Nucleic acid chains

End (Section 28.1) The end of a nucleic acid chain with a free hydroxyl group at C3. ... 

When working as a guest at the famous Salk Institute for Biomedical Research in La Jolla (California), Eschenmoser (now a professor emeritus) was able to study a series of sugar derivatives as possible candidates for pre-RNA models. It turned out that five atoms in the nucleic acid chain suffice, if they are present in an optimal extended form. This was shown using a polymer containing (L)-a-threofuranosyl-(3 2 )-oligonucleotides (TNA) (Fig. 6.18) (Schoning et al., 2000). 

It is the sequence of different bases in the oligonucleotide that is of functional importance and therefore the nucleic acid chain is usually expressed simply as its base sequence, e.g. 

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 ... 

Does intercalation of flat molecules into nucleic acid chains have a biochemical function Aromatic rings of amino acid side chains in proteins designed to interact with... 

Many enzymes are named by adding the suffix -ase to a word, or words, descriptive of the type of enzymatic activity. Thus, esterases hydrolyze esters, proteinoses hydrolyze proteins, reductases achieve reductions, and synthetases achieve syntheses of polypeptide chains, nucleic acid chains, and other molecules. 

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 ... 

Once the early code reader had been produced from RNA, which is the active component even in modern ribosomes, the potential information stored in the nucleic acid chains became defined and accessible and the protein products could be recruited as expeditors of the expression of a limitless reservoir of information. The reiteration of complementary strands of nucleic acids never stopped even when all possibilities of every possible protein plus all the failures were produced many times. All structural motifs were exhausted and all of them were potentially available to nascent cells they just had to be there to be collected in a grab-bag fashion. How much nucleic acid material was there Was it enough to buy all the tickets in the lottery ... 

Figure 8.1 The two sugars, five nitrogenous bases, and phosphate that occur in nucleic acids. Each fundamental unit of nucleic acid is a nucleotide, an example of which is shown. The single letter beside the structural formula of each of the nitrogenous bases is used to denote the base in shorthand representations of the nucleic acid chains.

The double helix has the ability to wind and unwind so that the nucleic acid chain can duplicate itself. That duplication process happens every time a cell divides. 

Figure 1.28 (a) The general structure of a nucleotide, (b) A schematic representation of a section of a nucleic acid chain, (c) The bases commonly found in DNA and RNA. These bases are indicated by the appropriate letter in the structures of Nucleic acids. Thymine is not found in RNA it is replaced by uracil, which is similar in shape and structure, (d) Examples of nucleosides found in DNA and RNA... 

Nucleic acids have a primary, secondary, and tertiary structure analogous to the classification of protein structure. The sequence of bases in the nucleic acid chain gives the primary structure of DNA or RNA. The sequence of bases is read in a 5 -> 3 direction, so that you would read the structure in the next figure as ACGT. See Figure 8-1. 

MB is used as a temporary stain to examine and verify DNA and RNA under a microscope or in a gel. MB is less sensitive as ethidium bromide, but does not intercalate into nucleic acid chains. Recent studies have shown that MB immobilized on metal oxide substrates can mediate NADH catalytic oxidation. 

Nucleic acid probes are commonly labeled by enzymatic incorporation of radiolabeled nucleotides or enzymatic addition of radiolabeled phosphate groups to the nucleic acid chain. Proteins, in particular immunoglobulins, are labeled commonly by direct... 

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