Types of Polynucleotides

Within cells, DNA is organized into tightly paeked structures called chromosomes. These chromosomes are duplieated before cells divide, 

RNA is a special macromolecule in biology because it is able to store and transmit information as well as catalyze some processes. One of these processes is protein synthesis where mRNA molecules direct the assembly of proteins on ribosomes. In contrast to DNA, it has a single strand structure. There are several types of RNA, which are differentiated by their functions. The three most common types are messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA). 

Messenger RNA can be considered the postal carrier because it earries the genetic information to the ribosome, the site of protein syn- 

In terms of green pol5mier chemistry, we are going to concentrate on the synthesis and degradation of these macromolecules. 

Francis Crick and James Watson established the double helix structure of DNA, using the x-ray pictures taken by Rosalind Franklin and Maurice Wilkins. 

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In other experiments (Walker etal. 1992) using another type of polynucleotide sequence, preferential fragmentations were seen at other sites, thus among others at sequence 5 TTTT. In both cases, the preferential cuts limit the number of cleaved polynucleotides and gel electrophoresis only revealed a small number of compounds. On the other hand, cleavage is statistical with the aglycon and this explains the presence of a good number of spots of uniform intensity. 

DNA is not normally broken down, except after cell death and during DNA repair. RNA is turned over in much the same way as protein. The enzymes involved in breaking down both types of polynucleotides are the nucleases, or more specifically deoxy-ribonucleases and ribonucleases, they hydrolyze DNA and RNA, respectively, to oligo-nucleotides which can be further hydrolyzed (Fig. 14-38) so eventually purines and pyrimidines are formed. 

The prefixes d and r, which represent deoxyribose of DNA and ribose of RNA respectively, are omitted where an implication of the type of polynucleotides is obvious from the context of nucleotides involved (i.e. T for DNA, while U for RNA). In the linear code representation, the nucleotide sequence is written from the left for the 5 -end to the right for the 3 -end (e.g. coding nucleotide sequence for human lysozyme (Pasta format))... 

Locked nucleic acids (LNA) (10.96d,e), are types of polynucleotide (RNA) chain in which eithCT the 2 or the 3 O atom is linked to the 4 C atom by a methylene bridge, thns restricting the conformation of the sugar ring. 

Four types of polynucleotide chains are found amongst these, for example. 

Although it is generally accepted that in vivo various types of polynucleotide polymerases exist (some using DNA as primer for RNA synthesis, others using RNA as primer), in vitro the activity of the enzymes is not necessarily restricted by the nature of the primer. In vitro both DNA and RNA may act as primers for certain RNA polymerases. 

Two types of polynucleotides may be distinguished through their structure deoxyribonucleic acids (DNA) with molecular weights as high as 100 million and ribonucleic acids (RNA) with molecular weights up to 500,000. 

Other results concerned with polynucleotide-programmed systems lead to a different conclusion inhibition by macrolides is at the level of the peptidyl transferase. This action depends on the macrolide used, and on the type of polynucleotide engaged. For example, erythromycin inhibits polylysyl-puromycin release (poly-A-programmed) but stimulates acetyl-phenylalanyl-puromycin formation (poly-U-programmed). 

Snake venom exonucleases can hydrolyze almost any type of polynucleotide of any chain length. The type of bases, linkages, and sugars do not have much effect on the rate of hydrolysis. Thus, the enzyme hydrolyzes RNA, DNA, synthetic polynucleotides, and native or denatured DNA. 

Certain types of molecules, especially polypeptides and polynucleotides, lend themselves to synthesis on solid supports. In such syntheses, the starting material is attached to a small particle (bead) or a surface and the molecule remains attached during the course of the synthetic sequence. Solid phase synthesis also plays a key role in creation of combinatorial libraries, that is, collections of many molecules synthesized by a sequence of reactions in which the subunits are systematically varied to create a range of structures (molecular diversity). 

In the reaction of unprotected uridine with tri(imidazolyl-l)phosphine (ratio 1 1.5) under mild conditions (THF, — 78° to 0 °C, 10 min) and subsequent oxidation with iodide, two types of polymers [(Up)n (n = 2-6) and (Up)nU (n = 2—5)] are formed. Additives such as metal cations or polynucleotides (poly U and poly A) acting as templates in the oxidation process showed a significant effect on the ratio of the 3, 5 -linked to 2, 5 -linked oligomer 17 177 ... 

The exact nature of the lesion in DNA is unknown, and so is the type of DNA that is attacked. Recent X-ray crystallographic studies, as well as other physicochemical studies, have made it clear that DNA is not simply a polynucleotide, folded as Watson and Crick (106) proposed. There are three main conformational types of DNA they each keep the hydrogen-bonded bases in the center of the helix, but may tilt them by a "propellor twist," may slide them from the center of the helix in the plane of the base pairs, and may vary the amount of rotation from one base pair to the next up the helical axes. 

A detailed discussion of the modes of occurrence and biological importance of the polynucleotides is outside the scope of this article. However, in examining the structures of polynucleotides, it is necessary to take into consideration the origins of the materials studied. The pioneer researches of Caspersson114 indicated that deoxyribonucleic acids are present exclusively in the nucleus, whereas ribonucleic acids are found chiefly in the cytoplasm and only to a small extent in the nucleus. This general outline of the distribution of nucleic acids within the cell has been confirmed and extended by more recent work,116 and it has been possible to isolate both types of nucleic acid from different cellular fractions of the same tissue.116... 

The bulk of all carbohydrates in nature exists in the form of polysaccharides. These are very large molecules formed by linking together long chains of monosaccharide units. These chains may be linear, like polypeptides or polynucleotides, or branched. They may contain a single type of monosaccharide unit, similar to polyglycine or polyA for example, or two or more types of monosaccharide, like nucleic acids (four types of nucleotides) or proteins (20 types of amino acids). However, polysaccharides that contain more than two types of monosaccharide are rare in nature. 

Metal ions can attach themselves at two different types of sites on a polynucleotide—i.e., the phosphate and the donor groups on the bases. Some of the metal ions do indeed bind at one site, and some metal ions at the other. Those binding to the phosphate will promote the cleavage of the phosphate bond, whereas metal ions binding on the base will inhibit such cleavage in a manner that illustrates one of Dr. Jones points very well. 

RNA also differs from DNA in that there are not the same regularities in the overall composition of its bases and it usually consists of a single polynucleotide chain. There are different types of RNA, which fulfill different functions. About 80% of the RNA in a cell is located in the cytoplasm in clusters closely associated with proteins. These ribonucleoprotein particles specifically are called ribosomes, and the ribosomes are the sites of most of the protein synthesis in the cell. In addition to the ribosomal RNA (rRNA),... 

The mechanism of action of spleen exonuclease is similar to that seen for venom exonuclease (19-21) but different from the processive type of attack exhibited by E. coli RNase II, sheep kidney exonuclease, and polynucleotide phosphorylase (22, 23), in which cases each polynucleotide molecule is completely degraded before the enzymes attack a new molecule. The results of Bernardi and Cantoni (12) contradict the previous beliefs that the enzyme has an intrinsic, though weak, endonucleolytic activity (5) and that a phosphate group in a terminal 5 position makes a polynucleotide chain completely resistant to the enzyme (15, 24, 25). 

The structural components of nucleic acids. Nucleic acids are long linear polymers of nucleotides, called polynucleotides, (a) The nucleotide consists of a five-carbon sugar (ribose in RNA or deoxyribose in DNA) covalently linked at the 5 carbon to a phosphate, and at the 1 carbon to a nitrogenous base. (b) Nucleotides are distinguished by the types of bases they contain. These are either of the two-ring purine type or of the one-ring pyrimidine type. 

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