Streptomycin-RNA Aptamer

Apr 20, 2024 • Linfei Li, Yuhang Luo

Timeline

Description

In 1998, Wallace et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for Streptomycin, In 2003, Tereshko et al. Tertiary structure of the aptamer was resolved for the first time. In 2007, de-los-Santos-Alvarez et al. Presented label-free modified RNA-aptasensor for the detection of small molecules in biological samples^[1,2,4].

SELEX

Starting with a pool of 1015 different DNA molecules, in vitro selection procedures were performed to select for RNAs with a high affinity to streptomycin Affinity chromatography was performed using dihydrostreptomycin coupled to sepharose RNA from the starting pool was applied to the dihydrostreptomycin column and was specifically eluted,RNAs from the three final pools were reversetranscribed, PCR-amplified, cloned, and subjected to sequence analysis. Of 99 clones sequenced (33 from each selection procedure), 43 were unique^[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'-GGAUCGCAUUUGGACUUCUGCC……CGGCACCACGGUCGGAUC-3'

3D visualisation

Used a 2.9 Å structure of a complex be tween the aminocyclitol antibiotic streptomycin in vitro selected RNA aptamer, solved using anomalous diffraction properties of Ba cations. which contains two asymmetric internal loops, adopts a distinct cation-stabilized fold involving a series of S-shaped backbone turns anchored by canonical and noncanonical pairs and triples. The streptomycin streptose ring is encapsulated by stacked arrays of bases from both loops at the elbow of the L-shaped RNA architecture. Specificity is defined by direct hydrogen bonds between all streptose functional groups and base edges that line the inner walls of the cylindrical binding pocket^[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: 1NTA by X-ray. Streptomycin(shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with Streptomycin^[2].

Ligand information

SELEX ligand

Wallace and colleagues, isolated small, streptomycin-binding RNA aptamers via in vitro selection. In addition, bluensomycin, a streptomycin analogue that does not inhibit splicing, was used in a counter-selection to obtain RNAs that bind streptomycin with high affinityand specificity. Although an RNA from the normal selection (motif 2) bound both antibiotics, an RNA from the counter-selection (motif 1) discriminated between streptomycin and bluensomycin by four orders of magnitude. The binding site of streptomycin on the RNAs was determined via chemical probing with dimethylsulfate and kethoxal. The minimal size required for drug binding was a 46- and a 41-mer RNA for motifs 1 and 2, respectively. Using Pb2+ cleavage in the presence and absence of streptomycin, a conformational change spanning the entire mapped sequence length of motif 1 was observed only when both streptomycin and Mg2+ were present. Both RNAs require Mg2+ for binding streptomycin.^[1].

Structure ligand

Streptomycin is an aminoglycoside antibiotic indicated to treat multi-drug resistant mycobacterium tuberculosis and various non-tuberculosis infections.-----From drugbank

PubChem CID	Molecular Formula	MW	CAS	Solubility	Drugbank ID
19649	C21H39N7O12	581.6 g/mol	57-92-1	40 g/L(at 20℃）	DB01082

Similar compound

We screened the compounds with great similarity to Streptomycin 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
ZINC8214681	Streptomycin	57-92-1	19649
ZINC36176697	2-[(1S,2R,3R,4R,5S,6S)-3-(diaminomethylideneamino)-4-[(2R,3S,4S,5S)-3-[(2R,3R,4S,5S,6S)-4,5-dihydroxy-6-(hydroxymethyl)-3-(methylamino)oxan-2-yl]oxy-4-formyl-4-hydroxy-5-methyloxolan-2-yl]oxy-2,5,6-trihydroxycyclohexyl]guanidine	NA	93190235
ZINC36176688	2-[(1S,2R,3R,4R,5S,6S)-3-(diaminomethylideneamino)-4-[(2R,3S,4R,5S)-3-[(2R,3R,4S,5S,6S)-4,5-dihydroxy-6-(hydroxymethyl)-3-(methylamino)oxan-2-yl]oxy-4-formyl-4-hydroxy-5-methyloxolan-2-yl]oxy-2,5,6-trihydroxycyclohexyl]guanidine	NA	93190230
ZINC8101190	2-[(1S,2R,3R,4R,5S,6S)-3-(diaminomethylideneamino)-4-[(2R,3S,4R,5R)-3-[(2R,3R,4S,5S,6S)-4,5-dihydroxy-6-(hydroxymethyl)-3-(methylamino)oxan-2-yl]oxy-4-formyl-4-hydroxy-5-methyloxolan-2-yl]oxy-2,5,6-trihydroxycyclohexyl]guanidine	NA	92328111
ZINC1078030477	2-[(1R,2S,3S,4S,5S,6R)-3-(diaminomethylideneamino)-4-[(2S,3S,4R,5R)-3-[(2S,3S,4S,5S,6S)-4,5-dihydroxy-6-(hydroxymethyl)-3-(methylamino)oxan-2-yl]oxy-4-formyl-4-hydroxy-5-methyloxolan-2-yl]oxy-2,5,6-trihydroxycyclohexyl]guanidine	NA	44120113
ZINC8214760	2-[(1R,2R,3S,4R,5R,6S)-3-(diaminomethylideneamino)-4-[(2R,3S,4R,5S)-3-[(2S,3S,4S,5R,6S)-4,5-dihydroxy-6-(hydroxymethyl)-3-(methylamino)oxan-2-yl]oxy-4-formyl-4-hydroxy-5-methyloxolan-2-yl]oxy-2,5,6-trihydroxycyclohexyl]guanidine	NA	2735213
ZINC253487932	2-[(1R,2S,3S,4S,5R,6R)-3-(diaminomethylideneamino)-4-[(2R,3S,4R,5R)-3-[(2S,3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(methylamino)oxan-2-yl]oxy-4-formyl-4-hydroxy-5-methyloxolan-2-yl]oxy-2,5,6-trihydroxycyclohexyl]guanidine	NA	124894813
ZINC253487934	2-[(1R,2S,3S,4S,5R,6R)-3-(diaminomethylideneamino)-4-[(2R,3S,4R,5R)-3-[(2S,3S,4R,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-(methylamino)oxan-2-yl]oxy-4-formyl-4-hydroxy-5-methyloxolan-2-yl]oxy-2,5,6-trihydroxycyclohexyl]guanidine	NA	124894815

References

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