DSSR-PyMOL cartoon-block schematics: PDB entry 6m0c

PDB-id

6m0c; DSSR-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

Solution NMR structures of DNA minidumbbell formed by 5'-cttg catg-3'.

Reference

Ngai CK, Lam SL, Lee HK, Guo P (2020): "High-Resolution Structures of DNA Minidumbbells Comprising Type II Tetraloops with a Purine Minor Groove Residue." J.Phys.Chem.B, 124, 5131-5138. doi: 10.1021/acs.jpcb.0c03163.

Abstract

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.