scholarly journals Ribozymes of the hepatitis delta virus: recent findings on their structure, mechanism of catalysis and possible applications.

2001 ◽  
Vol 48 (2) ◽  
pp. 409-418 ◽  
Author(s):  
J Ciesiolka ◽  
J Wrzesinski ◽  
M Legiewicz ◽  
B Smólska ◽  
M Dutkiewicz
Keyword(s):  
Hepatitis Delta Virus ◽  
Catalytic Properties ◽  
Rna Degradation ◽  
Base Catalysis ◽  
Rna Catalysis ◽  
X Ray ◽  
Rna Molecules ◽  
Mechanism Of Catalysis ◽  
Made In ◽  
Delta Virus

Although the delta ribozymes have been studied for more than ten years the most important information concerning their structure and mechanism of catalysis were only obtained very recently. The crystal structure of the genomic delta ribozyme turns out to be an excellent example of the extraordinary properties of RNA molecules to fold into uniquely compact structures. Details of the X-ray structure have greatly stimulated further studies on the folding of the ribozymes into functionally active molecules as well as on the mechanism of RNA catalysis. The ability of the delta ribozymes to carry out general acid-base catalysis by nucleotide side chains has been assumed in two proposed mechanisms of self-cleavage. Recently, considerable progress has been also made in characterizing the catalytic properties of trans-acting ribozyme variants that are potentially attractive tools in the strategy of directed RNA degradation.

Linkage between proton binding and folding in RNA: implications for RNA catalysis

2005 ◽  
Vol 33 (3) ◽  
pp. 466-470 ◽  
Author(s):  
P.C. Bevilacqua ◽  
T.S. Brown ◽  
D. Chadalavada ◽  
J. Lecomte ◽  
E. Moody ◽  
...  
Keyword(s):  
Hepatitis Delta Virus ◽  
Bond Cleavage ◽  
Rna Catalysis ◽  
Hepatitis Delta ◽  
Phosphodiester Bond ◽  
General Acid ◽  
Leaving Group ◽  
Context Specific ◽  
Do So ◽  
Delta Virus

Small ribozymes use their nucleobases to catalyse phosphodiester bond cleavage. The hepatitis delta virus ribozyme employs C75 as a general acid to protonate the 5′-bridging oxygen leaving group, and to accomplish this task efficiently, it shifts its pKa towards neutrality. Simulations and thermodynamic experiments implicate linkage between folding and protonation in nucleobase pKa shifting. Even small oligonucleotides are shown to fold in a highly co-operative manner, although they do so in a context-specific fashion. Linkage between protonation and co-operativity of folding may drive pKa shifting and provide for enhanced function in RNA.

RNA conformational requirements of self-cleavage of hepatitis delta virus RNA

1990 ◽  
Vol 10 (10) ◽  
pp. 5575-5579
Author(s):  
H N Wu ◽  
M M Lai
Keyword(s):  
Hepatitis Delta Virus ◽  
High Efficiency ◽  
Catalytic Rna ◽  
Heat Denaturation ◽  
Active Conformation ◽  
Hepatitis Delta ◽  
Rna Molecules ◽  
Virus Rna ◽  
Delta Virus

Hepatitis delta virus (HDV) RNA subfragments undergo self-cleavage at varying efficiencies. We have developed a procedure of using repeated cycles of heat denaturation and renaturation of RNA to achieve a high efficiency of cleavage. This effect can also be achieved by gradual denaturation of RNA with heat or formamide. These results suggest that only a subpopulation of the catalytic RNA molecules assumes the active conformation required for self-cleavage. This procedure could be of general use for detecting catalytic RNA activities.

scholarly journals Mechanisms of RNA catalysis

2011 ◽  
Vol 366 (1580) ◽  
pp. 2910-2917 ◽  
Author(s):  
David M. J. Lilley
Keyword(s):  
Distinct Species ◽  
Base Catalysis ◽  
Nucleophilic Attack ◽  
Phosphoryl Transfer ◽  
Rna Catalysis ◽  
Rna Molecules ◽  
General Base ◽  
General Acid ◽  
Guanine And Adenine ◽  
Self Splicing

Ribozymes are RNA molecules that act as chemical catalysts. In contemporary cells, most known ribozymes carry out phosphoryl transfer reactions. The nucleolytic ribozymes comprise a class of five structurally-distinct species that bring about site-specific cleavage by nucleophilic attack of the 2′-O on the adjacent 3′-P to form a cyclic 2′,3′-phosphate. In general, they will also catalyse the reverse reaction. As a class, all these ribozymes appear to use general acid–base catalysis to accelerate these reactions by about a million-fold. In the Varkud satellite ribozyme, we have shown that the cleavage reaction is catalysed by guanine and adenine nucleobases acting as general base and acid, respectively. The hairpin ribozyme most probably uses a closely similar mechanism. Guanine nucleobases appear to be a common choice of general base, but the general acid is more variable. By contrast, the larger ribozymes such as the self-splicing introns and RNase P act as metalloenzymes.

scholarly journals Impact of Methods on the Measurement of mRNA Turnover

2017 ◽  
Author(s):  
Takeo Wada ◽  
Attila Becskei
Keyword(s):  
Mrna Stability ◽  
Rna Degradation ◽  
Mrna Turnover ◽  
Gene Control ◽  
Cellular Activity ◽  
Transcription Inhibition ◽  
Rna Molecules ◽  
Metabolic Labelling ◽  
Differential Stability ◽  
Made In

The turnover of the RNA molecules is determined by the rates of transcription and RNA degradation. Several methods have been developed to study mRNA turnover since the beginnings of molecular biology. Here we summarize the main methods to measure RNA half-life: transcription inhibition, gene control and metabolic labelling. These methods were used to detect the cellular activity of the mRNAs degradation machinery, including the exo-ribonuclease Xrn1 and the exosome. Less progress has been made in the study of the differential stability of mature RNAs because the different methods have often yielded inconsistent results so that an mRNA considered to be stable can be classified as unstable by another method. Recent advances in the systematic comparison of different method variants in yeast have permitted the identification of the least invasive methodologies that reflect half-lives the most faithfully, which is expected to open the way for a consistent quantitative analysis of the determinants of mRNA stability.

scholarly journals General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility

2008 ◽  
Vol 112 (35) ◽  
pp. 11177-11187 ◽  
Author(s):  
Pavel Banáš ◽  
Lubomír Rulíšek ◽  
Veronika Hánošová ◽  
Daniel Svozil ◽  
Nils G. Walter ◽  
...  
Keyword(s):  
Active Site ◽  
Hepatitis Delta Virus ◽  
Base Catalysis ◽  
Hepatitis Delta ◽  
General Base ◽  
Hepatitis Delta Virus Ribozyme ◽  
Delta Virus

scholarly journals Properties of Subviral Particles of Hepatitis B Virus

2008 ◽  
Vol 82 (16) ◽  
pp. 7812-7817 ◽  
Author(s):  
Ning Chai ◽  
Ho Eun Chang ◽  
Emmanuelle Nicolas ◽  
Ziying Han ◽  
Michal Jarnik ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Hepatitis Delta Virus ◽  
Envelope Proteins ◽  
Infectious Particle ◽  
B Virus ◽  
Made In ◽  
Delta Virus ◽  
Bind Cell Surface ◽  
Subviral Particles

ABSTRACT In the sera of patients infected with hepatitis B virus (HBV), in addition to infectious particles, there is an excess (typically 1,000- to 100,000-fold) of empty subviral particles (SVP) composed solely of HBV envelope proteins in the form of relatively smaller spheres and filaments of variable length. Hepatitis delta virus (HDV) assembly also uses the envelope proteins of HBV to produce an infectious particle. Rate-zonal sedimentation was used to study the particles released from liver cell lines that produced SVP only, HDV plus SVP, and HBV plus SVP. The SVP made in the absence of HBV or HDV were further examined by electron microscopy. They bound efficiently to heparin columns, consistent with an ability to bind cell surface glycosaminoglycans. However, unlike soluble forms of HBV envelope protein that were potent inhibitors, the SVP did not inhibit the ability of HBV and HDV to infect primary human hepatocytes.

scholarly journals RNA conformational requirements of self-cleavage of hepatitis delta virus RNA.

1990 ◽  
Vol 10 (10) ◽  
pp. 5575-5579 ◽  
Author(s):  
H N Wu ◽  
M M Lai
Keyword(s):  
Hepatitis Delta Virus ◽  
High Efficiency ◽  
Catalytic Rna ◽  
Heat Denaturation ◽  
Active Conformation ◽  
Hepatitis Delta ◽  
Rna Molecules ◽  
Virus Rna ◽  
Delta Virus

Hepatitis delta virus (HDV) RNA subfragments undergo self-cleavage at varying efficiencies. We have developed a procedure of using repeated cycles of heat denaturation and renaturation of RNA to achieve a high efficiency of cleavage. This effect can also be achieved by gradual denaturation of RNA with heat or formamide. These results suggest that only a subpopulation of the catalytic RNA molecules assumes the active conformation required for self-cleavage. This procedure could be of general use for detecting catalytic RNA activities.

Microanalysis of precipitates in a ferritic steel

1978 ◽  
Vol 36 (1) ◽  
pp. 618-619
Author(s):  
J.M. Titchmarsh
Keyword(s):  
Ferritic Steel ◽  
Particle Identification ◽  
Energy Dispersive ◽  
Objective Lens ◽  
Ferritic Steels ◽  
Replica Technique ◽  
X Ray ◽  
Large Numbers ◽  
Scanning Transmission ◽  
Made In

The advances in recent years in the microanalytical capabilities of conventional TEM's fitted with probe forming lenses allow much more detailed investigations to be made of the microstructures of complex alloys, such as ferritic steels, than have been possible previously. In particular, the identification of individual precipitate particles with dimensions of a few tens of nanometers in alloys containing high densities of several chemically and crystallographically different precipitate types is feasible. The aim of the investigation described in this paper was to establish a method which allowed individual particle identification to be made in a few seconds so that large numbers of particles could be examined in a few hours.A Philips EM400 microscope, fitted with the scanning transmission (STEM) objective lens pole-pieces and an EDAX energy dispersive X-ray analyser, was used at 120 kV with a thermal W hairpin filament. The precipitates examined were extracted using a standard C replica technique from specimens of a 2¼Cr-lMo ferritic steel in a quenched and tempered condition.

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