PEARL-seq: A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions

被引：30

作者：

Mukherjee, Herschel ^{[1
]}

Blain, J. Craig ^{[1
]}

Vandivier, Lee E. ^{[1
]}

Chin, Donovan N. ^{[1
]}

Friedman, Jessica E. ^{[1
]}

Liu, Fei ^{[1
]}

Maillet, Ashley ^{[1
]}

Fang, Chao ^{[1
]}

Kaplan, Jenifer B. ^{[1
]}

Li, Jinxing ^{[2
]}

Chenoweth, David M. ^{[2
]}

Christensen, Allan Beck ^{[3
]}

Petersen, Lars Kolster ^{[3
]}

Hansen, Nils Jakob Vest ^{[3
]}

Barrera, Luis ^{[1
]}

Kubica, Neil ^{[1
]}

Kumaravel, Gnanasambandam ^{[1
]}

Petter, Jennifer C. ^{[1
]}

机构：

[1] Arrakis Therapeut, Waltham, MA 02451 USA

[2] Univ Penn, Dept Chem, Philadelphia, PA 19104 USA

[3] Vipergen, Copenhagen, Denmark

来源：

ACS CHEMICAL BIOLOGY | 2020年 / 15卷 / 09期

关键词：

SEQUENCE-BASED DESIGN; INDUCED FIT; TAR RNA; NMR; BINDING;

D O I：

10.1021/acschembio.0c00357

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

RNA is emerging as a valuable target for the development of novel therapeutic agents. The rational design of RNA-targeting small molecules, however, has been hampered by the relative lack of methods for the analysis of small moleculeRNA interactions. Here, we present our efforts to develop such a platform using photoaffinity labeling. This technique, termed Photoaffinity Evaluation of RNA Ligation-Sequencing (PEARL-seq), enables the rapid identification of small molecule binding locations within their RNA targets and can provide information on ligand selectivity across multiple different RNAs. These data, when supplemented with small molecule SAR data and RNA probing data enable the construction of a computational model of the RNA-ligand structure, thereby enabling the rational design of novel RNA-targeted ligands.

引用

页码：2374 / 2381

页数：8

共 50 条

[31] Covalent Small-Molecule-RNA Complex Formation Enables Cellular Profiling of Small-Molecule-RNA Interactions
Guan, Lirui
Disney, Matthew D.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2013, 52 (38) : 10010 - 10013
[32] Mapping small molecule-RNA binding sites via Chem-CLIP synergized with capillary electrophoresis and nanopore sequencing
Yang, Xueyi
Wang, Jielei
Springer, Noah A.
Zanon, Patrick R. A.
Jia, Yilin
Su, Xiaoxuan
Disney, Matthew D.
NUCLEIC ACIDS RESEARCH, 2025, 53 (06)
[33] Small molecule-RNA interaction: Spectroscopic and calorimetric studies on the binding by the cytotoxic protoberberine alkaloid coralyne to single stranded polyribonucleotides
Islam, Md Maidul
Kumar, Gopinatha Suresh
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 2009, 1790 (08): : 829 - 839
[34] Light-regulated RNA-small molecule interactions
Young, Douglas D.
Deiters, Alexander
CHEMBIOCHEM, 2008, 9 (08) : 1225 - 1228
[35] Small-molecule modulators of protein-RNA interactions
Byun, Wan Gi
Lim, Donghyun
Park, Seung Bum
CURRENT OPINION IN CHEMICAL BIOLOGY, 2022, 68
[36] expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform
Borrill, Philippa
Ramirez-Gonzalez, Ricardo
Uauy, Cristobal
PLANT PHYSIOLOGY, 2016, 170 (04) : 2172 - 2186
[37] sRNAflow: A Tool for the Analysis of Small RNA-Seq Data
Zayakin, Pawel
NON-CODING RNA, 2024, 10 (01)
[38] shortran: a pipeline for small RNA-seq data analysis
Gupta, Vikas
Markmann, Katharina
Pedersen, Christian N. S.
Stougaard, Jens
Andersen, Stig U.
BIOINFORMATICS, 2012, 28 (20) : 2698 - 2700
[39] Global Analysis of Small Molecule Interactions with Proteins
Li, X.
Snyder, M.
MOLECULAR & CELLULAR PROTEOMICS, 2009, : S14 - S14
[40] MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean
Zhang, Chunbao
Fu, Fuyou
Lin, Chunjing
Ding, Xiaoyang
Zhang, Jingyong
Yan, Hao
Wang, Pengnian
Zhang, Wei
Peng, Bao
Zhao, Limei
FRONTIERS IN GENETICS, 2021, 12

← 1 2 3 4 5 →