Penetration and DNA binding

Some allelochemicals such as sesquiterpene lactones or alkaloids penetrate into a cell, binding with various cellular compartments, and changing the cellular fluorescence excited by ultra-violet or violet light. This makes clear cellular mechanisms of actions for the allelochemicals. Sesquiterpene lactones azulene and proazulenes binds DNA-containing structures such as nuclei and chloroplasts, which fluoresce in blue (Roshchina, 2004). 

Vimses are made up of a protein capsule, some with a lipoprotein envelope around it, containing genetic material (either DNA or RNA), with maybe a few enzymes but very little else and hence they are not considered to be cells, but, rather, infectious particles. Viruses are able to bind to cell membranes, penetrate and infect cells of other organisms. Viruses are intracellular parasites they cannot replicate themselves without using the contents of the host cell to synthesize the cellular components necessary for their reproduction. This makes the development of effective antiviral drugs that do not damage healthy host cells very difficult. 

Another class of DNA-binding proteins are the restriction endonucleases which cleave DNA at specific sites. The recognition motif found in the complex between DNA and Eco R1 features a helices as well, but the interaction mode differs considerably from those found in the helix-turn-helix and zinc-finger proteins. In the Eco RI complex, a parallel bundle of four a helices penetrates the major groove, whereby only the ends of the helices interact with the DNA [99, 100]. In addition, an extension of the polypeptide chain of one of these helices wraps around the DNA and makes several contacts to bases. 

Doxorubicin is an antineoplastic/anthracycline antibiotic. It binds DNA and inhibits nucleic acid synthesis. Cell structure studies have demonstrated rapid cell penetration and perinuclear chromatin binding, rapid inhibition of mitotic activity and nucleic acid synthesis, and induction of mutagenesis and chromosomal aberrations. It is indicated in treatment of ovarian cancer in patients whose disease has progressed or recurred after platinum-based chemotherapy and in treatment of AIDS-related Kaposi s sarcoma in patients whose disease has progressed on prior combination chemotherapy or who are intolerant to such therapy. 

A possibility for differentiating between viable and nonviable cells uses ethidium bromide monoazide (EMA), a DNA binding dye that is used for the differentiation of living and dead cells in flow cytometry and PCR. Dead cells have membrane damage EMA penetrates and binds covalently to the bacterial DNA. This binding inhibits the amplification of the bound DNA so that the polymerase is sterically hindered (Wang Levin, 2005). 

There are both geometric and kinetic differences between the interactions of A- and A-[Ru(bpy)2(hpimp)]2+ hpimp=2-(2-hydroxyphenyl)imi-dazo [4,5-/]-1,10-phenanthroline and the hexanucleotide d(GTCGAC)2. The A-isomer penetrates more deeply into the major groove of the polynucleotide it also binds more rapidly than the A-isomer to DNA (156). 

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