significantly increased in phase 8, and sequencing of 21 clones from cycle 8 revealed approximately 50% of the RNA sequences^[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'-GGACUGGGCGAGAAGUUUAGUCC-3'

3D visualisation

Jiang, L and colleagues present the solution structure as determined by Specific features of aminoglycoside antibiotic–RNA recognition have been probed using chemical, biochemical,spectroscopic and computational approaches on both natural RNA targets and RNA aptamers identified through in vitro selection. Specifically G9, G10, A16, G18, U19 and U21 bind to the neomycin B complex (partial hydrogen bonding predicted to be generated by pymol, see references for more details). The PDB ID of this structure is 1NEM^[3].
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: 1NEM by NMR. NeomycinB (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with NeomycinB^[3].

Ligand information

SELEX ligand

Wallis and colleagues utilized several methodologies including isocratic elution from neomycin and equilibrium gel filtration techniques to determine the dissociation constant of the neomycin complex both on the column and in solution. These methods were employed to comprehensively assess the stability and affinity of the neomycin^[1].

Structure ligand

Neomycin is a broad-spectrum aminoglycoside antibiotic drug that is derived from the metabolic products of Streptomyces fradiae.5 Neomycin is a complex comprised of three components, neomycin A, B, and C.2 Neomycin B, also known as framycetin, is the most active component of the complex and neomycin C is the isomer of neomycin B, making these two stereoisomers the active components of neomycin.1,2 Neomycin A, or neamine, is a moiety that conjoins two molecules of neomycin B and C together.-----From drugbank

PubChem CID	Molecular Formula	MW	CAS	Solubility	Drugbank ID
8378	C23H46N6O13	614.6 g/mol	1404-04-2	50 mg/ml（at room temperature)	DB00994

Similar compound

We screened the compounds with great similarity to NeomycinB 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
ZINC71928291	Framycetin	119-04-0	8378
ZINC85536952	(2R,3R,4S,5R,6S)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2R,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol	NA	70685100
ZINC60183170	paromomycin	NA	165580
ZINC72186786	(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2S,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol	NA	24871322
ZINC261494548	(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1R,2S,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2S,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol	NA	125116806
ZINC245219488	(2R,3S,4R,5R,6S)-5-amino-2-(aminomethyl)-6-[(1S,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2S,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol	NA	124762241
ZINC245219490	(2R,3R,4R,5R,6S)-5-amino-2-(aminomethyl)-6-[(1S,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2S,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol	NA	124762243
ZINC169719177	(2R,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(1S,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,4S,5R)-4-[(2S,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxycyclohexyl]oxyoxane-3,4-diol	NA	124605136

References

[1] A novel RNA motif for neomycin recognition.
Wallis, M. G., von Ahsen, U., Schroeder, R., & Famulok, M.
Chemistry & biology, 2(8), 543–552 (1995)
[2] Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer.
Jiang, L., Majumdar, A., Hu, W., Jaishree, T. J., Xu, W., & Patel, D. J.
Structure (London, England : 1993), 7(7), 817–827 (1999)
[3] Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions.
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Nucleic acids research, 28(15), 2935–2942. (2000)
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