Difference between revisions of "Stusti 2018"
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== Riboswitch modeling: Mark Sinzger == | == Riboswitch modeling: Mark Sinzger == | ||
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== Protein- or tRNA-controlled RNA switches == | == Protein- or tRNA-controlled RNA switches == | ||
Revision as of 09:50, 16 July 2018
Contents
- 1 Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas
- 1.1 What makes RNA such a special molecule – specific chemical and structural features of RNA
- 1.2 RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair
- 1.3 Ribozymes (catalytically active RNAs) (Intro)
- 1.4 The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology
- 1.5 The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity
- 1.6 Protein independent ribozymes – about Hammerhead, Varkud satellite, hairpin ribozyme & Co
- 1.7 RNA-based second messengers
- 1.8 Riboregulation and virulence, targeting by antibiotics
- 1.9 Riboswitches
- 1.10 Riboswitch modeling: Mark Sinzger
- 1.11 Protein- or tRNA-controlled RNA switches
- 1.12 RNA thermometers
- 1.13 The RNA world and evolution
- 1.14 RNA modification
- 1.15 RNA degradation/processing
- 1.16 Regulation by non-coding RNA
- 1.17 RNA dependent DNA Polymerases - from telomerase to retroviruses
- 1.18 RNA dependent RNA Polymerases – the RNA replicase
- 1.19 CRISPR/Cas: Science – the bacterial “immune” system
- 1.20 CRISPR/Cas: Application and groundbreaking perspectives
- 1.21 The mysterious function and role of 6S-RNA and pRNA in bacteria
- 1.22 Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer
- 1.23 Outlook: Finding function in mystery transcripts – eRNAs, long-non coding (lncRNA) and circular RNA (circRNA)
- 1.24 Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways
Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas
What makes RNA such a special molecule – specific chemical and structural features of RNA
David A Hiller, Scott A Strobel
The chemical versatility of RNA.
Philos Trans R Soc Lond B Biol Sci: 2011, 366(1580);2929-35
[PubMed:21930584]
[WorldCat.org]
[DOI]
(I p)
RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair
Ribozymes (catalytically active RNAs) (Intro)
The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology
Meredith Root-Bernstein, Robert Root-Bernstein
The ribosome as a missing link in the evolution of life.
J Theor Biol: 2015, 367;130-158
[PubMed:25500179]
[WorldCat.org]
[DOI]
(I p)
Ingo Wohlgemuth, Corinna Pohl, Joerg Mittelstaet, Andrey L Konevega, Marina V Rodnina
Evolutionary optimization of speed and accuracy of decoding on the ribosome.
Philos Trans R Soc Lond B Biol Sci: 2011, 366(1580);2979-86
[PubMed:21930591]
[WorldCat.org]
[DOI]
(I p)
Thomas A Steitz
A structural understanding of the dynamic ribosome machine.
Nat Rev Mol Cell Biol: 2008, 9(3);242-53
[PubMed:18292779]
[WorldCat.org]
[DOI]
(I p)
The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity
Protein independent ribozymes – about Hammerhead, Varkud satellite, hairpin ribozyme & Co
RNA-based second messengers
Riboregulation and virulence, targeting by antibiotics
Riboswitches
Riboswitch modeling: Mark Sinzger
Christopher Schneider, Leo Bronstein, Jascha Diemer, Heinz Koeppl, Beatrix Suess
ROC'n'Ribo: Characterizing a Riboswitching Expression System by Modeling Single-Cell Data.
ACS Synth Biol: 2017, 6(7);1211-1224
[PubMed:28591515]
[WorldCat.org]
[DOI]
(I p)
Marco Barsacchi, Eva Maria Novoa, Manolis Kellis, Alessio Bechini
SwiSpot: modeling riboswitches by spotting out switching sequences.
Bioinformatics: 2016, 32(21);3252-3259
[PubMed:27378291]
[WorldCat.org]
[DOI]
(I p)
Chase L Beisel, Christina D Smolke
Design principles for riboswitch function.
PLoS Comput Biol: 2009, 5(4);e1000363
[PubMed:19381267]
[WorldCat.org]
[DOI]
(I p)
Protein- or tRNA-controlled RNA switches
RNA thermometers
Johanna Roßmanith, Franz Narberhaus
Exploring the modular nature of riboswitches and RNA thermometers.
Nucleic Acids Res: 2016, 44(11);5410-23
[PubMed:27060146]
[WorldCat.org]
[DOI]
(I p)
Satya Narayan, Mamta H Kombrabail, Sudipta Das, Himanshu Singh, Kandala V R Chary, Basuthkar J Rao, Guruswamy Krishnamoorthy
Site-specific fluorescence dynamics in an RNA 'thermometer' reveals the role of ribosome binding in its temperature-sensitive switch function.
Nucleic Acids Res: 2015, 43(1);493-503
[PubMed:25477380]
[WorldCat.org]
[DOI]
(I p)
The RNA world and evolution
RNA modification
RNA degradation/processing
Regulation by non-coding RNA
RNA dependent DNA Polymerases - from telomerase to retroviruses
RNA dependent RNA Polymerases – the RNA replicase
CRISPR/Cas: Science – the bacterial “immune” system
CRISPR/Cas: Application and groundbreaking perspectives
The mysterious function and role of 6S-RNA and pRNA in bacteria
Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer
Outlook: Finding function in mystery transcripts – eRNAs, long-non coding (lncRNA) and circular RNA (circRNA)
Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways
