Real time kinetic studies of the interaction between folded antisense and target RNAs using surface plasmon resonance

Journal of Molecular Biology

Volumn 310, Issue 5, 2001, Pages 1125-1134

  Nordgren, Sara ^a   Slagter J�ger, Jacoba G ^a   Wagner, E Gerhart H ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Antisense RNA; Binding intermediate; Binding kinetics; RNA RNA interaction; Surface plasmon resonance

Indexed keywords

COMPLEMENTARY RNA; NUCLEIC ACID;

ARTICLE; BINDING KINETICS; COMPLEX FORMATION; DISSOCIATION CONSTANT; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; RNA STRUCTURE; SURFACE PLASMON RESONANCE; TEMPERATURE DEPENDENCE;

EID: 0035958669     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4802     Document Type: Article

References (39)

1. Antisense RNA
2. Antisense RNA structure and function
3. Antisense RNA control in bacteria, phages, and plasmids
4. Insertion sequence IS10 anti-sense pairing initiates by an interaction between the 5′ end of the target RNA and a loop in the anti-sense RNA
5. Antisense RNA regulation in prokaryotes: Rapid RNA/RNA interaction facilitated by a general U-turn loop structure
6. An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment
7. Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA
8. The effect of loop size in antisense and target RNAs on the efficiency of antisense RNA control
9. Control of ColE1 plasmid replication. Intermediates in the binding of RNA I and RNA II
10. Control of replication of plasmid R1: Formation of an initial transient complex is rate-limiting for antisense RNA-target RNA pairing
11. Structural analysis of late intermediate complex formed between plasmid ColIb-P9 Inc RNA and its target RNA. How does a single antisense RNA repress translation of two genes at different rates?
12. Antisense RNA control of plasmid R1 replication. The dominant product of the antisense RNA-mRNA binding is not a full RNA duplex
13. Kissing and RNA stability in antisense control of plasmid replication
14. Control of ColE1 plasmid replication: Initial interaction of RNA I and the primer transcript is reversible
15. Control of replication of plasmid R1: Structures and sequences of the antisense RNA, CopA, required for its binding to the target RNA, CopT
16. Bulged-out nucleotides in an antisense RNA are required for rapid target RNA binding in vitro and inhibition in vivo
17. Complex formed by complementary RNA stem-loops and its stabilization by a protein: Function of CoIE1 Rom protein
18. Kinetic analysis of monoclonal antibody-antigen interactions with a new biosensor based analytical system
19. Surface plasmon resonance for detection and measurement of antibody-antigen affinity and kinetics
20. Control of replication of plasmid R1: Kinetics of in vitro interaction between the antisense RNA, CopA, and its target, CopT
21. Relaxation kinetics of dimer formation by self complementary oligonucleotides
22. Co-operative nonenzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic-oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH
23. Studies of the complex between transfer RNAs with complementary anticodons. 1. Origins of enhanced affinity between complementary triplets
24. Real-time kinetics of HIV-1 Rev-Rev response element interactions. Definition of minimal binding sites on RNA and protein and stoichiometric analysis
25. Kinetic and stoichiometric analysis for the binding of Escherichia coli ribonuclease HI to RNA-DNA hybrids using surface plasmon resonance
26. Activation of 2′-5′ oligoadenylate synthetase by single-stranded and double-stranded RNA aptamers
27. Pseudouridine synthetase Pus1 of Saccharomyces cerevisiae: Kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA
28. Kinetics for hybridization of peptide nucleic acids (PNA) with DNA and RNA studied with the BIAcore technique
29. Effect of substrate RNA sequence on the cleavage reaction by a short ribozyme
30. Interaction between hammerhead ribozyme and RNA substrates measured by a surface plasmon resonance biosensor
31. Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC
32. Copy mutants of plasmid R1: Effects of base-pair substitutions in the copA gene on the replication control system
33. Kinetic aspects of control of plasmid replication by antisense RNA
34. Analysis of mass transport-limited binding kinetics in evanescent wave biosensors
35. Mechanism and utility of an RNA-cleaving DNA enzyme
36. Complexes formed by complementary RNA stem-loops. Their formations, structures and interaction with ColE1 Rom protein
37. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli
38. Control of replication of plasmid R1: The duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III
39. Analysis of macromolecular interactions using immobilized ligands