Nucleic acids constructing

Villa R., Folini M., Lualdi S., Veronese S., Daidone M.C., Zaffaroni N. Inhibition of telomerase activity by a cell-penetrating peptide nucleic acid construct in human melanoma cells. FEB.S. Lett. 2000 473 241-248. 

Figure 1.42 The three pyrimidine bases common to nucleic acid construction. Cytosine and thymine are found in DNA, while in RNA, uracil residues replace thymine. The associated sugar groups are bound in N-glycosidic linkages to the N-l nitrogen.

Transfection—the introduction of a nucleic acid construct into a cell(s) so that it remains intact and maintains its function. 

First, given the wide range of prebiotic nucleic acids, ribose-based polymers may be the most eminently suited for catalysis. Eschenmoser has pointed out, for example, that nucleic acids constructed from hexose nucleotides form inflexible ribbon structures,61 poorly suited for convoluting into the complex shapes that are required for catalysis (e.g., the backbone of the projected tertiary structure of the Tetrahymena self-splicing intron folds back on itself a number of times).62 Conversely, backbones composed of acyclic nucleotides may be too flexible to adopt stable secondary structures (since a great deal of entropy would necessarily be lost on freezing into a given conformer). Ribose, on the other hand, has a limited flexibility because of its pseudorotation cycle, and RNA can adopt a variety of helical conformations. 

It should be noted first that the fact that only enantiomers of tlie same optical rotation sign are found in proteins and nucleic acids - the homo part of homochirality - may be viewed as a necessity, most probably a consequence of natural selection. Protein molecules containing both d- and L-amino acids, nucleic acid constructed with the two enantiomers of the pentoses, would lack some of their key biological properties. Life as we know it could not exist with heterochiral proteins or nucleic acids. The alleged mystery thus concerns the chirality part, the actual nature of the enantiomers used l- rather than D-amino acids, and d- rather than L-pentoses. 

Much has been written on this topic. Relevant to the subject of this chapter is the fact that there seems to be no compelling cosmic reason - there may be a local one - why fife should use one or the other enantiomer. The possibility of life forms similar to those we know, but functioning with proteins made of D-amino acids and with nucleic acids constructed with L-pentoses, is not ruled out in the present state of our knowledge. Whether D-amino acids could be used with D-pentoses, or the opposite, seems less likely if, as may well have been the case, steric interactions between the two kinds of molecule played an important role in the origin of life. 

An organism s nucleic acids construct its proteins. And, given that the proteins determine how the organism looks and behaves, no job could be more essential. 

EN] NUCLEIC ACID CONSTRUCTS AND METHODS FOR PRODUCING ALTERED SEED OIL... 

Small spherical viruses have a protein shell around their nucleic acid that is constructed according to icosahedral symmetry. Objects with icosahedral symmetry have 60 identical units related by fivefold, threefold, and twofold symmetry axes. Each such unit can accommodate one or severed polypeptide chains. Hence, virus shells are built up from multiples of 60 polypeptide chains. To preserve quasi-equivalent symmetry when packing subunits into the shell, only certain multiples (T = 1, 3, 4, 7...) are allowed. 

This chapter describes the chemistry of nucleotides and the m or classes of nucleic acids. Chapter 12 presents methods for determination of nucleic acid primary structure (nucleic acid sequencing) and describes the higher orders of nucleic acid structure. Chapter 13 introduces the molecular biology of recombinant DNA the construction and uses of novel DNA molecules assembled by combining segments from other DNA molecules. 

A rather limited collection of simple precursor molecules is sufficient to provide for the biosynthesis of virtually any cellular constituent, be it protein, nucleic acid, lipid, or polysaccharide. All of these substances are constructed from appropriate building blocks via the pathways of anabolism. In turn, the building blocks (amino acids, nucleotides, sugars, and fatty acids) can be generated from metabolites in the cell. For example, amino acids can be formed by amination of the corresponding a-keto acid carbon skeletons, and pyruvate can be converted to hexoses for polysaccharide biosynthesis. 

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. 

A typical procedure is shown in Figure 2. Other dyes besides ethidium can be used, although ethidium has an advantage in that its excitation emission bands are well removed from any protein absorbances. A standard curve can be constructed for the nucleic acid of concern and the limits of detection established. In Step 3, proteolytic enzymes may be substituted for heparin, or the step may be bypassed in the case of proteins which do not interfere. After measurement of the unknown sample the nucleic acid concentration may be simply calculated or read from the standard curve. 

Kristensen E. In vitro and in vivo studies on pharmacokinetics and metabolism of PNA constructs in rodents. In Peptide Nucleic Acids Methods and Protocols, Nielsen P. E. (Ed.). 2002, Humana Press (To-towa, N.J., United States) Copenhagen, pp. 259-269. 

To understand the extraordinary potential for DNA to be utilized as a material in construction processes, the general properties of this biomolecule will first be discussed. In addition, examples of naturally occurring nucleic acid-based nanostructures will be described that are of great importance both for cellular processes and conventional applications in molecular biotechnology. 

The use of DNA hybridization just described opens up a novel, uncomplicated, yet powerful strategy for supramolecular synthesis Many different devices are connected to a distinct sequence codon and are subsequently organized on a suitable template strand. The utilization of appropriate nucleic acid scaffolds should even allow the fabrication of highly complex supramolecular structures by means of a modular construction kit. For approximately 20 years, the work of Seeman and coworkers [8,27] have been engaged in the rational construction of ID, 2D, and 3D DNA frameworks. They use branched DNA... 

Bifunctional adamantyl, as a hydrophobic central core, can be used to construct peptidic scaffolding [151], as shown in Fig. 27. This is the reason why adamantane is considered one of the best MBBs. This may be considered an effective and practical strategy to substitute different amino acids or DNA segments on the adamantane core (Fig. 28). In other words, one may exploit nucleic acid (DNA or RNA) sequences as linkers and DNA hybridization (DNA probe) to attach to these modules with an adamantane core. Thus a DNA-adamantane-amino acid nanostructure may be produced. 

The reference standards are used to quantitate the standards that are employed in the kits to generate the standard curves. The kit standards are recombinant single-stranded DNA molecules that are added to either negative serum or plasma at known concentrations. Because the standard curve is not constructed with reference standards, Chiron initially chose to use the term equivalent to describe the units of nucleic acid quantitation in clinical samples. An equivalent was defined as the amount of nucleic acid in a clinical sample that gave a signal equal to one molecule of the reference standard nucleic acid. The term copy rather than equivalent is used to describe the units of nucleic acid quantitation in the HIV-1 bDNA assay. The terms are now used interchangeably. 

The latter is an interesting example of self-organizing chiral dendrimers. The construction of the dendrimer is based on the natural property of nucleic acids to recognize and specifically bind to complementary sequences. Pairwise hybridization of two designed DNA strands results in the formation of large monomers which have four single stranded arms and a double stranded waist (24, Fig. 12). 

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