8-Hydroxyguanine, an Oxidative DNA and RNA Modification

2016 ◽  
pp. 147-185 ◽  
Author(s):  
Hiroshi Kasai ◽  
Kazuaki Kawai
Keyword(s):  
Rna Modification ◽  
Dna And Rna

scholarly journals Mapping the epigenetic modifications of DNA and RNA

2020 ◽  
Vol 11 (11) ◽  
pp. 792-808 ◽  
Author(s):  
Lin-Yong Zhao ◽  
Jinghui Song ◽  
Yibin Liu ◽  
Chun-Xiao Song ◽  
Chengqi Yi
Keyword(s):  
Single Molecule ◽  
Detection Methods ◽  
Rna Modification ◽  
Rna Modifications ◽  
Single Molecule Sequencing ◽  
Dna And Rna ◽  
Third Generation Sequencing ◽  
Technological Advances ◽  
Long Read ◽  
High Throughput Detection

Abstract Over 17 and 160 types of chemical modifications have been identified in DNA and RNA, respectively. The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics. Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study. Here, we review the recent technological advances in this rapidly evolving field. We focus on high-throughput detection methods and biological findings for these modifications, and discuss questions to be addressed as well. We also summarize third-generation sequencing methods, which enable long-read and single-molecule sequencing of DNA and RNA modification.

DNA and RNA Modification Promoted by [Co(H2O)6]Cl2and KHSO5:  Guanine Selectivity, Temperature Dependence, and Mechanism

1996 ◽  
Vol 118 (10) ◽  
pp. 2320-2325 ◽  
Author(s):  
James G. Muller ◽  
Ping Zheng ◽  
Steven E. Rokita ◽  
Cynthia J. Burrows
Keyword(s):  
Temperature Dependence ◽  
Rna Modification ◽  
Dna And Rna

The chemical diversity of RNA modifications

2019 ◽  
Vol 476 (8) ◽  
pp. 1227-1245 ◽  
Author(s):  
R. Jordan Ontiveros ◽  
Julian Stoute ◽  
Kathy Fange Liu
Keyword(s):  
Human Cancer ◽  
Stem Cell Differentiation ◽  
Chemical Diversity ◽  
Rna Modification ◽  
Small Nuclear Rna ◽  
Disease States ◽  
Dna And Rna ◽  
Non Coding Rna ◽  
Important Means ◽  
A Site

AbstractNucleic acid modifications in DNA and RNA ubiquitously exist among all the three kingdoms of life. This trait significantly broadens the genome diversity and works as an important means of gene transcription regulation. Although mammalian systems have limited types of DNA modifications, over 150 different RNA modification types have been identified, with a wide variety of chemical diversities. Most modifications occur on transfer RNA and ribosomal RNA, however many of the modifications also occur on other types of RNA species including mammalian mRNA and small nuclear RNA, where they are essential for many biological roles, including developmental processes and stem cell differentiation. These post-transcriptional modifications are enzymatically installed and removed in a site-specific manner by writer and eraser proteins respectively, while reader proteins can interpret modifications and transduce the signal for downstream functions. Dysregulation of mRNA modifications manifests as disease states, including multiple types of human cancer. In this review, we will introduce the chemical features and biological functions of these modifications in the coding and non-coding RNA species.

scholarly journals ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data

2021 ◽  
Author(s):  
Leszek P Pryszcz ◽  
Eva Maria Novoa
Keyword(s):  
Rna Modification ◽  
Nanopore Sequencing ◽  
Computationally Efficient ◽  
Rna Modifications ◽  
Efficient Manner ◽  
Dna And Rna ◽  
File Formats ◽  
User Friendly ◽  
And Storage

DNA and RNA modifications can now be identified using Nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data. Here we present ModPhred, a versatile toolkit that facilitates DNA and RNA modification analysis from nanopore sequencing reads in a user-friendly manner. ModPhred integrates probabilistic DNA and RNA modification information within the FASTQ and BAM file formats, can be used to encode multiple types of modifications simultaneously, and its output can be easily coupled to genomic track viewers, facilitating the visualization and analysis of DNA and RNA modification information in individual reads in a simple and computationally efficient manner. ModPhred is available at https://github.com/novoalab/modPhred, is implemented in Python3, and is released under an MIT license.

scholarly journals Chemistry of Class 1 CRISPR-Cas effectors: Binding, editing, and regulation

2020 ◽  
Vol 295 (42) ◽  
pp. 14473-14487
Author(s):  
Tina Y. Liu ◽  
Jennifer A. Doudna
Keyword(s):  
Defense Mechanisms ◽  
Rna Modification ◽  
Nucleic Acid Detection ◽  
Control Of Gene Expression ◽  
Immune Systems ◽  
Adaptive Immune ◽  
Dna And Rna ◽  
Single Protein ◽  
Class 1 ◽  
Adaptive Immune Systems

Among the multiple antiviral defense mechanisms found in prokaryotes, CRISPR-Cas systems stand out as the only known RNA-programmed pathways for detecting and destroying bacteriophages and plasmids. Class 1 CRISPR-Cas systems, the most widespread and diverse of these adaptive immune systems, use an RNA-guided multiprotein complex to find foreign nucleic acids and trigger their destruction. In this review, we describe how these multisubunit complexes target and cleave DNA and RNA and how regulatory molecules control their activities. We also highlight similarities to and differences from Class 2 CRISPR-Cas systems, which use a single-protein effector, as well as other types of bacterial and eukaryotic immune systems. We summarize current applications of the Class 1 CRISPR-Cas systems for DNA/RNA modification, control of gene expression, and nucleic acid detection.

On the chemical nature of DNA and RNA modification by a hemin model system

Biochemistry ◽  
1990 ◽  
Vol 29 (20) ◽  
pp. 4783-4789 ◽  
Author(s):  
Reuel B. Van Atta ◽  
Jean Bernadou ◽  
Bernard Meunier ◽  
Sidney M. Hecht
Keyword(s):  
Chemical Nature ◽  
Model System ◽  
Rna Modification ◽  
Dna And Rna

High-resolution nucleic acid sequence mapping via in situ hybridization at the Electron Microscope level

1995 ◽  
Vol 53 ◽  
pp. 752-753
Author(s):  
B.A. Hamkalo ◽  
S. Narayanswami ◽  
A.P. Kausch
Keyword(s):  
Nucleic Acid ◽  
Interphase Nucleus ◽  
Genome Mapping ◽  
Precise Location ◽  
Electron Microscope Level ◽  
Rna Sequences ◽  
Fundamental Interest ◽  
Whole Cells ◽  
Dna And Rna

The availability of nonradioactive methods to label nucleic acids an the resultant rapid and greater sensitivity of detection has catapulted the technique of in situ hybridization to become the method of choice to locate of specific DNA and RNA sequences on chromosomes and in whole cells in cytological preparations in many areas of biology. It is being applied to problems of fundamental interest to basic cell and molecular biologists such as the organization of the interphase nucleus in the context of putative functional domains; it is making major contributions to genome mapping efforts; and it is being applied to the analysis of clinical specimens. Although fluorescence detection of nucleic acid hybrids is routinely used, certain questions require greater resolution. For example, very closely linked sequences may not be separable using fluorescence; the precise location of sequences with respect to chromosome structures may be below the resolution of light microscopy(LM); and the relative positions of sequences on very small chromosomes may not be feasible.

Scanning tunneling microscopy (STM) of DNA and RNA

1989 ◽  
Vol 47 ◽  
pp. 34-35
Author(s):  
Patricia G. Arscott ◽  
Gil Lee ◽  
Victor A. Bloomfield ◽  
D. Fennell Evans
Keyword(s):  
Molecular Structures ◽  
Inorganic Materials ◽  
Resolving Power ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Form And Function ◽  
Dna And Rna ◽  
Calf Thymus ◽  
And Function ◽  
The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

THE POSSIBLE INFLUENCE OF STEROID-RECEPTOR COMPLEXES ON THE INTERACTION OF DNA AND RNA POLYMERASES

1971 ◽  
Vol 68 (1_Supplb) ◽  
pp. S151
Author(s):  
Frank R. Mangan ◽  
W. I. P. Mainwaring
Keyword(s):  
Steroid Receptor ◽  
Rna Polymerases ◽  
Receptor Complexes ◽  
Dna And Rna
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