II-mini3-4 aptamer

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Description

 In 2008, Shinsuke Sando and Atsushi Narita et al. employed in vitro selection techniques to isolate aptamers with high-affinity binding sites for Hoechst derivatives. The aptamer binds the fluorophore with high affinity. The light-up RNA aptamer-Hoechst pair can be used as a fluorescent tag to monitor transcription processes[1].

SELEX

SELEX was performed with a library containing ~1015 random RNA molecules and for their ability to bind and activate the fuorophore ligand Hoechst derivatives. After six rounds of screening, researchers selected a number of sequences, including aptamer II, to characterize their affinity for the dye and its spectral properties[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[1].

II-mini3-4 aptamer: 5'-GCCAAGCAGGUUCGUUUUCGAAGCUUGGA-3'
aptamer II: 5'-GGGUGAUCAGAUUCUGAUCCAGGUUACCAAGCAGGUUCGGCCUCGUCUGAGGUGAAGCUUGGAUCCGUCGC-3'

 drawing


Ligand information

SELEX ligand

Hoechst stains are part of a family of blue fluorescent dyes used to stain DNA. These bis-benzimides were originally developed by Hoechst AG, which numbered all their compounds so that the dye Hoechst 33342 is the 33,342nd compound made by the company. There are three related Hoechst stains: Hoechst 33258, Hoechst 33342, and Hoechst 34580.The dyes Hoechst 33258 and Hoechst 33342 are the ones most commonly used and they have similar excitation-emission spectra.-----From Wikipedia
Name Molecular Formula MW CAS Solubility PubChem Drug ID
Hoechst 33258 C25H27Cl3N6O 533.9 g/mol 23491-45-4 NA 31953 NA
drawing

Similar compound

We screened the compounds with great similarity 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 Named CAS Pubchem CID Structure
NA Hoechst 33258 23491-45-4 31953 drawing
ZINC2047214 Bisbenzimide 23491-52-3 1464 drawing
ZINC4866194 Pyrazophos 13457-18-6 26033 drawing
ZINC3831047 Metahexamide 565-33-3 11259 drawing
NA Bisbenzimide ethoxide trihydrochloride 875756-97-1 16760503 drawing
ZINC2047210 Hoechst 34580 23555-00-2 448202 drawing
ZINC113618708 para-iodoHoechst 33258 158013-43-5 10437137 drawing
ZINC26503609 meta-Hoechst 132869-83-1 10410101 drawing
NA Nuclear yellow 74681-68-8 123837 drawing
ZINC31539673 Hoechst 33378 23491-51-2 193594 drawing


References

[1] Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA.
Sando, S., Narita, A., Hayami, M., & Aoyama, Y.
Chemical communications, (33), 3858–3860. (2008)