Conformational properties of DNA fragments containing GAC trinucleotide repeats associated with skeletal displasias

The human gene for cartilage oligomeric matrix protein contains five tandem repeats of the GAC trinucleotide. Its expansion by one repeat causes multi ple epiphyseal dysplasia, while expansion by two repeats or, remarkably, de letion of one repeat causes pseudoa-chondroplasia. Here we used CD spectros copy, PAGE and UV absorption spectroscopy to compare conformational propert ies of the DNA strands containing four, five, six and seven repeats of the GAC trinucleotide. The (GAC)(n) strands were found to form four distinct or dered conformations, depending on the solution conditions. The first was a foldback, stable at slightly alkaline pH values and low and medium ionic st rengths. Increasing salt concentration induced a transition of the foldback into an antiparallel right-handed homoduplex. Both the conformers containe d the Watson-Crick G(.)C pairs while the intervening adenines contributed l ittle to their B-like conformation. Thirdly, the strands associated into a parallel homoduplex stabilized by the hemiprotonated C+.C pairs and by the GpA steps that both favor the parallel DNA strand orientation. The parallel homoduplex was stable even at neutral pH. The fourth conformation was the left-handed Z-DNA, which formed easier with (GAC)(n) than with (GC)(n) of c omparable length, indicating that the adenines of (GAC)(n) promoted the lef t-handed duplex. The paper shows that stability of the above four conformer s strongly depends on the GAC repeat number.