Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group

1999 ◽  
Vol 121 (23) ◽  
pp. 5364-5372 ◽  
Author(s):  
Yingfu Li ◽  
Ronald R. Breaker
Keyword(s):  
Rna Degradation ◽  
Base Catalysis ◽  
Hydroxyl Group ◽  
Kinetics Of

Kinetics of cyclization of S-ethoxycarbonylmethylisothiouronium chloride to 2-imino-4-thiazolidone

1979 ◽  
Vol 44 (3) ◽  
pp. 912-917 ◽  
Author(s):  
Vladimír Macháček ◽  
Said A. El-bahai ◽  
Vojeslav Štěrba
Keyword(s):  
Hydrochloric Acid ◽  
Dilute Hydrochloric Acid ◽  
Base Catalysis ◽  
General Base ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Kinetics Of Formation ◽  
Acid Catalyzed ◽  
Rate Limiting ◽  
Kinetics Of

Kinetics of formation of 2-imino-4-thiazolidone from S-ethoxycarbonylmethylisothiouronium chloride has been studied in aqueous buffers and dilute hydrochloric acid. The reaction is subject to general base catalysis, the β value being 0.65. Its rate limiting step consists in acid-catalyzed splitting off of ethoxide ion from dipolar tetrahedral intermediate. At pH < 2 formation of this intermediate becomes rate-limiting; rate constant of its formation is 2 . 104 s-1.

Evidence for general base catalysis by protic solvents in a kinetic study of alcoholyses and hydrolyses of 1-(phenoxycarbonyl)pyridinium ions under both solvolytic and non-solvolytic conditions

2009 ◽  
Vol 74 (1) ◽  
pp. 43-55 ◽  
Author(s):  
Dennis N. Kevill ◽  
Byoung-Chun Park ◽  
Jin Burm Kyong
Keyword(s):  
Second Order ◽  
Base Catalysis ◽  
Substitution Reactions ◽  
Third Order ◽  
Methoxy Derivative ◽  
First Order ◽  
General Base ◽  
Protic Solvents ◽  
Kinetics Of ◽  
Pyridinium Ions

The kinetics of nucleophilic substitution reactions of 1-(phenoxycarbonyl)pyridinium ions, prepared with the essentially non-nucleophilic/non-basic fluoroborate as the counterion, have been studied using up to 1.60 M methanol in acetonitrile as solvent and under solvolytic conditions in 2,2,2-trifluoroethan-1-ol (TFE) and its mixtures with water. Under the non- solvolytic conditions, the parent and three pyridine-ring-substituted derivatives were studied. Both second-order (first-order in methanol) and third-order (second-order in methanol) kinetic contributions were observed. In the solvolysis studies, since solvent ionizing power values were almost constant over the range of aqueous TFE studied, a Grunwald–Winstein equation treatment of the specific rates of solvolysis for the parent and the 4-methoxy derivative could be carried out in terms of variations in solvent nucleophilicity, and an appreciable sensitivity to changes in solvent nucleophilicity was found.

c-myc RNA degradation in growing and differentiating cells: possible alternate pathways

1989 ◽  
Vol 9 (1) ◽  
pp. 288-295
Author(s):  
S G Swartwout ◽  
A J Kinniburgh
Keyword(s):  
Actinomycin D ◽  
Rna Degradation ◽  
Transcriptional Elongation ◽  
Rna Turnover ◽  
Rapid Degradation ◽  
Polyadenylated Rna ◽  
Myc Gene ◽  
Fail Safe ◽  
Kinetics Of ◽  
In Cells

Transcripts of the proto-oncogene c-myc are composed of a rapidly degraded polyadenylated RNA species and an apparently much more stable, nonadenylated RNA species. In this report, the extended kinetics of c-myc RNA turnover have been examined in rapidly growing cells and in cells induced to differentiate. When transcription was blocked with actinomycin D in rapidly growing cells, poly(A)+ c-myc was rapidly degraded (t1/2 = 12 min). c-myc RNA lacking poly(A) initially remained at or near control levels; however, after 80 to 90 min it was degraded with kinetics similar to those of poly(A)+ c-myc RNA. These bizarre kinetics are due to the deadenylation of poly(A)+ c-myc RNA to form poly(A)- c-myc, thereby initially maintaining the poly(A)- c-myc RNA pool when transcription is blocked. In contrast to growing cells, cells induced to differentiate degraded both poly(A)+ and poly(A)- c-myc RNA rapidly. The rapid disappearance of both RNA species in differentiating cells suggests that a large proportion of the poly(A)+ c-myc RNA was directly degraded without first being converted to poly(A)- c-myc RNA. Others have shown that transcriptional elongation of the c-myc gene is rapidly blocked in differentiating cells. We therefore hypothesize that in differentiating cells a direct, rapid degradation of poly(A)+ c-myc RNA may act as a backup or fail-safe system to ensure that c-myc protein is not synthesized. This tandem system of c-myc turnoff may also make cells more refractory to mutations which activate constitutive c-myc expression.

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.

Stress–response relationships related to ageing and death of orthodox seeds: a study comparing viability and RNA integrity in soya bean (Glycine max) cv. Williams 82

2020 ◽  
Vol 30 (2) ◽  
pp. 161-172
Author(s):  
Christina Walters ◽  
Margaret B. Fleming ◽  
Lisa M. Hill ◽  
Emma J. Dorr ◽  
Christopher M. Richards
Keyword(s):  
Degradation Kinetics ◽  
Rna Degradation ◽  
Soya Bean ◽  
Rna Integrity ◽  
Viability Loss ◽  
Rna Integrity Number ◽  
Oxidative Stresses ◽  
Degradation Rates ◽  
Highly Correlated ◽  
Kinetics Of

AbstractCharacterizing non-lethal damage within dry seeds may allow us to detect early signs of ageing and accurately predict longevity. We compared RNA degradation and viability loss in seeds exposed to stressful conditions to quantify relationships between degradation rates and stress intensity or duration. We subjected recently harvested (‘fresh’) ‘Williams 82’ soya bean seeds to moisture, temperature and oxidative stresses, and measured time to 50% viability (P50) and rate of RNA degradation, the former using standard germination assays and the latter using RNA Integrity Number (RIN). RIN values from fresh seeds were also compared with those from accessions of the same cultivar harvested in the 1980s and 1990s and stored in the refrigerator (5°C), freezer (−18°C) or in vapour above liquid nitrogen (−176°C). Rates of viability loss (P50−1) and RNA degradation (RIN⋅d−1) were highly correlated in soya bean seeds that were exposed to a broad range of temperatures [holding relative humidity (RH) constant at about 30%]. However, the correlation weakened when fresh seeds were maintained at high RH (holding temperature constant at 35°C) or exposed to oxidizing agents. Both P50−1 and RIN⋅d−1 parameters exhibited breaks in Arrhenius behaviour near 50°C, suggesting that constrained molecular mobility regulates degradation kinetics of dry systems. We conclude that the kinetics of ageing reactions at RH near 30% can be simulated by temperatures up to 50°C and that RNA degradation can indicate ageing prior to and independent of seed death.

Kinetics and Activation Parameters for the Alkaline Aqueous Rearrangement of Trichorfon [O,O-Dimethyl-(2,2,2-Trichloro-1-Hydroxyethyl) Phosphonate] to Dichlorvos [O,O-Dimethyl-O-(2,2-Dichloroethenyl)Phosphate]

2001 ◽  
Vol 36 (3) ◽  
pp. 589-604 ◽  
Author(s):  
Julian M. Dust ◽  
Christopher S. Warren
Keyword(s):  
Activation Energy ◽  
High Pressure ◽  
Activation Parameters ◽  
Base Catalysis ◽  
Rearrangement Product ◽  
Exponential Factor ◽  
First Order ◽  
Pseudo First Order ◽  
Order Plot ◽  
Kinetics Of

Abstract The kinetics of the alkaline rearrangement of O,O-dimethyl-(2,2,2-trichloro-1- hydroxyethyl)phosphonate, (trichlorfon, 1), the active insecticidal component in such formulations as Dylox, was followed at 25±0.5°C by high pressure liquid chromatography (UV-vis detector, 210 nm). The rearrangement product, O,Odimethyl- O-(2,2-dichloroethenyl)phosphate (dichlorovos, 2), which is a more potent biocide than trichlorfon, undergoes further reaction, and the kinetics, consequently, cannot be treated by a standard pseudo-first-order plot. A two-point van't Hoff (initial rates) method was used to obtain pseudo-first-order rate constants (kѱ) at 25, 35 and 45°C: 2.6 × 10-6, 7.4 × 10-6 and 2.5 × 10-5 s-1, respectively. Arrhenius treatment of this data gave an activation energy (Ea) of 88 kJ·mol-1 with a pre-exponential factor (A) of 5.5 × 109 s-1. Kinetic trials at pH 8.0 using phosphate and tris buffer systems show no buffer catalysis in this reaction and indicate that the rearrangement is subject to specific base catalysis. Estimates are reported for pseudo-first-order half-lives for trichlorfon at pH 8.0 for environmental conditions in aqueous systems in the Corner Brook region of western Newfoundland, part of the site of a recent trichlorfon aerial spray program.

scholarly journals Toxins from TA system of Helicobacter pylori and insight into mRNase activity

2014 ◽  
Vol 70 (a1) ◽  
pp. C828-C828
Author(s):  
Chinar Pathak ◽  
Hookang Im ◽  
Sun-bok Jang ◽  
Yeon-Jin Yang ◽  
Hye-Jin Yoon ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Active Site ◽  
Isothermal Calorimetry ◽  
Rna Degradation ◽  
Base Catalysis ◽  
Homology Search ◽  
Specific Sequence ◽  
General Base ◽  
Sequence Recognition ◽  
Calorimetric Studies

The toxin-antitoxin (TA) systems widely spread among bacteria and archaea are important for antibiotic resistance and virulence. The bacterial kingdom uses TA systems to adjust the global level of gene expression and translation through RNA degradation. The HP0892-HP0893 and HP0894-HP0895 toxin-antitoxin systems are the only two known TA systems belonging to Helicobacter pylori. In both of these TA systems, the antitoxin binds and inhibits the toxin and regulates the transcription of the TA operon. However, the precise molecular basis for interaction with substrate or antitoxin and the mechanism of mRNA cleavage remains unclear. Therefore, here an attempt was made to shed some light on the mechanism behind the TA system of HP0892-HP0893 and HP0894-HP0895. Here, we present the crystal structures of apo- and copper-bound HP0894 at 1.28 Å and 1.89 Å, respectively, and the crystal structure of the zinc-bound HP0892 toxin at 1.8 Å resolution. Reorientation of residues involving the mRNase active site was shown. Through the combined approach of structural analysis along with isothermal calorimetry studies and structural homology search, the amino acids involved in mRNase active site were monitored. In the mRNase active site of HP0894 toxin, His84 acts as a catalytic residue and reorients itself acting as a general acid in an acid-base catalysis reaction, while His47 and His60 stabilize the transition state. Glu58 acts as a general base, and substrate reorientation is caused by Phe88. In the mRNase active site of HP0892 toxin, the most catalytically important residue, His86, reorients itself to exhibit RNase activity while Glu58 acts as a general base. His47 and His60 are considered to be involved in enzymatic activity. Glu58 and Asp64 are involved in substrate binding and specific sequence recognition. The mutational constructs were used for isothermal calorimetric studies to analyze the effect of catalytic residues.

Kinetics and mechanism of the bromination of phenols in aqueous solution. Evidence of general base catalysis of bromine attack

1990 ◽  
Vol 68 (10) ◽  
pp. 1769-1773 ◽  
Author(s):  
Oswald S. Tee ◽  
N. Rani Iyengar
Keyword(s):  
Aqueous Solution ◽  
Kinetics And Mechanism ◽  
Base Catalysis ◽  
Hydroxyl Group ◽  
Molecular Bromine ◽  
Electrophilic Attack ◽  
General Base ◽  
Carboxylate Anions

The reactions of bromine with phenol, 4-bromophenol, and 4-methylphenol (p-cresol) in aqueous solution are catalyzed by carboxylate anions, confirming the suggestions of earlier work. The results are consistent with deprotonation of the phenol hydroxyl group by a general base occurring at more or less the same time as electrophilic attack by molecular bromine. Possible origins of the general base catalysis are discussed. Combined with earlier results, the present findings suggest that a protonated cyclohexadienone is not a mandatory intermediate in phenol bromination; it can be avoided in both the formation of and enolization of the cyclohexadienone intermediate by general catalysis. Keywords: bromination, phenol, mechanism, catalysis, kinetics.

Kinetics of the reaction of guanyl-O-methylisourea hydrochloride with dimethylformamide dimethylacetal

1986 ◽  
Vol 51 (9) ◽  
pp. 1964-1971
Author(s):  
Jaromír Kaválek ◽  
Josef Panchartek ◽  
Tomáš Potěšil ◽  
Vojeslav Štěrba
Keyword(s):  
Absorption Maximum ◽  
Base Catalysis ◽  
Dimethylformamide Dimethylacetal ◽  
Catalysis Mechanism ◽  
Kinetics Of

The reaction of guanyl-O-methylisourea hydrochloride (IV) with dimethylformamide (V) proceeds in two steps. The first step consists in the reaction of the imidoester with the imidatonium ion formed in a fast pre-equilibrium to give a conjugated system with the absorption maximum at 278 nm. The subsequent slower step consists in the cyclization to 2-amino-4-methoxy-1,3,5-triazine (VI). The rate of the first step is directly proportional to the concentrations of both hydrochloride IV and acetal V. Both the steps involve base catalysis. Mechanism of the whole reaction is suggested on the basis of the kinetic results.

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