Description

In 2008, Aoyama, Y. 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].

Structure

2D representation

The 2D structure of the figure is based on the article by online secondary structure prediction tool to draw. The figure shows the secondary structure prediction of the original aptamer sequence. The II-mini3-4 aptamer adopts a relatively simple secondary structure, with its core motif comprising a stem-loop featuring a central bulge. This functional domain was derived through truncation and optimisation of the primary nucleic acid library obtained via SELEX. The II-mini3-4 aptamer was named by Aoyama, Y. et al. in the article.^[1].

5'-GCCAAGCAGGUUCGUUUUCGAAGCUUGGA-3'

Following the SELEX procedure, the enriched nucleic acid library was subjected to high-throughput sequencing, generating a substantial population of raw sequence reads. The sequences presented herein represent additional high-affinity aptamers identified from this dataset.^[1].

5'-GGGUGAUCAGAUUCUGAUCCAGGUUACCAAGCAGGUUCGGCCUCGUCUGAGGUGAAGCUUGGAUCCGUCGC-3'

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

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.

Similar compound(s)

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.

ZINC ID	Name	CAS	Pubchem CID	Structure
not in ZINC	Hoechst 33258	23491-45-4	31953
ZINC2047214	Bisbenzimide	23491-52-3	1464
ZINC4866194	Pyrazophos	13457-18-6	26033
ZINC3831047	Metahexamide	565-33-3	11259
not in ZINC	Bisbenzimide ethoxide trihydrochloride	875756-97-1	16760503
ZINC2047210	Hoechst 34580	23555-00-2	448202
ZINC113618708	para-iodoHoechst 33258	158013-43-5	10437137
ZINC26503609	meta-Hoechst	132869-83-1	10410101
not in ZINC	Nuclear yellow	74681-68-8	123837
ZINC31539673	Hoechst 33378	23491-51-2	193594

References