How Does The Fluorescence Of Dna - Specific Dyes Depend On Base Composition And Base Sequence? Comparison Of The Sequenced Species Oryza Sativa And Arabidopsis Thaliana.
A MeisterInstitute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
It is well known that some of the DNA-binding dyes are base-specific. DAPI and the Hoechst dyes bind preferentially to adenine and thymine (AT), and mithramycin binds preferentially to guanine and cytosine (GC). The relationship between AT or GC frequency of the nuclear DNA and fluorescence intensity of these dyes is not quite clear, but it seems that 3-5 consecutive bases of the same type are necessary for binding (= binding length). This results in a non-linear relation between AT (or GC) frequency and fluorescence intensity, if random distribution of bases is assumed. However, because the bases are non-randomly distributed within the DNA sequence, the fluorescence intensity is expected to be not only a function of AT frequency, but also of the sequence. The first sequenced species of higher plants, Oryza sativa and Arabidopsis thaliana, give us the opportunity to verify this relation. The result is rather surprising: The binding length for all investigated dyes is near to 1, but in no way greater than 2. This is in contradiction to results obtained by other methods. The discrepancy may be due to the incomplete sequencing of the Arabidopsis genome which results in incorrect base composition (Bennett et al., 2003). An alternative reason would be that the simple theory of several consecutive bases of the same type binding one dye molecule is not correct.
1. Bennett MD, Leitch IJ, Price, HJ, Johnston JS. (2003). Annals of Botany 91: 547-557.