Degradation and modification of nucleic acids

Adams, Roger; Knowler, John T.; Leader, David P.

doi:10.1007/978-94-011-2290-0_4

Cited by 5 publications

(3 citation statements)

References 239 publications

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“…Contaminating RNases almost invariably cleave to yield 5′ hydroxyl and 2′, 3′ phosphate end groups, and very few RNases cleave the phosphodiester backbone through the same mechanism used by RNase III (32,33). To identify the end group of the reaction products we carried out two different kinds of experiments.…”

Section: Resultsmentioning

confidence: 99%

RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site

Beguiristain¹

2005

Nucleic Acids Research

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Here, we show that Escherichia coli Ribonuclease III cleaves specifically the RNA genome of hepatitis C virus (HCV) within the first 570 nt with similar efficiency within two sequences which are ∼400 bases apart in the linear HCV map. Demonstrations include determination of the specificity of the cleavage sites at positions C27 and U33 in the first (5′) motif and G439 in the second (3′) motif, complete competition inhibition of 5′ and 3′ HCV RNA cleavages by added double-stranded RNA in a 1:6 to 1:8 weight ratio, respectively, 50% reverse competition inhibition of the RNase III T7 R1.1 mRNA substrate cleavage by HCV RNA at 1:1 molar ratio, and determination of the 5′ phosphate and 3′ hydroxyl end groups of the newly generated termini after cleavage. By comparing the activity and specificity of the commercial RNase III enzyme, used in this study, with the natural E.coli RNase III enzyme, on the natural bacteriophage T7 R1.1 mRNA substrate, we demonstrated that the HCV cuts fall into the category of specific, secondary RNase III cleavages. This reaction identifies regions of unusual RNA structure, and we further showed that blocking or deletion of one of the two RNase III-sensitive sequence motifs impeded cleavage at the other, providing direct evidence that both sequence motifs, besides being far apart in the linear RNA sequence, occur in a single RNA structural motif, which encloses the HCV internal ribosome entry site in a large RNA loop.

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Section: Resultsmentioning

confidence: 99%

RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site

Beguiristain¹

2005

Nucleic Acids Research

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“…Contaminating RNases almost invariably cleave to yield 5Ј-hydroxyl and 3Ј-phosphate end groups (29), and very few other RNases and ribozymes cleave the phosphodiester backbone through the same mechanism used by RNase P (30).…”

Section: Direct Method: End Group Determination and Cleavage Precisiomentioning

confidence: 99%

Specific Cleavage of Hepatitis C Virus RNA Genome by Human RNase P

Nadal

Martell

Lytle³

et al. 2002

Journal of Biological Chemistry

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We have found that RNase P from HeLa cells specifically and efficiently cleaves hepatitis C virus (HCV) transcripts in vitro. The evidence includes identification of the 5-phosphate polarity of the newly generated termini at position A 2860 as well as immunological and biochemical assays. Active cleavage has been shown in five dominant sequences of HCV "quasispecies" differing at or near the position of cleavage, demonstrating that this is a general property of HCV RNA. During the analysis, a second cleavage event was found in the 3 domain of the internal ribosome entry site. We have found that HCV RNA competitively inhibits pre-tRNA cleavage by RNase P, suggesting that HCV RNA has structural similarities to tRNA. This finding sets HCV apart from other pathogens causing serious human diseases and represents the first description of human RNase P-viral RNA cleavage. Here we discuss the possible meaning of these RNase P-accessible structures built into the viral genome and their possible role in vivo. Moreover, such structures within the viral genome might be vulnerable to attack by therapeutic strategies.

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“…The breadth of DNA adductomics is dependent on the efficiency of digestion of chemically modified DNA, and adducts of different structures may require different cocktails of enzymes for quantitative digestion of DNA to the mononucleoside adducts (typical combinations of enzymes are nucleases or DNases used with phosphodiesterases and alkaline phosphatase). 85 …”

Section: Sample Source and Preparationmentioning

confidence: 99%

DNA Adductomics

Balbo

Turesky²,

Villalta³

2014

Chem. Res. Toxicol.

166

179

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Systems toxicology is a broad based approach to describe many of the toxicological features that occur within a living system under stress or subjected to exogenous or endogenous exposures. The ultimate goal is to capture an overview of all exposures and the ensuing biological responses of the body. The term “exposome” has been employed to refer to the totality of all exposures and systems toxicology investigates how the exposome influences health effects and consequences of exposures over a lifetime. The tools to advance systems toxicology include high-throughput transcriptomics, proteomics, metabolomics and adductomics, which is still in its infancy. A well-established methodology for the comprehensive measurement of DNA damage resulting from every day exposures is not fully developed. During the past several decades, the 32P-postlabeling technique has been employed to screen the damage to DNA induced by multiple classes of genotoxicants; however, more robust, specific, and quantitative methods have been sought to identify and quantify DNA adducts. While triple quadrupole and ion trap mass spectrometry, in particular when using multistage scanning (LC-MSn), have shown promise in the field of DNA adductomics, it is anticipated that high resolution and accurate mass LC-MSn instrumentation will play a major role in assessing global DNA damage. Targeted adductomics should benefit greatly from improved triple quadrupole technology. Once the analytical MS methods are fully mature, DNA adductomics along with other –omics tools will contribute greatly to the field of systems toxicology.

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Degradation and modification of nucleic acids

Cited by 5 publications

References 239 publications

RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site

RNase III cleavage demonstrates a long range RNA: RNA duplex element flanking the hepatitis C virus internal ribosome entry site

Specific Cleavage of Hepatitis C Virus RNA Genome by Human RNase P

DNA Adductomics

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