A purine and a backbone discontinuous site alter the structure and thermal stability of DNA minidumbbells containing two pentaloops.

Minidumbbell (MDB) is a noncanonical DNA structure found to form in several pyrimidine-rich short tandem repeats associated with neurodegenerative diseases. The most recently reported MDB contains two pentaloops formed by ATTCT repeats. Here, we studied the effects of a purine residue and a backbone discontinuous site on the structure and thermal stability of MDBs containing two pentaloops. It was found that a purine as the fourth loop residue improved the thermal stability of MDBs containing two regular pentaloops, while a backbone discontinuous site between the third and fourth, or between the fourth and fifth loop residues enhanced the thermal stability of MDBs containing a regular and a quasi pentaloops. The results of this study provide new insights into the sequence criteria and structural basis of MDBs.