Nucleic acid homology

Numerous organisms, both marine and terrestrial, produce protein toxins. These are typically relatively small, and rich in disulfide crosslinks. Since they are often difficult to crystallize, relatively few structures from this class of proteins are known. In the past five years two dimensional NMR methods have developed to the point where they can be used to determine the solution structures of small proteins and nucleic acids. We have analyzed the structures of toxins II and III of RadiarUhus paumotensis using this approach. We find that the dominant structure is )9-sheet, with the strands connected by loops of irregular structure. Most of the residues which have been determined to be important for toxicity are contained in one of the loops. The general methods used for structure analysis will be described, and the structures of the toxins RpII and RpIII will be discussed and compared with homologous toxins from other anemone species. 

Decoville, M., Giraud-Panis, M.J., Mosrin-Huaman, C., Leng, M., and Locker, D. (2000) HMG boxes of DSPl protein interact with the rel homology domain of transcription factors. Nucleic Acids Res. 28, 454-462. 

Sarnowski, T.J., Swiezewski, S., Pawlikowska, K., Kaczanowski, S., and Jerzmanowski, A. (2002) AtSWBB, an Arabidopsis homolog of SWI3, a core subunit of yeast Swi/Snf chromatin remodeling complex, interacts with FCA, a regulator of flowering time. Nucleic Acids Res. 30, 3412-3421. 

Figure 5. Summary of amino acid sequence homology between different xylose isomerases. The percent of homology was calculated by using the University of Wisconsin Genetics Computer Group, version 5, program (Devereux, L, Haeberli, P., and Smithies, O. Nucleic Acids Res. 12, 387-395, 1984). Reprinted with permission from ref. 22. Copyright 1990 American Society for Biochemistry and Molecular Biology.

Qaude, J. B., Suhre, K., Notredame, C., Qaverie, J. M., and Abergel, C. (2004) CaspR a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. 32, W606-609. 

Herzog ED, Takahashi JS, Block GD 1998 Clock controls circadian period in isolated suprachiasmatic nucleus neurons. Nat Neurosci 1 708—71 KobayashiK, Kanno S, Smit B, van der Horst GTJ, Takao M, Yasui A 1998 Characterization of photolyase/blue-hght receptor homologs in mouse and human cells. Nucleic Acids Res 26 5086-5092... 

The molecular weight or molar mass of proteins and nucleic acids (DNA, RNA) is identical for each specific species, e.g., the molecular weights of all casein molecules from a specific source are identical. These polymers are members of a homologous series and are said to be monodisperse or molecularly homogeneous. 

Fig. 26. Nucleic acid structures. A The structure of the four bases in DNA, guanine (G), cytosine (C) adenine (A) and thymine (T). Uracil (U) replaces thymine (T) in RNA. B The spontaneous attraction of A for T and C for G allows the recognition of homologous sequences in aqueous solutions and the strong and specific hybridization of one sequence with its homologous sequence. C DNA forms a double helix at body temperature, which can be denatured to separate the strands by heating. D single stranded mRNA structure.

The bottom-up synthesis of metallic nanowires was further applied to construct a nanotransistor device.93 The sequence-specific winding of the homologous nucleic acid carried by the RecA-protein into the duplex DNA was used to address the nucleic acid/protein complex on the DNA scaffold (Fig. 12.27). The subsequent association of the anti-RecA antibody to the protein DNA complex, followed by the association of the biotinylated antiantibody, and the linkage of streptavidin-modified carbon nanotube deposited the tubes in the specific domain of the DNA scaffold. The further... 

Hybridization measurements have been used in many studies of homology of nucleic acids from different species. A nucleic acid is cut (e.g., by sonic oscillation) into pieces of moderate length ( 1000 nucleotides) and is denatured. The denatured DNA fragments are mixed with denatured DNA of another species. Nucleotide sequences that are closely similar between species tend to hybridize, whereas sequences that are... 

Because of the different interactions involved in partition and adsorption processes, they may be applied to different separation problems. Partition processes are the most effective for the separation of small molecules, especially those in homologous series. Partition chromatography has been widely used for the separation and identification of amino acids, carbohydrates, and fatty acids. Adsorption techniques, represented by ion-exchange chromatography, are most effective when applied to the separation of macromolecules including proteins and nucleic acids. 

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