by PhilipJ on 1 February 2008
Double-stranded RNA is often a sign of trouble. Our transfer RNA and ribosomes do contain little hairpins that are double-stranded, but most of the free forms of RNA, messenger RNA molecules in particular, are single strands. Many viruses, however, form long stretches of double-stranded RNA as they replicate their genomes. When our cells find double-stranded RNA, it is often a sign of an infection, and they mount a vigorous response that often leads to death of the entire cell. However, plant and animal cells also have a more targeted defense that attacks the viral RNA directly, termed RNA interference.
RNA interference starts with a long double-stranded RNA, such as the ones formed as viruses replicate. The protein dicer, shown here at the top in blue from PDB entry 2ffl, cuts this RNA into small, distinctive pieces called small interfering RNA (siRNA), shown on the left from PDB entry 2f8s. Each siRNA is about 21 base pairs long and has a distinctive overhang of two base pairs on each strand, and a left-over phosphate at the other end of each strand. This makes them easy to recognize. In the dicer protein, notice how the four manganese ions (in magenta) are arranged. They are thought to make two offset cuts in the RNA double helix, forming the overhang.
Read the rest at David Goodsell’s site, here.