A Small Molecule Microarray Platform To Select RNA Internal Loop−Ligand Interactions

2007 ◽  
Vol 2 (11) ◽  
pp. 745-754 ◽  
Author(s):  
Jessica L. Childs-Disney ◽  
Meilan Wu ◽  
Alexei Pushechnikov ◽  
Olga Aminova ◽  
Matthew D. Disney
Keyword(s):  
Small Molecule ◽  
Microarray Platform ◽  
Internal Loop ◽  
Ligand Interactions ◽  
Rna Internal Loop

Photo-Cross-Linked Small-Molecule Microarrays as Chemical Genomic Tools for Dissecting Protein–Ligand Interactions

2006 ◽  
Vol 1 (6) ◽  
pp. 789-797 ◽  
Author(s):  
Naoki Kanoh ◽  
Aya Asami ◽  
Makoto Kawatani ◽  
Kaori Honda ◽  
Saori Kumashiro ◽  
...  
Keyword(s):  
Small Molecule ◽  
Protein Ligand Interactions ◽  
Chemical Genomic ◽  
Genomic Tools ◽  
Ligand Interactions

RNALigands: a database and web server for RNA - ligand interactions

RNA ◽  
2021 ◽  
pp. rna.078889.121
Author(s):  
Saisai Sun ◽  
Jianyi Yang ◽  
Zhaolei Zhang
Keyword(s):  
Secondary Structure ◽  
Small Molecules ◽  
Small Molecule ◽  
Neurological Diseases ◽  
Experimental Studies ◽  
Rna Structures ◽  
Structural Motifs ◽  
Rna Molecules ◽  
Small Molecule Ligands ◽  
Ligand Interactions

Motivation: RNA molecules can fold into complex and stable 3-D structures, allowing them to carry out important genetic, structural, and regulatory roles inside the cell. These complex structures often contain 3-D pockets made up of secondary structural motifs that can be potentially targeted by small molecule ligands. Indeed, many RNA structures in PDB contain bound small molecules, and high-throughput experimental studies have generated large number of interacting RNA and ligand pairs. There are considerable interests in developing small molecule lead compounds targeting viral RNAs or those RNAs implicated in neurological diseases or cancer. Results: We hypothesize that RNAs that have similar secondary structural motifs may bind to similar small molecule ligands. Towards this goal, we established a database collecting RNA secondary structural motifs and bound small molecules ligands. We further developed a computational pipeline, which takes input an RNA sequence, predicts its secondary structure, extracts structural motifs and searches the database for similar secondary structure motifs and interacting small molecules. We demonstrated the utility of the server by querying α-synuclein mRNA 5′ UTR sequence and finding potential matches which was validated as correct. Availability and Implementation: The server is publicly available at http://RNALigands.ccbr.utoronto.ca. The source code can also be downloaded at https://github.com/SaisaiSun/RNALigands.

Structure of an RNA Internal Loop Consisting of Tandem C-A+Base Pairs†,‡

Biochemistry ◽  
1998 ◽  
Vol 37 (34) ◽  
pp. 11726-11731 ◽  
Author(s):  
Se Bok Jang ◽  
Li-Wei Hung ◽  
Young-In Chi ◽  
Elizabeth L. Holbrook ◽  
Richard J. Carter ◽  
...  
Keyword(s):  
Base Pairs ◽  
Internal Loop ◽  
Rna Internal Loop
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