A possible mechanism responsible for the correction of transcription errors

Volloch, Vladimir; Rits, Sophia; Tumerman, L.A.

doi:10.1093/nar/6.4.1535

Cited by 16 publications

(15 citation statements)

References 24 publications

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“…Volloch et al (1979) reported that, under reaction conditions comparable to those used in our study, CTP and UTP were attacked only slightly; we find GTP to be attacked at about one-tenth the rate of ATP. Thus, it appears that ATP is the nucleotide triphosphate principally attacked by the NTPase.…”

Section: Discussionsupporting

confidence: 70%

Specificity of an Escherichia coli RNA Polymerase-Associated NTPase

et al. 1997

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Standard preparations of Escherichia coli RNA polymerase harbor a 70 kDa protein with NTPase (beta-gamma cleavage) activity that is not a recognized polymerase subunit. The NTPase activity of this component, before and after separation from the polymerase, is strongly dependent on the presence of DNA; single-stranded polydeoxynucleotides are more effective than double-stranded. ATP and GTP are cleaved, the latter much less readily. The NTPase as it occurs with the polymerase displays cleavage preference for NTPs that are not complementary to the DNA, a fact that has led to proposals for involvement of the NTPase in transcriptional error prevention [Volloch, V. Z., Rits, L. & Tumerman, L. (1979) Nucleic Acids Res. 6, 1535-1546; Libby, R. T., Nelson, J. L., Calvo, J. M., & Gallant, J. A. (1989) EMBO J. 8, 3253-3158]. We find, however, that the lesser cleavage in the presence of complementary DNA results from competition for the NTP between the processes of incorporation by the polymerase and of cleavage by the NTPase, operating on the same substrate pool. The greater cleavage with noncomplementary DNA occurs because of the lack of incorporation by the polymerase, which then does not compete with the NTPase for the substrate pool. Thus, these findings indicate that the cleavage preference of the NTPase for noncomplementary NTPs is not part of a mechanism for error prevention during transcription.

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Section: Discussionsupporting

confidence: 70%

Specificity of an Escherichia coli RNA Polymerase-Associated NTPase

et al. 1997

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“…There is evidence that another factor, an NTPase, may also be involved in assuring fidelity in RNA synthesis. This NTPase has been studied in several laboratories (37)(38)(39) and found to act preferentially on the incorrect NTP. Butzow and Stankis (40) have isolated the NTPase activity from RNA polymerase and we have obtained results against this preferential activity.…”

mentioning

confidence: 99%

A structural model for fidelity in transcription.

Eichhorn

Chuknyisky²,

Butzow³

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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Distances between the metal ions bound to the product terminus i site and the substrate i+l site ofEscherichia col RNA polymerase range from 5.0 to 5.6 A when the substrate is complementary to a template base and from 6.5 to 7.0 A for a noncomplementary relationship. The metal bound to the substrate at the i+1 site exhibits a constant distance to the three phosphates on the substrate regardless of complementarity, but the dice to base and ribose protons changes.The differences in these geometric parameters are explained by the ability of the enzyme to assume two conformations, one to place correct nucleotide substrates in optimal position for bond formation and the other to prevent incorrect nucleotides from assuming such a position. In this scheme a metal-riphosphate complex can move toward or away from the terminal 3' OH group of the growing RNA chain, to assure fidelity of transcription.The primary process responsible for ensuring the fidelity of transcription is the Watson-Crick base pairing between the DNA base to be copied and the base on the incoming nucleoside triphosphate (NTP). This process depends on the greater stability of Watson-Crick base pairs compared to others; yet the difference in stability is insufficient to account for the observed fidelity oftranscription (1-5). Consequently, there must be another factor in producing this fidelity. The enzyme RNA polymerase is present and required at the point of elongation, where an incoming NTP enters the system to be incorporated into the growing RNA chain. This enzyme is a versatile one that has a variety of known functions. To enhance fidelity, the enzyme would have to engage in another hitherto unknown function: to distinguish between NTPs with "correct" and "incorrect" bases and reject the incorrect bases, thus enhancing the incorporation of the correct bases. We have evidence that the enzyme performs this function through its ability to assume two conformations, one to promote elongation with the incoming NTP and the other to prevent it. To determine whether the RNA polymerase is performing in this way, we have been studying the relationship between two NTPs in the active site of the Escherichia coli enzyme (6, 7), one in the i site (where the growing RNA chain is located) and the other in the i+ 1 site (for the incoming NTP) (8). We are thus looking at a system poised for the formation of the first bond in RNA synthesis, leading to the dinucleotide in which the first two bases of the DNA have been transcribed. In our previous studies (6, 7), we have determined the geometric relationship between ATP substrates in both i and i+1 sites with poly(dAdT)'poly(dAdT) serving as a template (6, 7). We accomplished this by measuring distances by electron paramagnetic resonance (EPR) between the Zn(II) and Mg(II) ions in the two sites, both replaced by Mn(II). We then used distances measured in our laboratory (7) and elsewhere (9-11) between these metals and points on the two substrates to produce a model for the geometry between the two ATP molecules...

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“…Since, BACE acts on the first and rate‐limiting step in Aβ generation and the BACE deficiency almost abolishes Aβ generation in mouse . However, recently clinical trials suggest that BACE inhibition and other immunotherapies to reduce brain Aβ are insufficient to improve cognition in AD …”

Section: Resultsmentioning

confidence: 99%

Synthesis, Molecular Docking, and Preliminary Evaluation of 2‐(1,2,3‐Triazoyl)benzaldehydes As Multifunctional Agents for the Treatment of Alzheimer's Disease

et al. 2020

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We described here our results on the use of thiourea as a ligand in the copper catalysed azide‐alkyne cycloaddition (CuAAC) of 2‐azidobenzaldehyde with alkynes. Reactions were performed reacting 2‐azidobenzaldehyde with a range of terminal alkynes using 10 mol % of copper iodide as a catalyst, 20 mol % of thiourea as a ligand, triethylamine as base, DMSO as solvent at 100 °C under nitrogen atmosphere. The corresponding 2‐(1H‐1,2,3‐triazoyl)‐benzaldehydes (2‐TBH) were obtained in moderated to excellent yields and according our experiments, the use of thiourea decreases the formation of side products. The obtained compounds were screened for their binding affinity with multiple therapeutic targets of AD by molecular docking: β‐secretase (BACE), glycogen synthase kinase (GSK‐3β) and acetylcholinesterase (AChE). The three compounds with highest affinity, 5 a (2‐(4‐phenyl‐1H‐1,2,3‐triazol‐1‐yl)benzaldehyde), 5 b (2‐(4‐(p‐tolyl)‐1H‐1,2,3‐triazol‐1‐yl)benzaldehyde), and 5 d (2‐(4‐(4‐(tert‐butyl)phenyl)‐1H‐1,2,3‐triazol‐1‐yl)benzaldehyde) were selected and evaluated on its antioxidant effect, in view of select the most promising one to perform the in vivo validation. Due the antioxidant potential ally to the affinity with BACE, GSK‐3β and AChE, compound 5 b was evaluated in a mouse model of AD induced by intracerebroventricular injection of streptozotocin (STZ). Our results indicate that 5 b (1 mg/kg) treatment during 20 days is able to reverse the cognitive and memory impairment induced by STZ trough the modulation of AChE activity, amyloid cascade and GSK‐3β expression.

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A possible mechanism responsible for the correction of transcription errors

Cited by 16 publications

References 24 publications

Specificity of an Escherichia coli RNA Polymerase-Associated NTPase

Specificity of an Escherichia coli RNA Polymerase-Associated NTPase

A structural model for fidelity in transcription.

Synthesis, Molecular Docking, and Preliminary Evaluation of 2‐(1,2,3‐Triazoyl)benzaldehydes As Multifunctional Agents for the Treatment of Alzheimer's Disease

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