Phosphodiester link

Oligonucleotides contain about 50 or fewer nucleotides held together by phosphodiester links polynucleotides can contain thousands of nucleotides... 

Figure 14.15 Major types of modification potentially made to an oligo s phosphodiester linkage in order to increase their stability or enhance some other functional characteristic. The native phosphodiester link is shown to the left...

Bacteria contain enzymes that catalyse the breaking of phosphodiester links between nucleotides in DNA at specific sites, to which the enzyme is directed by a short sequence of bases. These are known as restriction enzymes and they have resulted in remarkable progress in analysing sequences of DNA fragments. They are endonucleases, i.e., they cleave DNA at the phosphodiester bonds within, rather than at the ends, of DNA chains. They cleave bonds such that sequences of nucleotides, typically 4-8 base pairs, are produced. These are the restriction sequences. 

Phosphodiester links within the chain (endonucleases) or at the end of a chain (exonucleases) for details of nucleases reactions see Appendix 10.1. 

The enzyme used is DNA ligase. It catalyzes the formation of a phosphodiester link between adjacent 5 -phosphoryl and 3 -hydroxyl groups in double-stranded DNA. DNA ligase from E. coli... 

DNA ligase catalyzes the covalent linkage of two segments of DNA. A phosphodiester link is formed between adjacent 5 -phosphoryl and 3 -hydroxyl groups within duplex DNA. In other words, DNA ligase... 

Finally, studies of the calcium dependent turnover of glucose-1-phosphate on phosphoglucomutase in rat cortical synaptosomes and in PC-12 cells suggest that the incorporation of phosphodiester-linked Glc is dependent on intracellular calcium levels [106]. Depolar-... 

The chemical synthesis of oligoribonucleotides containing vicinal 2, 5 - and 3, 5 -phosphodiester links, which are found at the branching site of lariat mRNA during mRNA splicing, has been reviewed.267 The synthesis of a substantial number of triribonucleoside diphosphates (184) has been reported analogues of (184 ... 

Coenzyme A, CoASH, is ubiquitously found in living organisms and consists of a phosphodiester linking adenosine and pantetheine residue with a reactive terminal thiol group ... 

In DNA and RNA, the chain of phosphodiester links and sugar rings is known as the phosphodiester backbone the bases may be regarded in both cases almost as side-chains . By convention, DNA or RNA chains begin at the 5 -end (i.e., where carbon atom C-5 of the terminal residue is not involved in a phosphodiester link) and terminate at the 3 -end (where carbon atom C-3 is not involved in a phosphodiester link). Each chain is therefore said to run by convention from S to S (5 —>-3 ). Several shorthand conventions are used to describe the sequences of deoxynucleotide or nucleotide residues in DNA and RNA respectively. These include the Fischer, linear alphabetic and condensed alphabetic conventions that draw upon the letter codes for bases and deoxynucleosides or nucleosides as described previously (Figure 1.59). 

Figure 1.58 Schematic illustration of formation of phosphodiester link from deoxynucleotides for generation of DNA. Identical link can be formed from nucleotides for the generation of RNA.

Figure 1.61 Conformational freedom is heavily restricted in nucleic acids owing to lack of free rotation about 0 —P and P—0 bonds, (a) Nucleic acid equivalent of the Ramachandran plot illustrating the theoretically allowed angles of C and a. (b) Free rotation is primarily damped owing to the gauche effect in which lone-pair-o- orbital overlaps in phosphodiester links generate double bond character in 0—P bonds that restrict free rotation (adapted from Govil, 1976 [Wiley]).

Figure 2.4 Comparison of PNA and DNA. PNA contains neither phosphodiester links nor the fi-D-2 -deoxyribofuranose rings. Instead the backbone consists of W-(2-aminoethyl)-glycine repeat units conjoined by peptide links. The main purine and pyrimidine bases of DNA are linked to the the PNA backbone by methylene carbonyl bridge linkages. Watson-Crick base-complementary PNA strands are capable of Watson-Crick base pairing and hence anti-parallel double helix formation.

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