7D0Z

NMR solution structures of the DNA minidumbbell formed by two CCTG repeats at pH 5

Summary for 7D0Z

• Entry DOI: 10.2210/pdb7d0z/pdb
• NMR Information: BMRB: 36380
• Descriptor: DNA (5'-D(*(DCZ)P*CP*TP*GP*CP*CP*TP*G)-3'), SODIUM ION (2 entities in total)
• Functional Keywords: minidumbbell, cctg, ph 5, dna
• Biological source: Homo sapiens
• Total number of polymer chains: 1
• Total formula weight: 2413.54

Authors

Guo, P.,Lam, S.L. (deposition date: 2020-09-12, release date: 2021-02-03, Last modification date: 2024-05-01)

Primary citation

Wan, L.,Yi, J.,Lam, S.L.,Lee, H.K.,Guo, P.
5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbells.
Chemistry, 27:6740-6747, 2021

PubMed Abstract: Minidumbbell (MDB) is a recently identified non-B DNA structure that has been proposed to associate with genetic instabilities. It also serves as a functional structural motif in DNA nanotechnology. DNA molecular switches constructed using MDBs show instant and complete structural conversions with easy manipulations. The availability of stable MDBs can broaden their applications. In this work, we found that substitutions of cytosine with 5-methylcytosine could lead to a significant enhancement in the thermal stabilities of MDBs. Consecutive methylations of cytosine in MDBs brought about cumulative stabilization with a drastic increase in the melting temperature by 23 °C. NMR solution structures of two MDBs containing 5-methylcytosine residues have been successfully determined and revealed that the enhanced stabilities resulted primarily from favorable hydrophobic contacts, more stable base pairs and enhanced base-base stackings involving the methyl group of 5-methylcytosine.

PubMed: 33501691
DOI: 10.1002/chem.202005410

Experimental method

SOLUTION NMR