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Showing 1 to 13 of 13 for “"modified bases"”.
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Methods to Probe the Function of Modified Bases in DNA
… and biological tools to probe the function of modified bases in DNA with specific exploration of the less well-studied T-modifications: 5-hmU, 5-fU and Base J. LCMS/MS techniques are first utilised to enable the accurate global quantification of T-modifications (5-hmU, 5-fU and Base J) in both …
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The versatile E. coli adaptive response protein AlkB mitigates toxicity and mutagenicity of etheno-, ethano-, and methyl-modified bases in vivo
The Escherichia coli AlkB protein is an exceptionally versatile DNA repair enzyme. Its expression is induced upon exposure to alkylating agents as part of the Ada-mediated adaptive response. This member of the ac-ketoglutarate/iron(II)-dependent dioxygenase family was originally discovered to …
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Study of DNA damage on DNA G-quadruplexes and biophysical evaluation of the effects of modified bases (lesions) on their conformation and stability
… to reactive oxygen species (ROS) results in the modified nucleobases (lesions) as well as strand scissions under physiological conditions. Due to its lowest oxidation potential (1.29 eV), guanine is the most easily oxidisable nucleobase. Furthermore, it has been observed that the 5'-guanine in …
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Exploring conformational variability of an rna domain in the ribosome: from structure and function to potential antibiotic targeting
<p>RNA in nature is modified at many specific sites to order to gain extra functions or to expand the genetic code. One of such RNAs is ribosomal RNA (rRNA), which contains several modified bases, particularly around the functionally significant sites. We have focused on understanding the …
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Single stranded DNA: A new model system for single molecule polymer dynamics
… Polymer chains are synthesized with amine modified bases incorporated along the backbone to facilitate labeling with fluorescent dyes. As proof-of-principle demonstration of this new chemical platform, we use epifluorescence microscopy to image individual ssDNA molecules stretching in an …
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Characterization of splicing mechanisms by single-molecule fluorescence
… for human snRNAs similar to yeast. Although unmodified snRNAs exhibit similar folding dynamics as yeast, modified bases destabilize the low FRET state of the U2-U6 complex. However, comparison of FRET and UV melting data suggests modified bases may be involved in protein recognition and/or …
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Novel regulatory mechanisms of mutagenic translesion DNA synthesis : characterization of REV1 in Saccharomyces cerevisiae
… agents that can cause a wide range of modified bases and aberrant DNA structures. To respond to the large diversity of DNA lesions that can be produced, cells possess a host of DNA repair and damage tolerance systems. The majority of these processes operate with exquisite accuracy to …
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A photochemical method for the detection of cytosine modifications in DNA
Covalent modifications to DNA bases represent an important form of epigenetic information which contributes to the regulation of gene expression in many cellular processes throughout development and differentiation. Aberrant modification patterns can also signal or drive the emergence of genetic …
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Chemical and Enzymatic Methods to Detect Chemical Modifications in Nucleic Acids
The bases of DNA and RNA are chemically modified in a variety of ways across all branches of life. DNA and RNA chemical modifications function as a layer of epigenetic information that regulate gene expression. Studies on the chemical reactivity of nucleic acids and the biochemical activity of …
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Structural studies of S-adenosyl-L-methionine radical enzymes involved in tRNA and natural product biosynthesis
… the key steps in the biosynthesis of the tRNA modified bases wybutosine and queuosine. TYWI catalyzes the formation of the characteristic imidazopurine ring of wybutosine through a disputed mechanism. Here, we have garnered support for one of the proposed mechanisms, through the identification …
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Characterisation of the Essential t<sup>6</sup>A tRNA Modification Enzymes and Evaluation as a Potential Novel Antimicrobial Target
<p>Modified bases in RNA molecules are common, with over one-hundred individual modifications reported to date. In transfer RNA (tRNA), these modifications help hold the molecule in its proper conformation, allow the aminoacyl-synthetases to attach the amino acid to the correct tRNA for transfer to …
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The Role of Base Modifications on Tyrosyl-tRNA Structure, Stability, and Function in Bacillus subtilis and Bacillus anthracis
… in Gram-negative bacteria, however, the role of modified bases in tRNAs as they relate to thermostability, structure, and transcriptional regulation in Gram-positive bacteria, such as Bacillus subtilis and Bacillus anthracis, are not well characterized. Infections by Gram-positive bacteria that …
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Development of functional DNA-based sensors and investigations into their mechanism
… of the DNAzyme. Kinetic assays with the PS modified bases have shown that there are specific bases on the enzyme strand which are important for activity mainly in the presence of Pb2+. The activities of the identical PS modified enzymes are, however, not significantly altered in the presence …