Polynucleotide chains

Adding nucleotides to the 3 oxygen of an existing structure is called elongation and leads ultimately to a polynucleotide The most important polynucleotides are ribonu cleic acid (RNA) and deoxyribonucleic acid (DNA) As we shall see m later sections the polynucleotide chains of DNA and some RNAs are quite long and contain hundreds of thousands of bases... 

In addition to hydrogen bonding between the two polynucleotide chains the double helical arrangement is stabilized by having its negatively charged phosphate groups on the outside where they are m contact with water and various cations Na" Mg and ammonium ions for example Attractive van der Waals forces between the... 

By analogy to the levels of structure of proteins the primary structure of DNA IS the sequence of bases along the polynucleotide chain and the A DNA B DNA and Z DNA helices are varieties of secondary structures... 

FIGURE 28 9 The new polynucleotide chain grows by reaction of its free 3 OH group with the 5 triphosphate of an appropriate 2 deoxyribonucleoside... 

Section 28 14 The nucleotide sequence of DNA can be determined by a technique m which a short section of single stranded DNA is allowed to produce its complement m the presence of dideoxy analogs of ATP TTP GTP and CTP DNA formation terminates when a dideoxy analog is incorporated into the growing polynucleotide chain A mixture of polynucleotides dif fermg from one another by an incremental nucleoside is produced and analyzed by electrophoresis From the observed sequence of the comple mentary chain the sequence of the original DNA is deduced... 

The nucleotides are linked together via the phosphate groups, which connect the 5 -hydroxyl group of one nucleotide and the 3 -hydroxyl group of the next to form a polynucleotide chain (Fig. la). DNA is not a rigid or static molecule rather, it can adopt a variety of hehcal motifs. 

Fig. 6. Elements of RNA stmcture (a) uracil (b) a Watson-Crick A—U base pair and (c) a polynucleotide chain which reads from 5 — 3 ACUG, and...

For a 3-cm-long molecule of DNA to fit inside a cell so tiny that we can only see it with a microscope, the polynucleotide chain must be folded into a more compact form. Not only must the DNA be compacted, it must be folded in a way that allows it to cany out its main functions. The way the chain is folded defines the tertiary structure of a nucleic acid. 

FIGURE 1.5 The DNA double helix. Two complementary polynucleotide chains running in opposite directions can pair through hydrogen bonding between their nitrogenous bases. Their complementary nucleotide sequences give rise to structural complementarity. 

FIGURE 11.17 3 -5 phosphodiester bridges link nucleotides together to form polynucleotide chains. 

FIGURE 11.29 The vicinal—OH groups of RNA are susceptible to nucleophilic attack leading to hydrolysis of the phosphodiester bond and fracture of the polynucleotide chain DNA lacks a 2 -OH vicinal to its 3 -0-phosphodiester backbone. Alkaline hydrolysis of RNA results in the formation of a mixture of 2 - and 3 -nucleoside monophosphates. 

FIGURE 11.30 Cleavage in polynucleotide chains a cleavage yields 5 -phosphate products, whereas h cleavage gives 3 -phosphate products. 

H bonding also vitally influences the conformation and detailed structure of the polypeptide chains of protein molecules and the complementary intertwined polynucleotide chains which form the double helix in nucleic acids.Thus, proteins are built up from polypeptide chains of the type shown at the top of the next column. 

Primer Short synthetic polynucleotide chain (generally about 18-25 bases) to which new deoxyribonucleotides can be added by DNA polymerase. 

A method has been developed which is designed to remove nucleotide residues singly from a polynucleotide chain, and it is anticipated that more precise information will shortly be forthcoming regarding the order in which the nucleotides are linked.220 The method is based on the fact that esters of 3-oxo alcohols are unstable toward alkali. In agreement with this, it is found that the products of the action of periodate on adenosine 5-phosphate (XXX) or adenosine 5-(benzyl hydrogen phosphate) are hydrolyzed under very mild conditions. Thus, after removal of terminal, singly-esterified phosphoryl residues from a polynucleotide chain, it is anticipated that periodate oxidation and hydrolysis will result in the removal of the... 

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