The thermodynamic principles of complementary binding of DNA or RNA strands are well known, thus the binding efficiency can be calculated for a given sequence. However, when a two-stranded molecule...Show moreThe thermodynamic principles of complementary binding of DNA or RNA strands are well known, thus the binding efficiency can be calculated for a given sequence. However, when a two-stranded molecule contains mismatches in the base pairs, e.g. a guanine opposite to thymine base, traditional models like the nearest-neighbour model do not suffice. The influence of the location of these mismatches on the binding efficiency, in particular, is not well understood. Understanding the binding behaviour of nucleotide strands is essential to the development of applications that require efficient and highly exclusive binding to specific sequences in RNA or DNA. Such an application is exon skipping, a gene correction therapy to treat Duchenne muscular dystrophy. An alternative model has recently been developed at Leiden University to explain this mismatch location dependency. This study is aimed at comparing its calculations with experimental results obtained by DNA encapsulated silver nanocluster fluorimetry. This type of fluorimetry uses a special labelling technique to relate the emitted intensity of various bulk samples to the binding efficiency. Mismatches are introduced in various locations, and the binding efficiency is measured to determine the dependency on the mismatch location. The binding efficiency as a function of the mismatch location shows a relation that resembles the calculations by the model. Improvements of the method are suggested based on the results, allowing for a valid evaluation of the model.Show less
