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XBA RNA aptamer
Description
In 1998, Daisuke Kiga et al.isolated RNAs that bind to xanthine (2,6-dioxypurine) from a population of 1012 random sequences by in vitro selection, he xanthine/guanine-binding RNAs is the same as a sequence in one of the internalloops of the hairpin ribozyme, except for a substitution that is neutral with respect to xanthine/guanine binding[1].SELEX
Kiga, D.& Yokoyama, S. In vitro screening of xanthine-binding RNAs by in vitro screening started with an RNA library of 60 nt random sequences flanked by two primer-binding regions, and sequence homologues of 36 clones were identified, with only the shortest aptamers having concordant sequence[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by ribodraw tool to draw.5'-GGCACGUGUAUUACCCUAGUGGUCGACGUGCC-3'
Ligand information
SELEX ligand
9H-xanthine is an oxopurine in which the purine ring is substituted by oxo groups at positions 2 and 6 and N-9 is protonated. It has a role as a Saccharomyces cerevisiae metabolite. It is a tautomer of a 7H-xanthine.-----From DrugBank
Guanine is a 2-aminopurine carrying a 6-oxo substituent. It has a role as a human metabolite, an algal metabolite, a Saccharomyces cerevisiae metabolite, an Escherichia coli metabolite and a mouse metabolite. It is a purine nucleobase, an oxopurine and a member of 2-aminopurines. It derives from a hydride of a 9H-purine.-----From DrugBank
| Name | Molecular Formula | MW | CAS | Solubility | PubChem | Drug ID |
|---|---|---|---|---|---|---|
| Xanthine | C5H4N4O2 | 152.11 g/mol | 69-89-6 | 69 mg/L (at 16 °C) | 1188 | DB02134 |
| Guanine | C5H5N5O | 151.13 g/mol | 73-40-5 | 2080 mg/L (at 37 °C) | 135398634 | DB02377 |
Similar compound
We screened the compounds with great similarity to 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. For another compound, we used a similar compound query method from the PubChem database.
| Source ligand | Zinc_id | Named | CAS | Pubchem CID | Structure |
|---|---|---|---|---|---|
| Xanthine (2,6-dioxypurine) | ZINC13517187 | Xanthine | 69-89-6 | 1188 |  |
| Xanthine (2,6-dioxypurine) | ZINC89203233 | 1,7-Dihydroimidazo[4,5-c]pyridine-4,6-dione | 73771-32-1 | 22086935 |  |
| Xanthine (2,6-dioxypurine) | ZINC95922756 | 7-amino-1H-imidazo[4,5-b]pyridin-5(4H)-one | 37660-70-1 | 45079066 |  |
| Xanthine (2,6-dioxypurine) | ZINC84403374 | Isoguanine | 3373-53-3 | 76900 |  |
| Xanthine (2,6-dioxypurine) | ZINC17174075 | Hypoxanthine, 2-fluoro- | 1480-90-6 | 135418579 |  |
| Xanthine (2,6-dioxypurine) | ZINC238514582 | 6-Chloro-1H-purin-2(3H)-one | 1146697-79-1 | 101216963 |  |
| Guanine | ZINC895129 | Guanine | 73-40-5 | 135398634 |  |
| Guanine | ZINC14982924 | 2-Methyl-7H-purin-6-ol | 5167-18-0 | 135449674 |  |
| Guanine | ZINC9974955 | 2-Bromohypoxanthine | 87781-93-9 | 135413991 |  |
| Guanine | ZINC100004527 | 7-Deazaguanine | 7355-55-7 | 135408714 |  |
| Guanine | ZINC16939736 | 5-amino-6H-[1,3]thiazolo[5,4-d]pyrimidin-7-one | nan | 335016 |  |
| Guanine | ZINC18102838 | 2-Amino-3,7-dihydropyrrolo[3,2-d]pyrimidin-4-one | nan | 135857139 |  |
| Guanine | ZINC116890271 | 5-amino-6H-[1,3]oxazolo[5,4-d]pyrimidin-7-one | nan | 49870045 |  |
References
[1] An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition.Kiga, D., Futamura, Y., Sakamoto, K., & Yokoyama, S.
Nucleic acids research, 26(7), 1755–1760 (1998)