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High-resolution Structures of DNA Minidumbbells Comprising Type II Tetraloops with a Purine Minor Groove Residue.

Minidumbbell (MDB) is a newly discovered DNA structure formed by native sequences, which serves as a possible structural intermediate causing repeat expansion mutation in the genome and also a functional structural motif in constructing DNA-based molecular switches. Up to now, all the reported MDBs containing two adjacent type II tetraloops were formed with pyrimidine-rich sequences 5'-YYYR YYYR-3' (Y and R represent pyrimidine and purine, respectively), wherein the second and sixth residues folded into the minor groove and interacted with each other. In this study, we have conducted a high-resolution nuclear magnetic resonance (NMR) spectroscopic investigation on alternative MDB-forming sequences and discovered that an MDB could also form stably with a purine in the minor groove, which has never been observed in any previously reported DNA type II tetraloops. Our refined NMR solution structures of the two MDBs formed by 5'-CTTG CATG-3' and 5'-CTTG CGTG-3' reveal that the sixth purine residue was driven into the minor groove via base-base stacking with the second thymine residue, and an adenine stacked better than a guanine. Results of our present research work expand the sequence criteria for the formation of MDBs and shed light to explore the significance of MDBs.