Biopolymers nucleic acids

Fundamental building blocks (amino acids, carbohydrates, lipids, nucleotides), organic and inorganic prosthetic groups, biopolymers (nucleic acids, peptides/ proteins, polysaccharides), membranes. 

G. Klebe, M. L. Verdonk, Biopolymers (Nucleic Acid Sciences) 2002, 99-110. Docking calculations using GOLD (G. Jones, P. Willett, R. C. Glen,... 

Klostermeier, D., Millar, D. P, Time resolved Fluorescence Resonance Energy Transfer a Versatile Tool for the Analysis of Nucleic Acids, Biopolymers (Nucleic Acid Sci.) 2002, 61, 159 179. 

The chapter concludes with a discussion of the nucleic acids, which are the genetic material of living systems and which direct the biosynthesis of proteins. These two types of biopolymers, nucleic acids and proteins, are the organic chemicals of life. 

The pathway of the book as a whole leads from less reactive, chiral molecules, which are useful as membrane components (lipids steroids, carbohydrates), to molecules that react reversibly with light and electrons and are helpful in energy conversion (carotenes, porphyrins, redoxactive vitamins), and finally to helical and reactive biopolymers (nucleic acids, proteins), which are used as frameworks for molecular machinery. Natural compounds that do not form important supramolecular assemblies or have not been used extensively as model compounds (e.g., alkaloids, antibiotics, metabolites) are not treated in separate chapters, but appear occasionally. 

Bergner, A., Gunther, J., Hendlich, M., Klebe, G., and Verdonk, M. (2001) Use of relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects. Biopolymers (Nucleic Acid Science), 61, 99-110. 

We have studied two of the three major kinds of biopolymers polysaccharides in Chapter 21 and proteins in Chapter 22. Now we will look at the third kind of biopolymer—nucleic acids. There are two types of nucleic acids deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DMA encodes an organism s entire hereditary information and controls the growth and division of cells. In all organisms (except certain viruses), the genetic information stored in DNA is transcribed into RNA. This information can then be translated for the synthesis of all the proteins needed for cellular structure and function. 

Biopolymers. Nucleic acids, proteins, and polysaccharides require special perception and heuristics to emphasize their polymeric nature and to orient the individual residues harmoniously. Like condensed-text organics, biopolymers may additionally contain textual regions. 

Nucleic acids are acidic substances present m the nuclei of cells and were known long before anyone suspected they were the primary substances involved m the storage transmission and processing of genetic information There are two kinds of nucleic acids ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) Both are complicated biopolymers based on three structural units a carbohydrate a phosphate ester linkage between carbohydrates and a heterocyclic aromatic compound The heterocyclic aro matic compounds are referred to as purine and pyrimidine bases We 11 begin with them and follow the structural thread... 

In this section we briefly consider the osmotic pressure of polymers which carry an electric charge in solution. These include synthetic polymers with ionizable functional groups such as -NH2 and -COOH, as well as biopolymers such as proteins and nucleic acids. In this discussion we shall restrict our consideration... 

Biopolymers are the naturally occurring macromolecular materials that are the components of all living systems. There are three principal categories of biopolymers, each of which is the topic of a separate article in the Eniyclopedia proteins (qv) nucleic acids (qv) and polysaccharides (see Carbohydrates Microbial polysaccharides). Biopolymers are formed through condensation of monomeric units ie, the corresponding monomers are amino acids (qv), nucleotides, and monosaccharides, for proteins, nucleic acids, and polysaccharides, respectively. The term biopolymers is also used to describe synthetic polymers prepared from the same or similar monomer units as are the natural molecules. 

There are approximately 20 common naturally occurring amino acids, hence 20 different R groups that appear as pendents on the polyamide chain. Many other amino acids have been isolated or prepared, each representing a variation in R. The number of isomeric stmctures is myriad. Protein biosynthesis is mediated by other biopolymers, the nucleic acids. 

Analytical techniques that utilise biopolymers, ie, natural macromolecules such as proteias, nucleic acids, and polysaccharides that compose living substances, represent a rapidly expanding field. The number of appHcations is large and thus uses hereia are limited to chiral chromatography, immunology, and biosensors. 

Biopolymers Naturally occurring macromolecules that include proteins, nucleic acids, and polysaccharides. 

Synthesis of reactive nucleic acids derivatives and their use for investigations of structure and functions of biopolymers 98UK688. 

The biological function of biopolymers such as polypeptides, proteins, nucleic acids etc. depends strongly on their ordered structure which is determined by the pattern of inter- and intramolecular interactions given by the primary structure. 

Just as proteins are biopolymers made of amino acids, nucleic acids are biopolv-mers made of nucleotides joined together to form a long chain. Each nucleotide is composed of a nucleoside bonded to a phosphate group, and each nucleoside is composed of an aldopentose sugar linked through its anomeric carbon to the nitrogen atom of a heterocyclic purine or pyrimidine base. 

These sorbents may be used either for selective fixation of biological molecules, which must be isolated and purified, or for selective retention of contaminants. Selective fixation of biopolymers may be easily attained by regulation of eluent polarity on the basis of reversed-phase chromatography methods. Effective isolation of different nucleic acids (RNA, DNA-plasmid) was carried out [115, 116]. Adsorption of nucleosides, nucleotides, tRN A and DNA was investigated. It was shown that nucleosides and nucleotides were reversibly adsorbed on... 

Current analytical methods have difficulty detecting picogram levels of nucleic acids, particularly when high levels of other biopolymers (e.g., proteins) are present. The most widely used assay method employed by the pharmaceutical industry involves a nick translation DNA hybridization method (1). This assay offers high sensitivity and selectivity but has a number of drawbacks. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

The development of DNA sensors and high-density DNA arrays has been prompted by the tremendous demands for innovative analytical tools capable of delivering the genetic information in a faster, simpler, and cheaper manner at the sample source, compared to traditional nucleic acid assays. Nanoparticle-biopolymer conjugates offer great potential for DNA diagnostics and can have a profound impact upon bioanalytical chemistry. Nanoparticle/polynucleotide assemblies for advanced electrical detection of DNA sequences have been reviewed by Wang [145]. 

Synthetic examples include the poly(meth)acrylates used as flocculating agents for water purification. Biological examples are the proteins, nucleic acids, and pectins. Chemically modified biopolymers of this class are carboxymethyl cellulose and the lignin sulfonates. Polyelectrolytes with cationic and anionic substituents in the same macromolecule are called polyampholytes. 

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