Nucleic acids defined

The melting temperature (T ) of nucleic acids defines the thermal point at which 50% of the complementary molecule dissociate/melt away from their cognate strands or anneal/hybridize the two strands. The capacity to estimate melting temperatures is important because it helps the researcher select strand separation/hybridization temperatures, such as in polymerase chain reaction and microarray assays. A good approximation of melting tonperature for oligonucleotides takes the expression (Wallance et al., 1979) ... 

ChemSketch has some special-purpose building functions. The peptide builder creates a line structure from the protein sequence defined with the typical three-letter abbreviations. The carbohydrate builder creates a structure from a text string description of the molecule. The nucleic acid builder creates a structure from the typical one-letter abbreviations. There is a function to clean up the shape of the structure (i.e., make bond lengths equivalent). There is also a three-dimensional optimization routine, which uses a proprietary modification of the CHARMM force field. It is possible to set the molecule line drawing mode to obey the conventions of several different publishers. 

Cellular Protein Biosynthesis. The process of cellular protein biosynthesis is virtually the same in all organisms. The information which defines the amino acid sequence of a protein is encoded by its corresponding sequence of DNA (the gene). The DNA is composed of two strands of polynucleotides, each comprising some arrangement (sequence) of the four nucleotide building blocks of the nucleic acids adenine (A), thymine (T),... 

For a 3-cm-long molecule of DNA to fit inside a cell so tiny that we can only see it with a microscope, the polynucleotide chain must be folded into a more compact form. Not only must the DNA be compacted, it must be folded in a way that allows it to cany out its main functions. The way the chain is folded defines the tertiary structure of a nucleic acid. 

Nucleic acids undergo heUx-to-coil transition with increasing temperature. The transition temperature Tm is defined as the temperature corresponding to which the hyperchromicity, H (absorbance at any temperature/absorbance at room temperature) is given by ... 

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. 

A standard curve is defined by light emission from the standards containing known concentrations of recombinant bacteriophage. A quadratic equation is used to fit the curve to the RLU of the four standards. A maximum of two points from different standards may be eliminated by the data management software in order to achieve the best curve fit. The concentration of the target nucleic acid in the sample is determined from this standard curve. An example of the output from the data management software for the second-generation HCV assay is shown in Fig. 6. 

Second is the application of a wide range of experimental designs and techniques. DNA CT is observed in a diverse array of systems over different distance and time regimes. Consequently, a versatile approach which draws upon complementary methods is required to explore different facets of this chemistry and develop a complete picture. We interrogate a variety of nucleic acid assemblies using spectroscopic, biochemical and electrochemical tools to define mechanistic features, exploit biological applications, and explore biological consequences of DNA CT. 

Nucleic acids, DNA and RNA, are attractive biopolymers that can be used for biomedical applications [175,176], nanostructure fabrication [177,178], computing [179,180], and materials for electron-conduction [181,182]. Immobilization of DNA and RNA in well-defined nanostructures would be one of the most unique subjects in current nanotechnology. Unfortunately, a silica surface cannot usually adsorb duplex DNA in aqueous solution due to the electrostatic repulsion between the silica surface and polyanionic DNA. However, Fujiwara et al. recently found that duplex DNA in protonated phosphoric acid form can adsorb on mesoporous silicates, even in low-salt aqueous solution [183]. The DNA adsorption behavior depended much on the pore size of the mesoporous silica. Plausible models of DNA accommodation in mesopore silica channels are depicted in Figure 4.20. Inclusion of duplex DNA in mesoporous silicates with larger pores, around 3.8 nm diameter, would be accompanied by the formation of four water monolayers on the silica surface of the mesoporous inner channel (Figure 4.20A), where sufficient quantities of Si—OH groups remained after solvent extraction of the template (not by calcination). 

Primeran oligonucleotide or pair of oligonucleotides used to direct an activity to a region of nucleic acid. With PCR (polymerase chain reaction), a pair of primers defines the area of the genome to be amplified. 

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