6FY6

Concerted dynamics of metallo-base pairs in an A/B-form helical transition (major species)

Summary for 6FY6

• Entry DOI: 10.2210/pdb6fy6/pdb
• Related: 6FY7 6RLS
• NMR Information: BMRB: 34244
• Descriptor: DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_major, MERCURY (II) ION (2 entities in total)
• Functional Keywords: metallated duplex dna, b-form helix, a-form helix, mercury(ii)-mediated base pair, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 8912.74

Authors

Schmidt, O.P.,Jurt, S.,Johannsen, S.,Karimi, A.,Sigel, R.K.O.,Luedtke, N.W. (deposition date: 2018-03-11, release date: 2019-10-09, Last modification date: 2024-05-15)

Primary citation

Schmidt, O.P.,Jurt, S.,Johannsen, S.,Karimi, A.,Sigel, R.K.O.,Luedtke, N.W.
Concerted dynamics of metallo-base pairs in an A/B-form helical transition.
Nat Commun, 10:4818-4818, 2019

PubMed Abstract: Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-Hg-T metallo base pairs separated by six canonical base pairs. NMR experiments reveal a 3:1 ratio of well-resolved structures in dynamic equilibrium. The major species contains two (N3)T-Hg-(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-Hg-(N4)C base pairs and greater A-form characteristics. Ten-fold different J coupling constants (N,Hg) are observed for (N3)C-Hg (114 Hz) versus (N4)C-Hg (1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-Hg-T base pairs are coupled to a global conformational exchange between the helices. These observations inspired the design of a repetitive DNA sequence capable of undergoing a global B-to-A-form helical transition upon adding Hg, demonstrating that C-Hg-T has unique switching potential in DNA-based materials and devices.

PubMed: 31645548
DOI: 10.1038/s41467-019-12440-x

Experimental method

SOLUTION NMR