1
|
Bohdan DR, Voronina VV, Bujnicki JM, Baulin EF. A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures. Nucleic Acids Res 2023; 51:8367-8382. [PMID: 37471030 PMCID: PMC10484739 DOI: 10.1093/nar/gkad605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
Understanding the 3D structure of RNA is key to understanding RNA function. RNA 3D structure is modular and can be seen as a composition of building blocks of various sizes called tertiary motifs. Currently, long-range motifs formed between distant loops and helical regions are largely less studied than the local motifs determined by the RNA secondary structure. We surveyed long-range tertiary interactions and motifs in a non-redundant set of non-coding RNA 3D structures. A new dataset of annotated LOng-RAnge RNA 3D modules (LORA) was built using an approach that does not rely on the automatic annotations of non-canonical interactions. An original algorithm, ARTEM, was developed for annotation-, sequence- and topology-independent superposition of two arbitrary RNA 3D modules. The proposed methods allowed us to identify and describe the most common long-range RNA tertiary motifs. Along with the prevalent canonical A-minor interactions, a large number of previously undescribed staple interactions were observed. The most frequent long-range motifs were found to belong to three main motif families: planar staples, tilted staples, and helical packing motifs.
Collapse
Affiliation(s)
- Davyd R Bohdan
- Department of Innovation and High Technology, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valeria V Voronina
- Department of Information Systems, Ulyanovsk State Technical University, Ulyanovsk 432027, Russia
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Eugene F Baulin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| |
Collapse
|
2
|
Hagler LD, Luu LM, Tonelli M, Lee J, Hayes SM, Bonson SE, Vergara JI, Butcher SE, Zimmerman SC. Expanded DNA and RNA Trinucleotide Repeats in Myotonic Dystrophy Type 1 Select Their Own Multitarget, Sequence-Selective Inhibitors. Biochemistry 2020; 59:3463-3472. [PMID: 32856901 DOI: 10.1021/acs.biochem.0c00472] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There are few methods available for the rapid discovery of multitarget drugs. Herein, we describe the template-assisted, target-guided discovery of small molecules that recognize d(CTG) in the expanded d(CTG·CAG) sequence and its r(CUG) transcript that cause myotonic dystrophy type 1. A positive cross-selection was performed using a small library of 30 monomeric alkyne- and azide-containing ligands capable of producing >5000 possible di- and trimeric click products. The monomers were incubated with d(CTG)16 or r(CUG)16 under physiological conditions, and both sequences showed selectivity in the proximity-accelerated azide-alkyne [3+2] cycloaddition click reaction. The limited number of click products formed in both selections and the even smaller number of common products suggests that this method is a useful tool for the discovery of single-target and multitarget lead therapeutic agents.
Collapse
Affiliation(s)
- Lauren D Hagler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Long M Luu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Marco Tonelli
- National Magnetics Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - JuYeon Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Samuel M Hayes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Sarah E Bonson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - J Ignacio Vergara
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
3
|
Hagler LD, Bonson SE, Kocheril PA, Zimmerman SC. Assessing the feasibility and stability of uracil base flipping in RNA–small molecule complexes using molecular dynamics simulations. CAN J CHEM 2020. [DOI: 10.1139/cjc-2019-0421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small molecules can be used to target RNAs that mediate disease. A fundamental understanding of binding interactions between RNA and small molecules and the structure of their complexes will further inform the design of new targeting agents. Two small molecule ligands were investigated for their ability to recognize the expanded CUG repeat sequence in RNA, the causative agent of myotonic dystrophy type 1. We report the use of molecular dynamics simulations to explore small molecule–RNA complexes and the finding of a stabilized base flipped conformation at UU mismatches. The results of this computational study support experimental observations and suggest that base flipping is feasible for CUG-repeat RNA.
Collapse
Affiliation(s)
- Lauren D. Hagler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sarah E. Bonson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Philip A. Kocheril
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Steven C. Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|