Results 11 to 20 of about 6,175 (141)

The global structure of the VS ribozyme. [PDF]

EMBO J, 2002
The VS ribozyme comprises five helical segments (II-VI) in a formal H shape, organized by two three-way junctions. It interacts with its stem-loop substrate (I) by tertiary interactions. We have determined the global shape of the 3-4-5 junction (relating helices III-V) by electrophoresis and FRET. Estimation of the dihedral angle between helices II and
Lafontaine DA, Norman DG, Lilley DM.
europepmc   +6 more sources

The complete VS ribozyme in solution studied by small-angle X-ray scattering. [PDF]

Structure, 2008
We have used small-angle X-ray solution scattering to obtain ab initio shape reconstructions of the complete VS ribozyme. The ribozyme occupies an electron density envelope with an irregular shape, into which helical sections have been fitted. The ribozyme is built around a core comprising a near-coaxial stack of three helices, organized by two three ...
Lipfert J, Ouellet J, Norman DG, Doniach S, Lilley DM.   +4 more
europepmc   +6 more sources

NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions. [PDF]

Biochemistry, 2014
Metal cations represent key elements of RNA structure and function. In the Neurospora VS ribozyme, metal cations play diverse roles; they are important for substrate recognition, formation of the active site, and shifting the pKa's of two key nucleobases that contribute to the general acid-base mechanism.
Bonneau E, Legault P.
europepmc   +4 more sources

The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure. [PDF]

RNA, 2015
As part of an effort to structurally characterize the complete Neurospora VS ribozyme, NMR solution structures of several subdomains have been previously determined, including the internal loops of domains I and VI, the I/V kissing-loop interaction and the III–IV–V junction.
Bonneau E, Girard N, Lemieux S, Legault P.   +3 more
europepmc   +5 more sources

Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. [PDF]

J Mol Biol, 2008
Non-coding RNAs of complex tertiary structure are involved in numerous aspects of the replication and processing of genetic information in many organisms; however, an understanding of the complex relationship between their structural dynamics and function is only slowly emerging.
Pereira MJ, Nikolova EN, Hiley SL, Jaikaran D, Collins RA, Walter NG.   +5 more
europepmc   +5 more sources

Enhancement of Neurospora VS ribozyme cleavage by tuberactinomycin antibiotics. [PDF]

The EMBO Journal, 1995
Several examples of inhibition of the function of a ribozyme or RNA-protein complex have shown that certain antibiotics can interact specifically with RNA. There are, however, few examples of antibiotics that have a positive, rather than a negative, effect on the function of an RNA.
D M De Abreu, Anthony Mittermaier, J E Olive, Richard A. Collins, A A Andersen, T Rastogi, T L Beattie   +6 more
openaire   +2 more sources

RNA-Puzzles Round IV:3D structure predictions of four ribozymes and two aptamers [PDF]

, 2020
International audienceRNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of ...
Adamiak, Ryszard W., Antczak, Maciej, Batey, Robert T., Boniecki, Michal J., Bujnicki, Janusz M., Chen, Shi-Jie, Cheng, Clarence Yu, Cheng, Yi, Chou, Fang-Chieh, Das, Rhiju, Ding, Feng, Dokholyan, Nikolay V., Geniesse, Caleb, Golden, Barbara L., Huang, Lin, Jiang, Yangwei, Joshi, Astha, Krokhotin, Andrey, Lilley, David M., Liu, Yijin, Magnus, Marcin, Mailhot, Olivier, Major, Francois, Mann, Thomas H., Miao, Zhichao, Patel, Dinshaw J., Piatkowski, Pawel, Pluta, Radoslaw, Popenda, Mariusz, Ren, Aiming, Sarzynska, Joanna, Sun, Lizhen, Szachniuk, Marta, Tian, Siqi, Wang, Jian, Wang, Jun, Watkins, Andrew M., Westhof, Eric, Wiedemann, Jakub, Xiao, Yi, Xu, Xiaojun, Yesselman, Joseph D., Zhang, Dong, Zhang, Yi, Zhang, Zhenzhen, Zhao, Chenhan, Zhao, Peinan, Zhou, Yuanzhe, Zok, Tomasz, Zyla, Adriana   +49 more
core   +3 more sources

The contribution of 2'-hydroxyls to the cleavage activity of the Neurospora VS ribozyme [PDF]

Nucleic Acids Research, 2002
We have used nucleotide analog interference mapping and site-specific substitution to determine the effect of 2'-deoxynucleotide substitution of each nucleotide in the VS ribozyme on the self-cleavage reaction. A large number of 2'-hydroxyls (2'-OHs) that contribute to cleavage activity of the VS ribozyme were found distributed throughout the core of ...
Richard A. Collins, Soraya Yekta, Vanita D. Sood   +2 more
openaire   +3 more sources

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone [PDF]

Chemistry & Biology, 1998
The catalytic activity of RNA enzymes is thought to require divalent metal ions, which are believed to facilitate RNA folding and to play a direct chemical role in the reaction.We have found that the hammerhead, hairpin and VS ribozymes do not require divalent metal ions, their mimics such as [Co(NH3)6]3+, or even monovalent metal ions for efficient ...
Murray, James B, Seyhan, Attila A, Walter, Nils G, Burke, John M, Scott, William G   +4 more
openaire   +4 more sources

Rearrangement of a Stable RNA Secondary Structure during VS Ribozyme Catalysis [PDF]

Molecular Cell, 2000
The Neurospora VS ribozyme recognizes and cleaves a substrate RNA that contains a GC-rich stem loop. In contrast to most RNA secondary structures that are stable during tertiary or quaternary folding, this substrate undergoes extensive ribozyme-induced rearrangement in the presence of magnesium in which the base pairings of at least seven of the ten ...
Angela A. Andersen, Richard A. Collins
openaire   +3 more sources