Nucleic acid, helical specificity

Seeman, N.C., Rosenberg, J.M., Rich, A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA 73 804-809, 1976. 

Acridine dyes used as antiseptics, i.e. proflavine and acriflavine, will react specifically with nucleic acids, by fitting into the double helical structure of this unique molecule. In so doing they interfere with its function and can thereby cause cell death. 

Depending upon chemical structure and the conformations that are possible, polysaccharides in solution may develop secondary structures such as helices, tertiary structures formed from junction zones or by double helix or triple helix unions and even quaternary structures from the cross linking of tertiary structures. Polysaccharides thus mimic proteins and nucleic acids, which are specific types of sugar-phosphoric acid copolymers. 

Figure 1. Catalysis and template action of RNA and proteins. Catalytic action of one RNA molecule on another one is shown in the simplest case, the "hammerhead ribozyme." The substrate is a tridecanucleotide forming two double-helical stacks together with the ribozyme (n = 34) in the confolded complex. Tertiary interactions determine the detailed structure of the hammerhead ribozyme complex and are important for the enzymatic reaction cleaving one of the two linkages between the two stacks. Substrate specificity of ribozyme catalysis is caused by secondary structure in the cofolded complex between substrate and catalyst. Autocatalytic replication of oligonucleotide and nucleic acid is based on G = C and A = U complementarity in the hydrogen bonded complexes of nucleotides forming a Watson-Crick type double helix. Gunter von Kiedrowski s experi-...

At present, there are only a few cases known of sequence-specific hydration of double helical nucleic acids. With the availability of more crystal structure data, new information concerning sequence-specific hydration is expected. This kind of hydration can have an influence on the recognition of nucleic acids by proteins, and is therefore of great interest. 

The existence of specific base-pairing interactions was discovered in the course of studies directed at determining the three-dimensional structure of DNA. Maurice Wilkins and Rosalind Franklin obtained x-ray diffraction photographs of fibers of DNA (Figure 5.10). The characteristics of these diffraction patterns indicated that DNA was formed of two chains that wound in a regular helical structure. From these and other data, James Watson and Francis Crick inferred a structural model for DNA that accounted for the diffraction pattern and was also the source of some remarkable insights into the functional properties of nucleic acids (Figure 511). 

The immunospecihcally purified antibodies have been particularly useful in physicochemical studies of the antibody-nucleic acid interaction for some purposes, the monovalent Fab fragments of the purified antibodies have been used. - The use of absorbed and purified antibodies also ensures the specificity of immunofluorescent and serological measurements of helical nucleic acids of a given class in the presence of other nucleic acid forms. 

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