Nucleic acids biology

Discussion in this section is confined to the matter mentioned in the introduction, which has provided such a fresh and energetic impetus to this whole subject, namely the direct and quantitative correlation between the amounts of several specific and identifiable photoproducts formed in the photolysis of nucleic acids and the amount of inactivation of the nucleic acid biological function. This specific area, however, is one which has drawn much attention, and to which several of the recent reviews are devoted.8,10,113"90 There is little need to extend these excellent articles, and so a comprehensive survey of the literature will not be attempted here, but merely a summary and interpretation. 

Zhang, L., Goldhammer, C., Henkel, B., et al. (1994) Peptides, proteins and nucleic acids. Biological and biomedical applications, in Innovation and Perspectives in Solid Phase Synthesis (Epton, R., ed.), Mayflower Worldwide Ltd, Birmingham, UK, pp. 711-716. 

Hyde, C. Johnson, T. Owen, D. Quibel, M. Sheppard, R. C., In Innovation and Perspectives in Solid Phase Peptide Synthesis Peptides, Proteins and Nucleic Acids, Biological and Biomedical Applications, Epton, R., Ed. Mayflower Worldwide Birmingham, UK,... 

Base Polyad Motifs in Nucleic Acids - Biological Significance, Occurrence in Three-Dimensional Experimental Structures and Computational Studies (M. Meyer J. Stthnel)... 

Base Polyad Motifs in Nucleic Acids — Biological Significance,... 

Jagger J Ultraviolet inactivation of biological systems. In Photochemistry and Photobiology of Nucleic Acids Biology. Volume II. Edited by Wang SY. New York Academic Press 1976 147—186. 

Kochoyan, M., Leroy, J.L. Hydration and solution structure of nucleic acids. Current Opinion in Structural Biology 5 (1995) 329-333... 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

PDB files were designed for storage of crystal structures and related experimental information on biological macromolecules, primarily proteins, nucleic acids, and their complexes. Over the years the PDB file format was extended to handle results from other experimental (NM.R, cryoelectron microscopy) and theoretical methods... 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

Many biochemical databases with sophisticated topics have been developed for solving various problems. Since 1996 the first issue of each journal volume of Nucleic Acid Research has been reserved for the presentation of molecular biology databases [28]. A comprehensive catalog on the Internet is DBCAT, currently listing 511 databases [29, 30). 

EMBL (European Molecular Biology Laboratory) [33] is a nucleotide sequence database provided from the online host EBl. Release 73 (December, 2002) consists of over 20 million nucleotide sequences with more than 28 billion nucleotides. The information includes sequence name, species, sequence length, promoter, taxonomy, and nucleic acid sequence. 

The unique combination of organic chemistry and molecular biology which is nowadays applied in nucleic acid synthesis and analysis led to a great interest in nucleic acid bioorganic chemistry. We give a few examples of recent synthetic endeavours in this field. 

Nobel-laureate Richard Feynman once said that the principles of physics do not preclude the possibility of maneuvering things atom by atom (260). Recent developments in the fields of physics, chemistry, and biology (briefly described in the previous sections) bear those words out. The invention and development of scanning probe microscopy has enabled the isolation and manipulation of individual atoms and molecules. Research in protein and nucleic acid stmcture have given rise to powerful tools in the estabUshment of rational synthetic protocols for the production of new medicinal dmgs, sensing elements, catalysts, and electronic materials. 

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