Nucleic acids measurement

All biochemical laboratory activities, whether in education, research, or industry, are replete with techniques that must be carried out almost on a daily basis. This chapter outlines the theoretical and practical aspects of some of these general and routine procedures, including use of buffers, pH and other electrodes, dialysis, membrane filtration, lyophilization, centrifugal concentration, and quantitative methods for protein and nucleic acid measurement. 

For the determination of the antiplasmodial activity of the compounds, the multi-resistant Dd2 strain of Plasmodium falciparum was used and [8-3H]-hypoxanthine incorporated into the parasitic nucleic acids measured. The plasmodia were incubated with 0.3% parasitemia and an erythrocyte hematocrit of 2.5% in the presence of different concentrations of selected experimental agents in a final volume of 200 xl. The medium employed was RPMI 1640 containing 10% of heat-treated human serum and 3 mg/1 of gentamycin. In the incubations, the concentrations of the compounds varied from 0.3 to 100 xM. After 48 hours, each batch was treated with 50 xl [8-3H]hypoxanthine and incubated additional 18 hours. Testing results are provided in Table 1. 

The polymerase chain reaction (PCR), branched-DNA analyses, and related techniques are highly sensitive methods to quantify both viral RNA and provi-ral DNA. Proviral DNA is a measure of the number of cells infected, whereas viral RNA reflects production of virions. As with the measurement of viral products, one cannot easily determine whether the nucleic acids measured represent infectious viruses. A number of commercially available technologies, exist for the measurement of HIV nucleic acids, since this methodology is now the standard of care for AIDS patients. Laboratories performing their own quantitative analyses have generally used a modification of the quantitative competitive (QC)-PCR (66). 

One of the first scarming adiabatic calorimeters designed in the past was the DASM IM microcalorimeter [107], used to determine the apparent molar heat capacity and conformational changes of proteins and nucleic acids. Measurements are performed in the temperature interval from 10 to 100°C, the shield heating rate can vary from 0.1 deg-min to 2 deg-min", and the sensitivity of the instmment is 4-10 cal-deg". A... 

M.C. Cheung, R. LaCroix, B.K. McKenna, L. Liu, J. Winkelman, D.J. Ehrlich, Intracellular protein and nucleic acid measured in eight cell types using deep-ultraviolet mass mapping. Cytometry A 83, 540-551 (2013)... 

The NAs such as DNA usually used in the experiments consist of 10" -1 o nucleotides. Thus, they should be considered as macrosystems. Moreover, in experiments with wet NA samples macroscopic quantities are measured, so averaging should also be performed over all nucleic acid molecules in the sample. These facts justify the usage of the macroscopic equations like (3) in our case and require the probabilities of finding macromolecular units in the certain conformational state as variables of the model. 

Fohc acid is a precursor of several important enzyme cofactors required for the synthesis of nucleic acids (qv) and the metaboHsm of certain amino acids. Fohc acid deficiency results in an inabiUty to produce deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and certain proteins (qv). Megaloblastic anemia is a common symptom of folate deficiency owing to rapid red blood cell turnover and the high metaboHc requirement of hematopoietic tissue. One of the clinical signs of acute folate deficiency includes a red and painhil tongue. Vitamin B 2 folate share a common metaboHc pathway, the methionine synthase reaction. Therefore a differential diagnosis is required to measure foHc acid deficiency because both foHc acid and vitamin B 2 deficiency cause... 

One of the most important and exciting advances in modern biochemistry has been the application of spectroscopic methods, which measure the absorption and emission of energy of different frequencies by molecules and atoms. Spectroscopic studies of proteins, nucleic acids, and other biomolecules are providing many new insights into the structure and dynamic processes in these molecules. 

Microarray hybridization is a process by which nucleic acids are detected by hybridizing with complementary sequences bound to wafers at specific array coordinates. Hundreds to thousands of gene products may be measured in a single experiment. 

Besides trace metals, adsorptive stripping voltammetry has been shown to be highly suitable for measuring organic compounds (including cardiac or anticancer drugs, nucleic acids, vitamins, and pesticides) that exhibit surface-active properties. 

A great deal of our knowledge about the interior of solids has come from x-ray diffraction. This important technique is used to determine the arrangement of atoms in solid compounds and to measure bond lengths and angles. Almost all recent advances in molecular biology have stemmed from the application of this technique to determine the structures of molecules such as proteins and nucleic acids. 

Several other techniques for have evolved for biochemical assays. In chapter 2 of this book, Omann and Sklar report on a method of fluoroimmunoassay where the bound and unbound antigen are separated by the quenching of fluorescence that accompanies antibody binding. Then, in chapter 3, Holl and Webb show how they achieved a sensitive measurement of nucleic acids by the enhancement in fluorescence that accompanies the binding of fluorescent dyes to nucleic acids. Chandler et al, also used fluorescence enhancement to monitor calcium mobility in neutrophil cells. 

It should be pointed out that when using ethidium bromide the sensitivity of the assays varies depending on the physical state of the nucleic acids (see Table I). Ethidium does not discriminate between RNA and DNA, although dyes are available which bind DNA exclusively, so the relative amounts of each may be determined by taking two sets of measurements. Alternatively, nucleases (DNA-ase or RNA-ase) can be used to exclusively remove one or the other in a mixture. Nucleic acids from different sources (see Table II) also show a variation in sensitivity, and the fluorescence assay lacks the selectivity of the hybridization technique. Nevertheless, for rapid screening or quality-control applications the fluorescence assay is still the method of choice. 

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. 

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. 

Since the pioneering work of Kleymann et al. (2002), Betz et al. (2002), Baumeister et al. (2007), and Crute et al. (2002), who showed that compounds identified as inhibitors of the helicase-primase enzyme complex could alleviate herpesvirus-induced disease in animal models, the attention of researchers developing antiviral compounds has been drawn more and more towards the virus-encoded helicases, particularly those of Herpes viruses and of RNA viruses such as Hepatitis C Virus (HCV) and SAKS coronavirus (SARS-CoV). Enzyme activity is usually assayed by measuring NTPase activity in the presence of an appropriate nucleic acid co-substrate although, more recently, novel fiuorimetric and luminescence principles have been applied to the measurement of strand unwinding and/or translocation of the protein along the nucleic acid (Frick 2003, 2006). 

The refinement of other analytical methods, such as electrophoresis [34,36], the various techniques of optical spectroscopy [103-105], and nuclear magnetic resonance [201], is supplemented by the recent advances in real-time affinity measurements [152,202], contributing to the understanding of biomolecular reactivity. Taken together, the improvement of analytical methods will eventually allow a comprehensive characterization of the structure, topology, and properties of the nucleic acid-based supramolecular components under consideration for distinctive applications in nanobiotechnology. 

Human tissues can synthesize purines and pyrimidines from amphibolic intermediates. Ingested nucleic acids and nucleotides, which therefore are dietarily nonessential, are degraded in the intestinal tract to mononucleotides, which may be absorbed or converted to purine and pyrimidine bases. The purine bases are then oxidized to uric acid, which may be absorbed and excreted in the urine. While little or no dietary purine or pyrimidine is incorporated into tissue nucleic acids, injected compounds are incorporated. The incorporation of injected [ H] thymidine into newly synthesized DNA thus is used to measure the rate of DNA synthesis. 

This technique provides an easy and convenient method to evaluate the association of small molecules to various polymorphic forms of nucleic acid structures from the measurement of absorbance changes in the absorption maximum of the hgand, where the nucleic acid has no absorbance. Information about overall DNA/RNA base preference and nature of binding can also... 

The previous biomarkers relate to phenotypic assessments of microbial diversity and most will probably measure a restricted part of the total microbial pool, since not alt markers will be expressed uniformly by every cell. In contrast, methods involving the detection of nucleic acids may be directly applicable to all microorganisms provided that the complete extraction of DNA (lysis of cells) or permea-bilization of cells can be achieved. 

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