Polymers, biological nucleic acids

Polymers, either natural or synthetic, have become an integral part of our daily life and also have a vital role in industry and the economy. Natural polymers like nucleic acids, proteins, polysaccharides, etc., have specific roles such as transportation, processing and manipulation of biological information, or and to act as fuel for cellular activity and to provide structural elements in living systems [1]. On the other hand, synthetic polymers like nylon, polyethylene, and polyurethane have penetrated our daily lives in such a way that they have become... 

FIGURE 1.10 The sequence of monomeric units in a biological polymer has the potential to contain information if the diversity and order of the units are not overly simple or repetitive. Nucleic acids and proteins are information-rich molecules polysaccharides are not. 

The nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are biological polymers that act as chemical carriers of an organism s genetic information. Enzyme-catalyzed hydrolysis of nucleic acids yields nucleotides, the monomer units from which RNA and DNA are constructed. Further enzyme-catalyzed hydrolysis of the nucleotides yields nucleosides plus phosphate. Nucleosides, in turn, consist of a purine or pyrimidine base linked to Cl of an aldopentose sugar—ribose in RNA and 2-deoxyribose in DNA. The nucleotides are joined by phosphate links between the 5 phosphate of one nucleotide and the 3 hydroxyl on the sugar of another nucleotide. 

Most biological polymers, such as proteins and nucleic acids and some synthetic polymers, have relatively inflexible chains. For rigid particles, the size is no longer of predominant importance, because the polymer chain is no longer in the form of a flexible random coil instead, shape becomes an important parameter. Following are some theoretical proposals for the estimation of the shape factor p from the viscosity measurement (table 4). The term f/fo is sometimes denoted as p, Perrin constant. 

The investigations directed at the synthesis of thymine-substituted polymers demonstrate that the type of functional groups displayed by nucleic acid bases are compatible with ROMP. Moreover, the application of MALDI-TOF mass spectrometry to the analysis of these polymers adds to the battery of tools available for the characterization of ROMP and its products. The utility of this approach for the creation of molecules with the desired biological properties, however, is still undetermined. It is unknown whether these thymine-substituted polymers can hybridize with nucleic acids. Moreover, ROMP does not provide a simple solution to the controlled synthesis of materials that display specific sequences composed of all five common nucleic acid bases. Nevertheless, the demonstration that metathesis reactions can be conducted with such substrates suggests that perhaps neobiopolymers that function as nucleic acid analogs can be synthesized by such processes. 

Fluorescence is also a powerful tool for investigating the structure and dynamics of matter or living systems at a molecular or supramolecular level. Polymers, solutions of surfactants, solid surfaces, biological membranes, proteins, nucleic acids and living cells are well-known examples of systems in which estimates of local parameters such as polarity, fluidity, order, molecular mobility and electrical potential is possible by means of fluorescent molecules playing the role of probes. The latter can be intrinsic or introduced on purpose. The high sensitivity of fluo-rimetric methods in conjunction with the specificity of the response of probes to their microenvironment contribute towards the success of this approach. Another factor is the ability of probes to provide information on dynamics of fast phenomena and/or the structural parameters of the system under study. 

Ion-exchange resins are cross-linked polymers which are typically polystyrene, cellulose or agarose based. Polystyrene is hydrophobic in nature and useful for inorganic ions and small molecules while cellulose and agarose are hydrophilic and more useful for the larger, biologically important molecules, e.g. proteins and nucleic acids, which either would be adversely affected by a hydrophobic environment or could not gain access to the small pore structure. 

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