Literature DB >> 21163353

GNRA/receptor interacting modules: versatile modular units for natural and artificial RNA architectures.

Junya Ishikawa1, Yuki Fujita, Yuri Maeda, Hiroyuki Furuta, Yoshiya Ikawa.   

Abstract

Interactions between GNRA tetraloops and their receptors are found frequently as modular units in various types of naturally occurring structured RNAs. Due to their functional importance, GNRA/receptor interactions have been studied extensively with regard to their 3D structures and biochemical and biophysical properties. Artificial non-natural GNRA/receptor modules have also been generated not only to obtain a better understanding of this class of motifs in natural RNA structures but also for application of these modular units to the design and construction of artificial RNA structures that can be used as platforms to generate functional RNAs applicable for nanobiotechnology. In this review, we present a survey of structures, functions, and analyses as well as artificial generation and application of GNRA/receptor interacting modules.
Copyright © 2010 Elsevier Inc. All rights reserved.

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Year:  2010        PMID: 21163353     DOI: 10.1016/j.ymeth.2010.12.011

Source DB:  PubMed          Journal:  Methods        ISSN: 1046-2023            Impact factor:   3.608


  13 in total

1.  Self-replication reactions dependent on tertiary interaction motifs in an RNA ligase ribozyme.

Authors:  Rei Ohmori; Hirohide Saito; Yoshiya Ikawa; Yoshihiko Fujita; Tan Inoue
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2.  Increased Flexibility between Stems of Intramolecular Three-Way Junctions by the Insertion of Bulges.

Authors:  Carolyn E Carr; Luis A Marky
Journal:  Biophys J       Date:  2018-06-19       Impact factor: 4.033

3.  Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.

Authors:  Namita Bisaria; Max Greenfeld; Charles Limouse; Dmitri S Pavlichin; Hideo Mabuchi; Daniel Herschlag
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-04       Impact factor: 11.205

4.  Deducing putative ancestral forms of GNRA/receptor interactions from the ribosome.

Authors:  Erin R Calkins; Paul Zakrevsky; Vasken L Keleshian; Eduardo G Aguilar; Cody Geary; Luc Jaeger
Journal:  Nucleic Acids Res       Date:  2019-01-10       Impact factor: 16.971

5.  Attenuation of loop-receptor interactions with pseudoknot formation.

Authors:  Kirill A Afonin; Yen-Ping Lin; Erin R Calkins; Luc Jaeger
Journal:  Nucleic Acids Res       Date:  2011-11-10       Impact factor: 16.971

6.  Corroboration of Zn(ii)-Mg(ii)-tertiary structure interplays essential for the optimal catalysis of a phosphorothiolate thiolesterase ribozyme.

Authors:  Tzu-Pin Wang; Yu-Chih Su; Yi Chen; Scott Severance; Chi-Ching Hwang; Yi-Ming Liou; Chia-Hui Lu; Kun-Liang Lin; Rui Jing Zhu; Eng-Chi Wang
Journal:  RSC Adv       Date:  2018-09-21       Impact factor: 3.361

7.  Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway.

Authors:  Steve Bonilla; Charles Limouse; Namita Bisaria; Magdalena Gebala; Hideo Mabuchi; Daniel Herschlag
Journal:  J Am Chem Soc       Date:  2017-12-15       Impact factor: 15.419

8.  Artificial RNA Motifs Expand the Programmable Assembly between RNA Modules of a Bimolecular Ribozyme Leading to Application to RNA Nanostructure Design.

Authors:  Md Motiar Rahman; Shigeyoshi Matsumura; Yoshiya Ikawa
Journal:  Biology (Basel)       Date:  2017-10-30

9.  Programmable folding of fusion RNA in vivo and in vitro driven by pRNA 3WJ motif of phi29 DNA packaging motor.

Authors:  Dan Shu; Emil F Khisamutdinov; Le Zhang; Peixuan Guo
Journal:  Nucleic Acids Res       Date:  2013-09-30       Impact factor: 16.971

10.  Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square and pentagon nanovehicles.

Authors:  Emil F Khisamutdinov; Hui Li; Daniel L Jasinski; Jiao Chen; Jian Fu; Peixuan Guo
Journal:  Nucleic Acids Res       Date:  2014-08-04       Impact factor: 16.971

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