DNA-binding substances

Berberine is an organic compound classified as benzylisoquinoline alkaloid. Chemically, it is a quaternary ammonia compound.

DAPI (pronounced 'DAPPY', /ˈdæpiː/), or 4′,6-diamidino-2-phenylindole, is a fluorescent stain that binds strongly to adenine–thymine-rich regions in DNA. It is used extensively in fluorescence microscopy. As DAPI can pass through an intact cell membrane, it can be used to stain both live and fixed cells, though it passes through the membrane less efficiently in live cells and therefore provides a marker for membrane viability.

small structural protein motif found mostly in transcriptional genes

Pentamidine is an antimicrobial medication used to treat African trypanosomiasis, leishmaniasis, Balamuthia infections, babesiosis, and to prevent and treat pneumocystis pneumonia (PCP) in people with poor immune function. In African trypanosomiasis it is used for early disease before central nervous system involvement, as a second line option to suramin. It is an option for both visceral leishmaniasis and cutaneous leishmaniasis. Pentamidine can be given by injection into a vein or muscle or by inhalation.

200px|thumb|The λ repressor of bacteriophage lambda employs two helix-turn-helix motifs (left; green) to bind [[DNA (right; blue and red). The λ repressor protein in this image is a dimer.]]

group of fluorescent dyes for DNA staining

DNA-binding structural motif

transcription regulator protein

Phenanthridine is a nitrogen heterocyclic compound with the formula . It is a colorless solid, although impure samples can be brownish. It is a precursor to DNA-binding fluorescent dyes through intercalation. Examples of such dyes are ethidium bromide and propidium iodide. Phenanthridine was discovered by Amé Pictet and H. J. Ankersmit in 1891.

chemical compound

family of proteins

Netropsin (also termed congocidine or sinanomycin) is a polyamide with antibiotic and antiviral activity. Netropsin was discovered by Finlay et al., and first isolated from the actinobacterium Streptomyces netropsis. It belongs to the class of pyrrole-amidine antibiotics.

Bisbenzimide (Hoechst 33342) is an organic compound used as a fluorescent stain for DNA in molecular biology applications. Several related chemical compounds are used for similar purposes and are collectively called Hoechst stains.

regions of biomolecules capable of binding to DNA

In molecular biology, the HMG-box (high-mobility group box) is a protein domain which is involved in DNA binding. The domain is composed of approximately 75 amino acid residues that collectively mediate the DNA-binding of chromatin-associated high-mobility group proteins. HMG-boxes are present in many transcription factors and chromatin-remodeling complexes, where they can mediate non-sequence or sequence-specific DNA binding.