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The nonfunctional DNA in bacterial genomes is mostly located in the intergenic fraction of non-coding DNA but in eukaryotic genomes it may also be found within introns. There are many examples of functional DNA elements in non-coding DNA, and it is erroneous to equate non-coding DNA with junk DNA.
Pseudogenes are a type of junk DNA. Most non-bacterial genomes contain many pseudogenes, often as many as functional genes. This is not surprising, since various biological processes are expected to accidentally create pseudogenes, and there are no specialized mechanisms to remove them from genomes.
Non-functional DNA is rare in bacterial genomes which typically have an extremely high gene density, with only a few percent being not protein-coding. [60] However, in most animal or plant genomes, a large fraction of DNA is non-functional, given that there is no obvious selective pressure on these sequences.
Non-B DNA can be classified into several types, including A-DNA, Z-DNA, H-DNA, G-quadruplexes, and Triplexes (Triple-stranded DNA).. A-DNA is a right-handed double helix structure for RNA-DNA duplexes and RNA-RNA duplexes that is less common than the more well-known B-DNA structure.
Different TLRs in human detect different PAMPS: lipopolysaccharides by TLR4, viral dsRNA by TLR3, viral ssRNA by TLR7/TLR8, viral or bacterial unmethylated DNA by TLR9. TLR9 has evolved to detect CpG DNA commonly found in bacteria and viruses and to initiate the production of IFN (type I interferons ) and other cytokines. [44]
The A form occurs under non-physiological conditions in partly dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, and in enzyme-DNA complexes. [ 54 ] [ 55 ] Segments of DNA where the bases have been chemically modified by methylation may undergo a larger change in conformation and adopt ...