Molecular sequences used

An alternative approach to peptide sequencing uses a dry method in which the whole sequence is obtained from a mass spectrum, thereby obviating the need for multiple reactions. Mass spec-trometrically, a chain of amino acids breaks down predominantly through cleavage of the amide bonds, similar to the result of chemical hydrolysis. From the mass spectrum, identification of the molecular ion, which gives the total molecular mass, followed by examination of the spectrum for characteristic fragment ions representing successive amino acid residues allows the sequence to be read off in the most favorable cases. 

The next lines, the OS (Organism Species) and OC (Organism Classification), describe the species from which the protein has been derived. The OS line shows the scientific name of the organism and, if existing, the common English name. The OC lines give the taxonomic tree. SWISS-PROT, as well as the DDBJ/EMBL/GenBank nucleotide sequence databases, uses the NCBI taxonomy to standardize the taxonomies of the molecular sequence databases. 

Karlin, S., and Altschul, S. F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U.S.A. 87, 2264-2268. 

DNA arrays have been also generated by Dip-Pen Nanolithography (DPN) [80]. DPN involves the transfer of NAs directly from a coated Atomic Force Microscope (AFM) tip to the substrate of interest by virtue of direct molecular diffusion. Using this technique, thiol-modified ONDs have been patterned onto gold substrates and acrylamide-modified ONDs onto glass sHdes that were previously modified with mercaptopropyltrimethoxysilane. Feature sizes ranging from many micrometers to less than 100 nanometers could be obtained. The deposition of two different OND sequences onto the same substrate has also been reported [80], but the appHcation of this principle to the fabrication of high-density arrays remains to be addressed. 

Weiner, A. M., Leaird, D. E., Wiederrecht, G. P, and Nelson, K. A. 1990. Femtosecond pulse sequences used for optical manipulation of molecular motion. Science 247 1317-19. 

Fig. 25. The development of lamellar molecular crystals using polypeptides with a repeating sequence. The correct folding of these macromolecules produced by molecular biology gives peptide nanostructures, bearing specific functional groups in a well-defined spatial relationship. (Reproduced with the permission of Ref. 63)...

Retrieve the amino acid sequences of liver alcohol dehydrogenase from six organisms to perform phylogenetic analysis. Compare phylogenetic results from Fitch-Margoliash methods without (Fitch) versus with (Kisch) molecular clock using the Dayhoff PAM 001 matrix. 

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