Bulk nucleic acids

There are several different methods based on 16S rRNA sequences that can be used to study bacterial community structure. The first approach involves extracting bulk nucleic acids from samples and then using this material in subsequent molecular analyses. A large number of these methods involve the polymerase chain reaction (PCR). Using PCR, target gene sequences... 

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. 

As a result many different functioning structures may appear within the transient architecture of liquid water. This makes it possible for liquid water to perform in several roles. Water is thus comparable to a supramolecular assembly, and indeed it has been postulated to act as a template for macromolecular systems (e.g. nucleic acids) which have evolved and have breathed life into non-purposive molecular assemblies. In Table 1 we compare some characteristics and attributes of bulk water and the molecule of H2O. 

ASAXS provides valuable spatial information about ions associated to nucleic acids. Because ion resonance is X-ray energy specific, a particular ionic species can be targeted in ASAXS experiments (even in conditions where there are multiple ionic species in the bulk solution). In this section, we provide several examples of how ASAXS experiments can be used to study counterion atmospheres around DNA and RNA. 

Substrate channeling is a process by which two or more sequential enzymes in a pathway interact to transfer a metabolite (or intermediate) from one enzyme to another without allowing free diffusion of the metabolite into bulk solvent. (Ovadi, 1991 Srere, 1987 Anderson, 1999). The substrate tunneling is one of fundamental process of regulating enzymatic processes in cells. Glycolysis, biosynthesis of nucleic acids, aminoacids, and fatty acids are found to be among these processes. 

If intermolecular associations are formed, hydration water molecules are removed from the interacting parts of the surface of a protein or a nucleic acid. This occurs, if the macromolecules form complexes with other macromolecules or with small substrates as, for instance, in enzymatic reactions (see Fig. 23.11). Because the contact between these interacting molecules is direct, water of hydration molecules have to be displaced from both partners. The question arises whether the water molecules located at the surface jump into the bulk water or whether they glide along the surface of the macromolecule and give way to the incoming, interacting molecules. 

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