Nucleic acid sequencing structure

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. 

This assay system developed by Chaires [136] is a new, powerful and effective tool based on the fundamental thermodynamic principle of equilibrium dialysis for the discovery of ligands that bind to nucleic acids with structural and sequence selectivity. Here, identical concentrations of various nucleic acid samples are dialysed in dispodialysers against a common ligand solution. At equilibrium, the contents of the ligand bound to each nucleic acid are determined and this is correlated directly to the ligand s specificity to a particular sequence. 

The database would present all known protein sequences and structures nucleic acid sequences exosporium structure metric parameters such as mean density and size spectral properties such as the fluorescence, fluorescence... 

Both the nucleic acid sequences and the protein sequences derived from the biological information are collected in most such databases. Large amounts of data in these databases need to be sorted, stored, retrieved, and analyzed. Selection of subsets of data for particular analysis should also be done. IT providers designed such a data warehouse and developed an interface that provides an important benefit to researchers by making it easy to access the existing information and also to submit new entries (i.e., datamining) (Table 5.6). Middlewares and structured query language (SQL) softwares were developed for this purposes. The former one is used... 

The formation of aptamer-substrate complexes was also followed by the use of redox-active intercalators73 (Fig. 12.18d). A nucleic acid hairpin structure that contained in its single-stranded loop the antithrombin base sequence was assembled on a Au electrode, and methylene blue was intercalated as a redox label in the double-stranded stem of the hairpin structure. The hairpin was, then, opened in the presence of thrombin, by generating the respective G-quadruplex-thrombin complex, and as a result, the redox label was removed from the nucleic structure, showing a decrease in the voltammetric response with the increase in the concentration of thrombin. This method enabled the analysis of thrombin with a detection limit that corresponded to... 

Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences... 

BLAST Chime Entrez (NCBI) FASTA GenBank (NCBI) Molecules R Us RasMol (Ras Mac) SRS (EMBL) Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross referencing databases... 

The polynucleotide chain has a directional sense with 5 and 3 ends. Either of these ends may contain a free hydroxyl group or a phosphorylated hydroxyl group. The structure shown in figure 25.3 contains a phosphate group on the 5 end but none on the 3 end. By convention, one writes a nucleic acid sequence from the 5 to the 3 end so that a comparable structure is written pTpApCpG. With no... 

Direct labeling of a biomolecule involves the introduction of a covalently linked fluorophore in the nucleic acid sequence or in the amino acid sequence of a protein or antibody. Fluorescein, rhodamine derivatives, the Alexa, and BODIPY dyes (Molecular Probes [92]) as well as the cyanine dyes (Amersham Biosciences [134]) are widely used labels. These probe families show different absorption and emission wavelengths and span the whole visible spectrum (e.g., Alexa Fluor dyes show UV excitation at 350 nm to far red excitation at 633 nm). Furthermore, for differential expression analysis, probe families with similar chemical structures but different spectroscopic properties are desirable, for example the cyanine dyes Cy3 and Cy5 (excitation at 548 and 646 nm, respectively). The design of fluorescent labels is still an active area of research, and various new dyes have been reported that differ in terms of decay times, wavelength, conjugatibility, and quantum yields before and after conjugation [135]. New ruthenium markers have been reported as well [136]. 

The advances in protein, and especially DNA, sequencing technology means that there is now a vast amount of primary structural information relating to biological macromolecules and it is hence essential for laboratories in the field to make use of computers to analyse data on protein and nucleic acid sequences. At present (June 1994) there are more than 80000 sequences in the OWL protein sequence database [8] and there are more than 170000 nucleic acid sequences in the EMBL (European Molecular Biology Laboratory) database [9]. 

The most obvious data in a typical 3D structure record are the atomic coordinate data, the locations in space of the atoms of a molecule represented by (x, y, z) triples, and distances along each axis to some arbitrary origin in space. The coordinate data for each atom are attached to a list of labeling information in the structure record such as that derived from the protein or nucleic acid sequence. 

More detailed RT-PCR analyses of mRNA from a variety of tissues have revealed additional structural complexity and identification of a large number of alternatively spliced subunit transcripts that differ in variable domain nucleic acid sequence (Tombes et al. 2003). These subunit variants are expressed in a tissue-specific manner. For example, the 6i subunit mRNA is expressed predominantly in brain, whereas S2 and 63 variants are expressed in rat aortic smooth muscle,... 

Human apoA-I is a major constituent of HDL, with an Mr of approximately 28,300, calculated from the known primary structure (Bl, B43). ApoA-I is initially synthesized as a 267-amino-acid precursor protein, pre-pro-apoA-I (G25, G26), containing an 18-amino-acid prepeptide and a 6-amino-acid propeptide [determined by nucleic acid sequence analysis of cloned apoA-I (L6), and by isolating the primary translation product of human intestinal apoA-I mRNA (G25)]. 

The structures of the rRNAs were generated and sequences compared using the University of Wisconsin Genetics Computer Group Nucleic Acid sequence analysis package29 and the University of Georgia Biological Structure and Sequence Computation Facility. 

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