Detection and analysis of hairpin II, an essential metastable structural element in viroid replication intermediates

Nucleic Acids Research

Volumn 30, Issue 15, 2002, Pages 3349-3359

  Schröder, Astrid R W ^a,b   Riesner, Detlev ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

^b SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; RNA; RNA POLYMERASE;

ARTICLE; BIOPHYSICS; COMPLEX FORMATION; CONTROLLED STUDY; GC RICH SEQUENCE; IN VITRO STUDY; IN VIVO STUDY; METHODOLOGY; NONHUMAN; PLANT CELL; POTATO; POTATO SPINDLE TUBER; PRIORITY JOURNAL; RNA ANALYSIS; RNA REPLICATION; RNA STRUCTURE; TEMPERATURE; VIROID;

POTATO SPINDLE TUBER VIROID; SOLANUM; SOLANUM TUBEROSUM; VIROIDS;

EID: 0036682130     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkf454     Document Type: Article

References (47)

1. Viroids
2. A proposed scheme for viroid classification and nomenclature
3. A replication cycle for viroids and other small infectious RNAs
4. Small catalytic RNAs
5. Replication of avocado sunblotch viroid: Evidence for a symmentric pathway with two rolling circles and hammerhead ribozyme processing
6. Nucleotide sequence and secondary structure of potato spindle tuber viroid
7. Structure and structure formation of viroids
8. Viroid replication is inhibited by a-Amanitin
9. Involvement of nuclear DNA-dependent RNA polymerases in potato spindle tuber viroid replication: A reevalution
10. Linear oligomeric potato spindle tuber viroid (PSTV) RNAs are accurately processed in vitro to the monomeric circular viroid proper when incubated with a nuclear extract from healthy potato cells
11. Switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation
12. Oligomeric potato spindle tuber viroid RNA does not process autocatalytically under conditions where other RNAs do
13. Only one of four possible secondary structures of the central conserved region of potato spindle tuber viroid is a substrate for processing in a potato nuclear extract
14. Transcription of potato spindle tuber viroid by RNA polymerase II starts predominantly at two specific sites
15. Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA
16. Restoration of secondary hairpin II is associated with restoration of infectivity of nonviable recombinant viroid
17. Multiple pathways of reversion in viroids for conservation of structural elements
18. Sequential folding of transfer RNA: A nuclear magnetic resonance study of successive longer tRNA fragments with a common 5′ end
19. Sequential folding of a messenger RNA molecule
20. Secondary structure formation during RNA synthesis
21. Description of RNA folding by 'simulated annealing'
22. Dynamic competition between alternative structures in viroid RNA simulated by an RNA folding algorithm
23. Temperature-gradient gel electrophoresis: Analysis of conformational transitions, sequence variations and protein-nucleic acid interactions
24. Viroid: From thermodynamics to cellular structure and function
25. Analysis of RNA structures by temperature-gradient gel electrophoresis: Viroid replication and processing
26. Physical basis and biological examples of metastable RNA structures
27. Formation of metastable RNA structures by sequential folding during transcription: Time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis
28. Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts
29. Correlation between bending of the VM region and pathogenicity of different Potato Spindle Tuber Viroid strains
30. Base-pair probability profiles of RNA secondary structures
31. Structure of viroid replicative intermediates: Physico-chemical studies on SP6 transcripts of cloned oligomeric potato spindle tuber viroid
32. Continuous replication of potato spindle tuber viroid (PSTV) in permanent cell cultures of potato and tomato
33. Die Struktur der intermediären Ribonucleinsäuren bei der Replikation von Viroiden
34. Longer than unit length viroid minus strands are present in RNA from infected plants
35. RNA intermediates in potato spindle tuber viroid replication
36. Detection of complementary RNA intermediates of viroid replication by Northern blot hybridization
37. Untersuchungen zum Replikationsmechanismus des Potato-Spindle-Tuber-Viroids (PSTV) an isolierten Zellkernen und Zellkernextrakten aus Solanum demissum
38. Chemical mapping of co-existing structures
39. Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure
40. Complementary oligonucleotide binding to the anticodon loop of fMet-transfer RNA
41. Probing dynamic changes in rRNA conformation in the 30S subunit of the Escherichia coli ribosome
42. Kinetics of an RNA conformational switch
43. Mutations at position 13 and/or 914 in Escherichia coli 16S ribosomal RNA interfere with the initiation of protein synthesis
44. Slow folding kinetics of RNase P RNA
45. Recognition and cleavage of hairpin structures in nucleic acids by oligodeoxynucleotides