Uracil is a rare base in DNA and its presence can provide a biological starting point for mutagenesis or cell death. This chapter will cover various ways in which uracil may be introduced in DNA, removed from DNA and the consequences of its occurrence. The focus of the chapter is a class of...

Proteins are classified as members of the APOBEC family based on the occurrence of a signature amino acid sequence and its characteristic three‑dimensional fold known as a zinc‑dependent deaminase domain (ZDD). This domain enables APOBEC proteins to bind nucleic acids and in most cases,...

Nucleoside deaminases that act on RNA and DNA play important roles in proteome diversification, mRNA stability and innate immunity. Adenosine deaminases that act on RNA (ADARs) or tRNA (ADATs) fall into one branch of a phylogenetic tree that catalyzes the hydrolytic deamination of adenosine (A)...

RNA editing is widespread throughout the human transcriptome. The major editing event is the deamination of adenosine to inosine. The enzymes responsible are ADARs and they deaminate specific adenosines in double‑stranded RNA. When editing occurs within a coding region it can result in another...

Base J (β‑D‑glucopyranosyloxymethyluracil) is the only hyper‑modified DNA base known in eukaryotes. It is present in the nuclear DNA of all flagellated protozoa of the order of the Kinetoplastida and in the closely related unicellular alga Euglena gracilis. Base J is a minor constituent of...

RNA modification enzymes in the manifestation of methyltransferases play a major role in antibiotic resistance in bacteria. The ribosome modifications are almost exclusively methylation of either the 2′‑O‑ribose position or various positions on the bases. A wealth of information on...

DNA Restriction-Modification systems are found in most bacteria. The Type I, II and III systems modify specific nucleotide sequences within the host genome using a methyltransferase. The absence of this specific methylation pattern on invading foreign DNA triggers the destruction of the invading...

The spliceosomal U snRNAs, which are essential for pre‑mRNA splicing, contain a number of posttranscriptionally modified nucleotides, in particular pseudouridine. The location of many of the pseudouridine residues has been conserved throughout evolution. The pseudouridylation of spliceosomal...

Several hundreds of genomes from the three Domains of life have been sequenced so far leading to the identification of an impressive list of new genes. When structural genomics programs were launched at the beginning of this decade, several research groups proposed to study specific targets...

Pseudouridylation, the isomerization of uridine to pseudouridine, is the most frequent posttranscriptional modification of RNA, such that pseudouridine has even been termed the fifth nucleotide. Whereas eubacteria employ single protein enzymes to identify and modify target uridines,...

Methylation at the 2‘-O-ribose position is an abundant nucleotide modification of both eukaryal and archaeal RNAs. The methyltransferase responsible for this modification is frequently a ribonucleoprotein (RNP) complex consisting of a box C/D guide RNA and associated core proteins. These RNP...

The ribosome is a large macromolecular machine that carries out template‑directed protein synthesis by translating the sequence of triplet codons found in an mRNA to the sequence of amino acids forming a protein molecule. The ribosome decodes the genetic information with remarkable accuracy and...

Structural and functional studies have illustrated how the T4Dam DNA‑(adenine N6)‑methyltransferase recognizes its GATC target sites, showing that the TC part of the target sequence is contacted by a b‑hairpin loop formed by an amino acid motif conserved in the Dam family of DNA MTases....

Eukaryotic DNA methylation is performed by DNA‑methyltransferases that catalyze transfer of a methyl group from S‑adenosyl‑L‑methionine to carbon 5 of cytosine bases in DNA, giving rise to 5‑methylcytosine (5‑meC). Cytosine methylation is used as an epigenetic mark for maintenance of...

Methylation of the 30S ribosomal subunit RNA (16S rRNA) is a significant mechanism of resistance to ribosome‑targeting antibiotics in both producer and pathogenic bacteria. Antibiotic resistance phenotypes may arise through both loss of intrinsic methylation or by site‑specific modification...

Mature tRNA is normally extensively modified and extremely stable. Recent evidence suggests that tRNA species that are incompletely modified in the yeast Saccharomyces cerevisiae can undergo different types of quality control checks, leading to their decay. In one pathway, pre-tRNAiMet lacking...

The recognition of the correct substrate and rejection of the incorrect substrate by RNA‑modifying enzymes is of great importance to the process of posttranscriptional base modification. Between 2001 and 2008, structures of nine different rRNA and tRNA base‑modifying enzymes in complex with...

The alkb gene was discovered more than two decades ago as a methylation sensitive mutant of Escherichia coli, suggesting that the corresponding protein (EcAlkB) may be involved in removing methyl lesions from DNA. However, it took several years to establish that this was indeed the case; EcAlkB...

With over 800 genome sequences available and thousands more in the pipeline (see Genome Online Database for latest number updates www.genomeonline.org), the genetic information used by most biologists/biochemists is now derived mainly from genomic sequences that have been annotated in silico....

DNA modification and repair enzymes are capable of rotating a DNA base to an extrahelical state, an event commonly referred to as \'base flipping,\' and perform a specific chemical reaction. Several experimental approaches have been applied to understand the kinetic, mechanistic and structural...

The methylation of mammalian DNA, primarily at CpG dinucleotides, has long been recognized to play a major role in controlling gene expression among other functions. Given their importance, it is surprising how many basic questions remain to be answered about the proteins responsible for this...

This chapter provides a review of recent advances in the molecular basis of transfer RNA (tRNA) processing events. tRNAs are transcribed into precursors that must undergo removal of 5′ and 3′ leader sequences, addition of a universally conserved CCA sequence, removal of introns and covalent...

The most prominent source of information on prokaryotic DNA modifications is REBASE (http://rebase.neb.com/rebase/rebase.html), which exhaustively covers restriction endonucleases and DNA methyltransferases. As of September 2008, it contains entries for almost 4000 restriction endonucleases (most...

Chemically simple modified ribonucleotides, such as pseudouridines and methylated nucleotides, show a widespread, almost ubiquitous distribution over almost every class of RNAs in all domains of life. Many modifications are thought to contribute to modulation and stabilization of RNA structure....

In general RNA modification reactions are catalyzed by enzymes acting posttranscriptionally on RNA substrates. From an enzymological perspective RNA modification is a major source of fascinating enzymes catalyzing a variety of interesting reactions with very high specificity since the chemical...

The continuous advancement in comprehension of biological processes is strongly dependent on the continuous development of novel molecular tools, including in particular chemically synthesized nucleic acids. Progress in nucleic acid biochemistry has been and will continue to be the basis of...

The most dramatic and localized enzyme‑induced conformational distortion to the helical structure of DNA is base flipping, in which a nucleobase is unpaired, removed from the stack and further rotated out 180˚ to assume a fully extrahelical position. Since its first demonstration in crystal...

Among RNAs, the transfer RNAs are those showing the highest level of posttranscriptional modifications. After an overview on early data, the chapter discusses the present knowledge on the role modified nucleosides have on tRNA structure and function with emphasis on tRNA aminoacylation. The...

In this chapter, the history of DNA modifying enzymes is briefly summarized with a focus on DNA methyltransferases. The current understanding of methylation in prokaryotes and eukaryotes is summarized and recent findings in both areas discussed. The future outlook for research for both kingdoms...

This chapter provides a short review of the structural biology of RNA modification enzymes, focused on comparative aspects. All modifications are introduced by protein enzymes, from relatively simple standalone catalytic domains to subunits of protein complexes or ribonucleoprotein particles....

RNA editing occurs in humans by single base deamination, Cytidine-to-Uridine or Adenosine-to-Inosine. These changes create codons for a different amino acid, stop codons or even new splice‑site allowing protein diversity generated from a single gene. Despite the abundance of these...

Nucleoside modification in tRNA is an essential process in the maturation of tRNA and results in the production of over 100 chemically distinct modified nucleosides. The 7‑deazaguanosine modified nucleosides queuosine and archaeosine are two of the most structurally complex modified nucleosides...

In this chapter, we will discuss the conformational mechanisms of the structurally poorly characterized EcoRI adenine methyltransferase and those of the structurally well‑characterized HhaI cytosine methyltransferase. The various techniques used to visualize conformational changes such as DNA...

Pseudouridine (Ψ) synthases are the enzymes responsible for the most abundant and phylogenetically conserved posttranscriptional modification of cellular RNAs. These enzymes catalyze an isomerization reaction of specific uridine residues within an RNA chain. Sequence and structure analyses have...

Enzymatic methylation of the C5 atom of uridyl to form (ribo)thymidyl occurs during the metabolism of DNA and RNA in all organisms. The first enzyme found to catalyze this fundamental reaction was thymidylate synthase ThyA that uses methylene tetrahydrofolate as carbon source and reducing agent...

KsgA is a ribosomal RNA methyltransferase that modifies two adjacent adenosines in the small subunit. It was originally identified by virtue of the fact that its absence in several bacteria provides resistance to the antibiotic kasugamycin. The ksgA gene appears to be ubiquitously spread...

S‑adenosyl‑l‑methionine (AdoMet, also abbreviated SAM or SAMe, 1) is one of the most versatile biomolecules in nature and one of the most widely used enzyme substrate, second perhaps only to adenosine triphosphate (ATP).1‑3 AdoMet acts as a cofactor in a myriad of enzyme catalyzed...

An RNA/protein world (probably cellular) is widely accepted as a probable step in the early evolution of life. During subsequent life evolution various enzymes emerged that allowed some organisms to generate deoxyribonucleotides from ribonucleotide precursors and to synthesize DNA molecules using...

Wyosine derivatives are tricyclic ribonucleosides present exclusively at position 37 of tRNA specific for phenylalanine in most Eukarya (cytoplasmic only) and Archaea, but not Bacteria. They occur by posttranscriptional modification of encoded guanosine in the tRNA precursor. Depending on the...

The amount of experimental information available in the field of RNA modifications is overwhelming. This expertise is mostly scattered in publications and laboratory centers worldwide. There are few web resources dealing with this topic and therefore it is difficult to find a good entry point...

Chemically altered nucleosides derived from canonical ribo‑ or deoxyribonucleoside‑derivatives of adenosine, cytosine, guanosine, and uridine or thymidine are found in all types of nucleic acids, DNA and RNAs. They are particularly abundant in noncoding RNAs, such as transfer RNAs and...

The importance of establishing and maintaining proper DNA methylation patterns is most dramatically highlighted by disturbances causing or contributing to human diseases. Mutations in components of the DNA methylation machinery underlie several inherited syndromes such as Immunodeficiency,...

Redesigning enzyme catalysis is of general interest in biological research and biotechnology. Enzymes often possess some degree of substrate promiscuity that can be exploited to change the course of enzymatic reactions. In this chapter we discuss examples of modified substrates for various...

Sulfur is an essential element for all living organisms. Several modified nucleosides containing sulfur atoms are found in tRNA molecules, namely 2‑thiocytidine (s2C), 2‑thiouridine (s2U) derivatives, 4‑thiouridine (s4U) and 2‑methylthioadenosine (ms2A) derivatives. Especially, 2‑thio...

Solid phase synthesis is an efficient method for the preparation of short RNAs of below 40 nucleotides in length, or DNA of up to 200 nucleotides in length. The obtained yields are suitable for material‑intensive biophysical methods like NMR and crystallography and allow the convenient...

Posttranscriptional modification of the wobble uridine at position 34 in the anticodon of tRNA allows accurate and efficient decoding of the genetic code. In particular, decoding of the synonymous two‑codon sets specific for Leu, Gln, Lys, Glu and Arg primarily depends on the presence of a...

Posttranscriptional modification of the wobble uridine at position 34 in the anticodon of tRNA allows accurate and efficient decoding of the genetic code. In particular, decoding of the synonymous two‑codon sets specific for Leu, Gln, Lys, Glu and Arg primarily depends on the presence of a...