In vitro selection of allosteric ribozymes that sense the bacterial second messenger c-di-GMP

Methods in Molecular Biology

Volumn 1111, Issue , 2014, Pages 209-220

  Furukawa, Kazuhiro ^a   Gu, Hongzhou ^a   Breaker, Ronald R ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Allosteric ribozyme; Aptamer; Cyclic di GMP; Hammerhead ribozyme; In vitro selection

Indexed keywords

APTAMER; COMPLEMENTARY DNA; CYCLIC DI GUANOSINE PHOSPHATE; DNA; DOUBLE STRANDED DNA; GUANOSINE PHOSPHATE; HAMMERHEAD RIBOZYME; RIBOZYME; RNA; RNA POLYMERASE; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; DNA TEMPLATE; ENZYME ACTIVITY; HIGH THROUGHPUT SCREENING; IN VITRO SELECTION; NONHUMAN; PRIORITY JOURNAL; SECOND MESSENGER;

ALLOSTERIC REGULATION; APTAMERS, NUCLEOTIDE; BASE SEQUENCE; CYCLIC GMP; GENETIC ENGINEERING; POLYMERASE CHAIN REACTION; RIBOSWITCH; RNA, CATALYTIC;

EID: 84934436676     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-755-6_15     Document Type: Article

References (23)

1. Breaker RR (2004) Natural and engineered nucleic acids as tools to explore biology. Nature 432:838-845
2. Famulok M (2005) Allosteric aptamers and aptazymes as probes for screening approaches. Annu Rev Microbiol 59:487-517
3. Tang J, Breaker RR (1997) Rational design of allosteric ribozymes. Chem Biol 4:453-459
4. Tang J, Breaker RR (1998) Mechanism for allosteric inhibition of an ATP-sensitive ribozyme. Nucleic Acid Res 26:4214-4221
5. Soukup GA, Breaker RR (1999) Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization. Structure 7:783-791
6. Soukup GA, Breaker RR (1999) Engineering precision RNA molecular switches. Proc Natl Acad Sci U S A 96:3584-3589
7. Koizumi M, Soukup GA, Kerr JNQ, Breaker RR (1999) Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nat Struct Biol 6:1062-1071
8. Gu H, Furukawa K, Breaker RR (2012) Engineered allosteric ribozymes that sense the bacterial second messenger cyclic diguanosyl 5monophosphate. Anal Chem 84:4935-4941
9. Wieland M, Benz A, Klauser B, Hartig JS (2009) Artificial ribozyme switches containing natural riboswitch aptamer domains. Angew Chem Int Ed 48:2715-2718
10. Win MN, Smolke CD (2007) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci U S A 104:14283-14288
11. Ogawa A, Maeda M (2008) An artificial aptazyme-based riboswitch and its cascading system in E. coli. Chembiochem 9:206-209
12. Robertson MP, Ellington AD (1999) In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat Biotechnol 17:62-66
13. Najafi-Shoushtari SH, Famulok M (2005) Competitive regulation of modular allosteric aptazymes by a small molecule and oligonucleotide effector. RNA 11:1514-1520
14. Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR (2010) An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science 329:845-848
15. Hengge R (2009) Principles of c-di-GMP signaling in bacteria. Nat Rev Microbiol 7:263-273
16. Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR (2008) Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321:411-413
17. Mayer G, Famulok M (2006) Highthroughput-compatible assay for glmS riboswitch metabolite dependence. Chembiochem 7:602-604
18. Lünse CE, Schmidt MS, Wittman V, Mayer G (2011) Carba-sugars activate the glmSriboswitch of Staphylococcus aureus. ACS Chem Biol 6:675-678
19. Furukawa K, Gu H, Sudarsan N, Hayakawa Y, Hyodo M, Breaker RR (2012) Identification of ligand analogues that control c-di-GMP riboswitches. ACS Chem Biol 7:1436-1443
20. Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA (2009) Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol 16:1218-1223
21. Kulshina N, Baird NJ, Ferré-D'Amaré AR (2009) Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat Struct Mol Biol 16:1212-1217
22. Forster AC, Symons RH (1987) Selfcleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell 50:9-16
23. Fedor MJ, Uhlenbeck OC (1992) Kinetics of intermolecular cleavage by hammerhead ribozymes. Biochemistry 31:12042-12054