Chloroplast DNA is also circular and present in multiple copies. 

Early studies of chloroplast DNA utilized isodensity centrifugation as the main tool for its isolation. 

Although this approach works well with unicellular plants in higher plants most of the isolated DNA components initially believed to be chloroplast DNA turned out not to be chloroplast DNA  at all. 

These early experiments, in which DNA prepared from isolated chloroplast was analyzed by cesium chloride isodensity centrifugation, revealed the presence of three DNA components: a major component with a density of about 1.696g/cm that was thought to represent contaminating nuclear DNA, and two minor DNA components denser than nuclear DNA that were thought to represent chloroplast DNA.

But in 1971 the chloroplast DNA of the alga Euglena was isolated as a single large circle, suggesting that the linear typical plant leaf cell contains about 10,000 chloroplast DNA circles distributed among 50 to 100 chloroplasts, giving each chloroplast between 100 to 200 DNA molecules. 

  • Depending on the organism. chloroplast DNA contains anywhere from 70,000 to more than 5,00,000 base pairs, with an average of 1,50,000 base pairs being typical for the chloroplasts of higher plants; the presence of DNA in chloroplasts is not indisputable evidence that this DNA contains genes governing chloroplast traits. 
  • Independent support for the existence of circular DNA in chloroplasts has come from the genetic studies of Ruth Sagar, who employed the antibiotic streptomycin to induce mutations in chloroplast genes of the green alga Chlamydomonas.

Inverted repeats

  • Many chloroplast DNAs contain two inverted repeats, which separate a long single copy section (LSC) from a short single copy section (SSC).
  • The inverted repeats vary wildly in length, ranging from 4,000 to 25,000 base pairs long each. in plants, each being 20,000–25,000 base pairs long. 
  • The inverted repeat regions usually contain three ribosomal RNA and two tRNA genes, but they can be expanded or reduced to contain as few as four or as many as over 150 genes. 
  • While a given pair of inverted repeats are rarely completely identical, they are always very similar to each other, apparently resulting from concerted evolution.
  • The inverted repeat regions are highly conserved among land plants, and accumulate few mutations. 
  • Similar inverted repeats exist in the genomes of cyanobacteria It is possible that the inverted repeats help stabilize the rest of the chloroplast genome, as chloroplast DNAs which have lost some of the inverted repeat segments tend to get rearranged more.

Linear structure

  • Chloroplast DNAs have long been thought to have a circular structure, but some evidence suggests that chloroplast DNA more commonly takes a linear shape. 
  • Over 95% of the chloroplast DNA in corn chloroplasts has been observed to be in branched linear form rather than individual circles.


  • New chloroplasts may contain up to 100 copies of their DNA, though the number of chloroplast DNA copies decreases to about 15–20 as the chloroplasts age. 
  • They are usually packed into nucleoids which can contain several identical chloroplast DNA rings. Many nucleoids can be found in each chloroplast. 
  • Though chloroplast DNA is not associated with true histones, in red algae, a histone-like chloroplast protein (HC) coded by the chloroplast DNA that tightly packs each chloroplast DNA ring into a nucleoid has been found.
  • In primitive red algae, the chloroplast DNA nucleoids are clustered in the center of a chloroplast, while in green plants and green algae, the nucleoids are dispersed throughout the stroma.
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