Nucleic acid phosphodiester bonds

En me Mechanism. Staphylococcal nuclease (SNase) accelerates the hydrolysis of phosphodiester bonds in nucleic acids (qv) some 10 -fold over the uncatalyzed rate (r93 and references therein). Mutagenesis studies in which Glu43 has been replaced by Asp or Gin have shown Glu to be important for high catalytic activity. The enzyme mechanism is thought to involve base catalysis in which Glu43 acts as a general base and activates a water molecule that attacks the phosphodiester backbone of DNA. To study this mechanistic possibiUty further, Glu was replaced by two unnatural amino acids. 

The result was quite disappointing, as instead of the required 3 -5 -phosphodiester linkage, which is found in nucleic acids today, the main products obtained were those with the unnatural 2 -5 -bond between the nucleotides. Further experiments showed that the presence of divalent metal ions had a clear positive effect on the matrix-dependent polycondensation. The addition of l-10mMPb2+ to 100 mM of poly(U) as the matrix and 50 mM of ImpA monomer caused the yield of oligomeric product (pentamers and longer) to increase by a factor of four (Sleeper et al., 1979). 

Another important group of hydrolytic enzymes are phospho- and cyclophosphodiesterases. They catalyze the hydrolysis of phospho-diester bonds and many of the most relevant biological substrates are nucleic acids. Phospholipase C and D are also important examples. Initial attempts to measure phosphodiesterase activity placed a phosphodiester between a fluorophore and a quencher and the probe was tested in vitro [146], This system was slightly modified by Caturla and used for the identification of catalysts with phosphodiesterase activity [147], More recently, Nagano and co-workers used a coumarin donor and fluorescein as a FRET... 

In RNA, the base T found in DNA is replaced by uracil, which is similar in structure to T, but lacks the methyl group. The nucleotides in nucleic acids are linked by phosphodiester bonds between the 3 -hydroxyl of one nucleoside and the 5 -hydroxyl of the sugar of its neighbour in the sequence, as was first shown by Alexander Todd3 in 1952 (Figure 4.13). 

Nucleic acids are polymers of nucleotides joined by 3, 5 -phosphodiester bonds that is, a phosphate group links the 3 carbon of a sugar to the 5 carbon of the next sugar in the chain. Each strand has a distinct 5 end and 3 end, and thus has polarity. A phosphate group is often found at the 5 end, and a hydroxyl group is often found at the 3 end. 

Polymerases are enzymes that synthesize nucleic acids by forming phosphodiester (PDE) bonds. Nucleases are enzymes that hydrolyze PDE bonds. 

Many examples of catalytic nucleic acids obtained by in vitro selection demonstrate that reactions catalyzed by ribozymes are not restricted to phosphodiester chemistry. Some of these ribozymes have activities that are highly relevant for theories of the origin of life. Hager et al. have outlined five roles for RNA to be verified experimentally to show that this transition could have occurred during evolution [127]. Four of these RNA functionalities have already been proven Its ability to specifically complex amino acids [128-132], its ability to catalyze RNA aminoacylation [106, 123, 133], acyl-transfer reactions [76, 86], amide-bond formation [76,77], and peptidyl transfer [65,66]. The remaining reaction, amino acid activation has not been demonstrated so far. 

Now that we have the monomers, which are pretty complex in this case, it remains to define how they are joined together to create the polymer. The amino acids in proteins are linked by peptide bonds. The nucleotides in nucleic acids are linked by phosphodiester bonds, as is shown in figure 12.2. These DNA phosphodiester bonds are very stable. Indeed, samples of largely intact DNA can be recovered from organisms that have been extinct for thousands of years. This remarkable stability should not come as a surprise the central importance of DNA in all forms of life requires that it be stable to various sorts of insults. 

A nucleotide consists of a heterocyclic base linked to a sugar (ribose or deoxyribose) and a phosphate group also linked to the sugar (Figure 10.6). Nucleic acids are polymers of nucleotides linked together by phosphodiester bonds (Figure 10.7). The enzymes that catalyse the breakdown of nucleic acids to nucleotides are nucleases. 

Nucleases that hydrolyse phosphodiester bonds, within the nucleic acid chain are endonucleases (Figure 10.8). Apart from specificity for DNA or RNA shown by some, nucleases, these enzymes show specificity for ... 

The nucleic acid polymer is formed when the nucleotides attach to one another through phosphodiester bonds, which connect the 3 -OH group of one nucleotide to the 5 -OH group of another nucleotide through the phosphate group. The order of the nucleotides in the chain is the primary structure of the DNA or RNA molecule, and it can be represented in short-hand notation with only the base pair designation... 

Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids... 

FIGURE 8-7 Phosphodiester linkages in the covalent backbone of DNA and RNA. The phosphodiester bonds (one of which is shaded in the DNA) link successive nucleotide units. The backbone of alternating pentose and phosphate groups in both types of nucleic acid is highly polar. The 5 end of the macromolecule lacks a nucleotide at the 5 position, and the 3 end lacks a nucleotide at the 3 position. 

Nucleotides are the building blocks of nucleic acids their structures and biochemistry were discussed in chapter 23. When a 5 -phosphomononucleotide is joined by a phosphodiester bond to the 3 -OH group of another mononucleotide, a dinucleotide is formed. The 3 -5 -linked phosphodiester intemucleotide structure of nucleic acids was firmly established by Lord Alexander Todd in 1951. Repetition of this linkage leads to the formation of polydeoxyribonucleotides in DNA or polyribonucleotides in RNA. The structure of a short polydeoxyribonucleotide is shown in figure 25.3. The polymeric structure consists of a sugar phosphate diester backbone with bases attached as distinctive side chains to the sugars. 

Why is the bond holding nucleotides together in nucleic acids called a phosphodiester bond ... 

RNA and DNA polymerases catalyze the same reaction mechanistically, involving hydrolysis of a nucleotide triphosphate to release pyrophosphate and form a phosphodiester bond. In both cases, the order of nucleotide addition is specified by the template, and synthesis of the growing nucleic acid chain is in a 5 to 3 direction (the enzymes move in a 3 to 5 direction along the template strand). In addition to the obvious difference in substrates (RNA polymerase utilizes ribonucleotides, whereas DNA polymerase utilizes deoxyribonucleotides), these two enzymes differ in their requirements for initiating synthesis ... 

Nuclease. An enzyme that cleaves phosphodiester bonds of nucleic acids. 

Buzayan, J.M., Hampel, A. and Bruening, G. (1986) Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res., 14, 9729-9743. 

EXONUCLEASE An enzyme that digests a nucleic acid (e.g., DNA) by removing nucleotides from the ends of strands or internal strand breaks (i.e., it does not cleave internal phosphodiester bonds). (See also ENDONUCLEASE) EXPOSURE Amount of material ingested, inhaled, or otherwise received by an organism. (See also DOSE) FIDELITY The biochemical concept that describes the accuracy of the enzymatic copying of DNA or ENA. 

Polynucleotide polymerases, or nucleotidyl transferases, are enzymes that catalyze the template-instructed polymerization of deoxyribo- or ribonu-cleoside triphosphates into polymeric nucleic acid - DNA or RNA. Depending on their substrate specificity, polymerases are classed as RNA- or DNA-dependent polymerases which copy their templates into RNA or DNA (all combinations of substrates are possible). Polymerization, or nucleotidyl transfer, involves formation of a phosphodiester bond that results from nucleophilic attack of the 3 -OH of primer-template on the a-phosphate group of the incoming nucleoside triphosphate. Although substantial diversity of sequence and function is observed for natural polymerases, there is evidence that many employ the same mechanism for DNA or RNA synthesis. On the basis of the crystal structures of polymerase replication complexes, a two-metal-ion mechanism of nucleotide addition was proposed [1] during this two divalent metal ions stabilize the structure and charge of the expected pentacovalent transition state (Figure B.16.1). 

The nucleases are enzymes that hydrolyse nucleic acids, either deoxyribonucleases (DNases) that have DNA as the substrate or ribonucleases (RNases) that have ribonucleic acids as the substrate. The DNases hydrolyse the phosphodiester linkages between the deoxyribose molecules of DNA, and similarly, the RNases attack the equivalent bonds in RNA. There are many nucleases found in mammalian tissues, and as in the case of the peptidases, they can be divided into the categories endo and exo based on whether they attack bonds in the interior of the nucleic acid molecule or remove nucleosides from the end termini of the chains. They... 

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