5XK0

Structure of 8-mer DNA2

PDB DOI: https://doi.org/10.2210/pdb5XK0/pdb
NAKB: 5XK0

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

Deposited: 2017-05-04 Released: 2017-12-06
Deposition Author(s): Liu, H.H., Gan, J.H.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.196
R-Value Work: 0.180
R-Value Observed: 0.181

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A DNA Structure Containing AgI -Mediated G:G and C:C Base Pairs

Liu, H.H., Shen, F.S., Haruehanroengra, P., Yao, Q.Q., Cheng, Y.S., Chen, Y.Q., Yang, C., Zhang, J., Wu, B.X., Luo, Q., Cui, R.X., Li, J.X., Ma, J.B., Sheng, J., Gan, J.H.

(2017) Angew Chem Int Ed Engl 56: 9430-9434

PubMed: 28635152 Search on PubMed
DOI: https://doi.org/10.1002/anie.201704891
Primary Citation of Related Structures:
5XJZ, 5XK0, 5XK1

PubMed Abstract:
Metal-mediated base pairs have been extensively utilized in many research fields, including genetic-code extension, novel therapeutics development, and nanodevice design. Compared to other cations, Ag ^I is more flexible in pairing with natural base pairs. Herein, we present a DNA structure containing two C-Ag ^I -C pairs and the first reported G-Ag ^I -G pair in a short 8mer DNA strand. This structure not only provides detailed insight into these Ag ^I -mediated base-pairing patterns in DNA, but also represents the first nonhelical DNA structure driven by heavy-metal ions, thus further contributing to the structural diversity of DNA. This unique complex structure is highly sequence-dependent, thus implying functional potentials as a new DNA aptamer that can bind and recognize silver ions. These results not only advance our understanding of the interactions between Ag ^I and nucleobases, but also provide a unique structural component for the rational design of new DNA nanodevices.

Organizational Affiliation

State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200433, China.