XBA RNA aptamer

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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., Futamura, Y., Sakamoto, K., and Yokoyama, S. used SELEX to isolate RNA aptamers that bind to xanthine from a population of 10¹² random sequences. After multiple rounds of selection, a representative xanthine-binding RNA (designated as XBA) was identified with a dissociation constant (Kd) of 3.3 µM for xanthine[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'

drawing

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

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 Molecular Formula Molecular Weight CAS Solubility PubChem Drugbank 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
drawing

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.

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.

Source ligand ZINC ID Name CAS Pubchem CID Structure
Xanthine (2,6-dioxypurine) ZINC89203233 1,7-Dihydroimidazo[4,5-c]pyridine-4,6-dione 73771-32-1 22086935 drawing
Xanthine (2,6-dioxypurine) ZINC95922756 7-amino-1H-imidazo[4,5-b]pyridin-5(4H)-one 37660-70-1 45079066 drawing
Xanthine (2,6-dioxypurine) ZINC84403374 Isoguanine 3373-53-3 76900 drawing
Xanthine (2,6-dioxypurine) ZINC17174075 Hypoxanthine, 2-fluoro- 1480-90-6 135418579 drawing
Xanthine (2,6-dioxypurine) ZINC238514582 6-Chloro-1H-purin-2(3H)-one 1146697-79-1 101216963 drawing
Guanine ZINC895129 Guanine 73-40-5 135398634 drawing
Guanine ZINC14982924 2-Methyl-7H-purin-6-ol 5167-18-0 135449674 drawing
Guanine ZINC9974955 2-Bromohypoxanthine 87781-93-9 135413991 drawing
Guanine ZINC100004527 7-Deazaguanine 7355-55-7 135408714 drawing


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)