DNA-RNA interactions

Ni(II)-Xaa-Xaa-His metallopeptide-DNA/RNA interactions (Xaa = any a-amino acid residue) 99ACR827. 

Appropriately designed biophysical studies can elucidate the mode(s), the binding affinities and the nature of the ligand-nucleic acid interaction that give rise to the observed selectivity and specificities. Thus, it is worthwhile to describe briefly the various physical techniques used to study alkaloid-DNA/RNA interactions. 

Living arrays Yeast colonies expressing GAL4 fusion proteins Yeast colonies with transposon disruptions protein—protein and protein—DNA/RNA interactions phenotype analysis... 

FIGURE 7.41. Formation of DNA-streptavidin networks (left, bars = 100 nm) and the spatial arrangement of gold (a-e) and antibody (f) bounded streptavidin molecules by DNA-RNA interactions (right). 

The fluorescent ddA 5 -triphosphate derivative (163) was shown to be an effective substrate for terminal transferase, and various DNA polymerases. The resultant DNA could then be detected by fluorescence spectroscopy. A molecular beacon DNA probe incorporating a donor and a quencher dye has been reported, " which shows high sensitivity and dynamic range. Such molecular beacons are anticipated to have use in DNA/RNA and pro-tein/DNA/RNA interactions. 

Under the conditions used in most of the hybridization experiments, only DNA sequences hybridize which exist in many copies ( repetitive sequences, Britten and Kohne, 1968). Nonrepetitive DNA sequences hybridize only at extremely high RNA-DNA ratios (Gelderman et al, 1971). But under these conditions the specificity of the DNA-RNA interaction is lower thus, sequences which are similar but not identical also hybridize. Finally, it should be mentioned that the amount of RNA synthesized per genome in very early stages of sea urchin embryos is larger than in later stages (Brandhorst and Humphreys, 1971). Whether more species with different base sequences or more copies of the same species are synthesized is unknown. 

Messenger RNA (mRNA) (Section 28.11) A polynucleotide of ribose that reads the sequence of bases in DNA and interacts with tRNAs in the ribosomes to promote protein biosynthesis. 

The multiprotein unit that synthesize RNA by copying the sequence information from the leading strand of the DNA. Its activity is tightly controlled by phosphorylation of the C-termal domain (CTD), access to DNA and interaction by general and sequence specific transcription factors and coactivators and corepressors. 

Bates et al. reported the construction and characterization of a gold nanoparticle wire assembled using Mg -dependent RNA-RNA interactions for the future assembly of practical nanocircuits [31]. They used magnesium ion-mediated RNA-RNA loop-receptor interactions, in conjunction with 15 nm or 30 nm gold nanoclusters derivatized with DNA to prepare self-assembled nanowires. A wire was deposited between lithographically fabricated nanoelectrodes and exhibited non-linear activated conduction by electron hopping at 150-300 K (Figure 16). 

The general types of protein-protein interactions that occur in cells include receptor-ligand, enzyme-substrate, multimeric complex formations, structural scaffolds, and chaperones. However, proteins interact with more targets than just other proteins. Protein interactions can include protein-protein or protein-peptide, protein-DNA/RNA or protein-nucleic acid, protein-glycan or protein-carbohydrate, protein-lipid or protein-membrane, and protein-small molecule or protein-ligand. It is likely that every molecule within a cell has some kind of specific interaction with a protein. 

Now that you understand the basis for the interactions between functional groups in water, you also understand the basis for most interactions DNA-DNA, DNA-RNA, DNA-protein, RNA-protein, protein-protein, protein-ligand, enzyme-substrate (Get the picture ), antibody-antigen, protein-chromatography column—it s all the same stuff. 

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