6RLS | pdb_00006rls

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

PDB DOI: https://doi.org/10.2210/pdb6RLS/pdb
BMRB: 34398
NAKB: 6RLS

Classification: DNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2019-05-02 Released: 2019-10-09
Deposition Author(s): Schmidt, O.P., Jurt, S., Johannsen, S., Karimi, A., Sigel, R.K.O., Luedtke, N.W.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

wwPDB Validation 3D Report Full Report

Validation slider image for 6RLS

This is version 1.2 of the entry. See complete history.

Literature

Concerted dynamics of metallo-base pairs in an A/B-form helical transition.

Schmidt, O.P., Jurt, S., Johannsen, S., Karimi, A., Sigel, R.K.O., Luedtke, N.W.

(2019) Nat Commun 10: 4818-4818

PubMed: 31645548 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-019-12440-x
Primary Citation Related Structures:
6FY6, 6FY7, 6RLS

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 ^II-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 ^II-(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-Hg ^II-(N4)C base pairs and greater A-form characteristics. Ten-fold different ¹J coupling constants ( ¹⁵N, ¹⁹⁹Hg) are observed for (N3)C-Hg ^II (114 Hz) versus (N4)C-Hg ^II (1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-Hg ^II-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 ^II, demonstrating that C-Hg ^II-T has unique switching potential in DNA-based materials and devices.

Organizational Affiliation

Department of Chemistry, University of Zurich, Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 8.51 kDa
Atom Count: 564
Modeled Residue Count: 28
Deposited Residue Count: 28
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(CPGPTPCPTPCPAPTPGPAPTPAPCPG)-3')_apo	A, B	14	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 20
Selection Criteria: structures with the lowest energy

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-10-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	165949

Revision History (Full details and data files)

Version 1.0: 2019-10-09
Type: Initial release
Version 1.1: 2019-11-13
Changes: Database references
Version 1.2: 2024-05-15
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.