The Use of Netropsin with CsCl Gradients for the Analysis of DNA and Its Application to Restriction Nuclease Fragments of Ribosomal DNA from Physarum polycephalum

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Abstract
Netropsin binds to DNA in CsCl density gradients and reduces the density of the DNA. The DNA is saturated at a netropsin/DNA weight ratio of about 6 and the change in density, .DELTA..rho., at saturation is given by .DELTA..rho. = -109 (dA + dT content)1.87 mg/ml for the 6 DNA tested covering dA + dT contents from 0.28-0.69. At lower netropsin/DNA ratios the observed density shifts are consistent with a 2-site model for netropsin binding to DNA. Netropsin approximately doubles the resolution of P. polycephalum nucleolar satellite DNA from main-band DNA. The fragments of P. polycephalum nucleolar satellite DNA obtained with the restriction endonuclease HindIII [Haemophilus influenzae EC 3.1.4.-] do not separate on CsCl gradients, even in the presence of netropsin, which shows that the transcribed and non-transcribed sequences in this DNA have similar nucleotide compositions.