Assay for determing the nucleic acid sequence in a region of a nucleic acid test substance having a known normal sequence and a known possible mutation at at least one target nucleotide position. Oligonucleotide probes are selected to anneal to immediately adjacent segments of a substantially complementary test DNA or RNA molecule. The target probe has an end region wherein one of the end region nucleotides is complementary to the normal or abnormal nucleotide at the corresponding target nucleotide position. A linking agent is added under conditions such that when the target nucleotide is correctly base paired, the probes are covalently joined and if not correctly base paired, the probes are incapable of being covalently joined under such conditions. The presence or absence of linking is detected as an indication of the sequence of the target nucleotide.