Results 11 to 20 of about 692,533 (307)

Probing complex RNA structures by mechanical force [PDF]

European Physical Journal E 12 (2003) 605-615, 2003
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices.
A. Xayaphoummine, Allemand, Cluzel, Cocco, D. Chatenay, Essevaz-Roulet, Evers, Fersht, Fontana, Gerland, Gutell, H. Isambert, Isambert, J-F. Léger, J. Robert, Kellermayer, Liphardt, Lubensky, Léger, Mathews, Montanari, Nowotny, Onoa, Powers, Rief, Rief, Rief, S. Harlepp, Smith, Svoboda, T. Marchal, Treiber, Treiber, Wimberly, Woodson, Xayaphoummine, Yusupov   +36 more
arxiv   +5 more sources

Systematic identification of gene families for use as markers for phylogenetic and phylogeny- driven ecological studies of bacteria and archaea and their major subgroups [PDF]

, 2013
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses.
Eisen, Jonathan A., Jospin, Guillaume, Wu, Dongying   +2 more
core   +13 more sources

Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling

Frontiers in Cellular and Infection Microbiology, 2022
Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies.
Vitor Heidrich, Vitor Heidrich, Lilian T. Inoue, Paula F. Asprino, Fabiana Bettoni, Antonio C. H. Mariotti, Diogo A. Bastos, Denis L. F. Jardim, Marco A. Arap, Anamaria A. Camargo   +9 more
doaj   +1 more source

Mediating Ribosomal Competition by Splitting Pools [PDF]

LCSS Vol 5 Issue 5 (Nov 2020), 2020
Synthetic biology constructs often rely upon the introduction of "circuit" genes into host cells, in order to express novel proteins and thus endow the host with a desired behavior. The expression of these new genes "consumes" existing resources in the cell, such as ATP, RNA polymerase, amino acids, and ribosomes. Ribosomal competition among strands of
arxiv   +1 more source

Exclusion model of mRNA translation with collision-induced ribosome drop-off [PDF]

J. Phys. A: Math. Theor. 56 385601 (2023), 2023
The translation of messenger RNA transcripts to proteins is commonly modeled as a one-dimensional totally asymmetric exclusion process with extended particles. Here we focus on the effects of premature termination of translation through the irreversible detachment of ribosomes.
arxiv   +1 more source

Functional Modification of 16S Ribosomal RNA by Kethoxal [PDF]

Proceedings of the National Academy of Sciences, 1972
Kethoxal reacts with 30S ribosomal subunits to give totally inactive particles, as measured by in vitro protein synthesis. It is postulated that functional modification occurs at the binding site for transfer RNA since ( a ) loss of specific binding of transfer RNA, but not binding of ...
Jonathan B. Chaires, Harry F. Noller
openaire   +3 more sources

Role of 16‐S RNA in Ribosome Messenger Recognition [PDF]

European Journal of Biochemistry, 1980
The deoxyoctanucleotide (5′‐3′)d(A‐A‐G‐G‐A‐G‐G‐T), which is complementary to the 3′ end of 16‐S RNA, inhibits the formation of the complex between the 30‐S subunit and MS2 RNA described in the preceding paper. If the complex is preformed, the octanucleotide cannot prevent entry of the complex into the ribosome cycle upon supplementation with the ...
Jan van Duin, Gijs A. van der Marel, Gerrit P. Overbeek, G. H. Veeneman, Jacques H. van Boom, Claude Backendorf   +5 more
openaire   +3 more sources

A model for the study of ligand binding to the ribosomal RNA helix h44. [PDF]

, 2010
Oligonucleotide models of ribosomal RNA domains are powerful tools to study the binding and molecular recognition of antibiotics that interfere with bacterial translation.
Dibrov, Sergey M, Hermann, Thomas, Parsons, Jerod   +2 more
core   +3 more sources

Recognition of Ribosomal RNA Sites in DNA, I. Analysis of the E. coli System [PDF]

, 1965
The evidence recently presented of specific hybridization between bacterial ribosomal RNA and homologous DNA1-3 has indicated the possibility of a biochemical approach to the problem of the identification of ribosomal RNA sites in DNA.
Attardi, Giuseppe, Huang, Pien Chien, Kabat, Susan   +2 more
core   +1 more source

Ribosomal Protein S12 Hastens Nucleation of Co-Transcriptional Ribosome Assembly

Biomolecules, 2023
Ribosomal subunits begin assembly during transcription of the ribosomal RNA (rRNA), when the rRNA begins to fold and associate with ribosomal proteins (RPs). In bacteria, the first steps of ribosome assembly depend upon recognition of the properly folded
Margaret L. Rodgers, Yunsheng Sun, Sarah A. Woodson   +2 more
doaj   +1 more source