Nucleic acid cleavage structures

Structure of a Cu -Kanamycin complex with nucleic acid cleavage properties.-... 

These results indicate that RNA in a DNA-RNA hybrid is protected from cleavage Ly Eu(L1)3+ under conditions where nearly all other sites in tRNAphe are cleaved. We cannot rule out poorer binding of the metal complex to the hybrid than to RNA alone. There is ample precedence for binding of Eu(III) ions to double-stranded nucleic acids (34). Eu(III) is also known to bind well to pockets in highly structured RNAs such as tRNA (31). It is not known how the europium complex will bind to these different structures. 

Metal ions are usually required to promote and stabilize functionally active or native conformations of nucleic acids, as well as to mediate nucleic acid-protein interactions. However, metal ions can also cause structural transformation of nncleic acids, or denature their native structures. In addition to structural roles, some metal compounds can indnce cleavage (i.e. scission, fragmentation, or depolymerization) and modification (withont cleavage) of nucleic acids. Metal-nucleic acid interactions can be either nonspecific or dependent on the chemical nature of nucleotide residues, nucleic acid sequence, or secondary and/or tertiary structure of nucleic acids. The specificity of these interactions is dependent... 

Just as metal ions can bind nucleic acids both specifically and nonspecifically, they can promote both specific and nonspecific cleavage of nucleic acids. The rate and specificity of the cleavage reactions varies markedly with the identity of both metal ions and nucleic acid structures, as well as with the couditions of experimeuts. Higher pH, temperature, and concentrations of metal ions could enhance the rate of the polynucleotide cleavage but would decrease the specificity. 

Viadiu H, Aggarwal AK. Structure of BamHI bound to nonspecific DNA a model for DNA sliding. Molec. Cell 2000 5 889-895. Sidorova NY, Muradymov S, Rau DC. Trapping DNA-protein binding reactions with neutral osmolytes for the analysis by gel mobility shift and self-cleavage assays. Nucleic Acids Res. 2005 33 5145-5155. 

Proteolytic enzymes have been used extensively in the study of protein structui e. First, of course, purified proteases have been employed to catalyze the cleavage of specific peptide bonds in proteins in the process of establishing amino acid sequences and distributions. Within the last few years it has also become apparent that proteolytic enzymes can be utilized to obtain at least semiquantitative information about protein (and nucleic acid) configuration (or secondary-tertiary structure) as well as about amino acid sequence. This use of proteases can be divided into two general areas ... 

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