5L2G

Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 9th Position

• PDB DOI:  https://doi.org/10.2210/pdb5L2G/pdb
• BMRB: 30151
• NAKB: 5L2G

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


• Deposited: 2016-08-01 Released: 2016-12-21 
• Deposition Author(s): Miears, H.L., Hoppins, J.J., Gruber, D.R., Kasymov, R.D., Johnson, E.C., Zharkov, D.O., Smirnov, S.L.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 18 
• Conformers Submitted: 9 
• Selection Criteria: structures with the lowest energy 

Literature

Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.

Gruber, D.R., Toner, J.J., Miears, H.L., Shernyukov, A.V., Kiryutin, A.S., Lomzov, A.A., Endutkin, A.V., Grin, I.R., Petrova, D.V., Kupryushkin, M.S., Yurkovskaya, A.V., Johnson, E.C., Okon, M., Bagryanskaya, E.G., Zharkov, D.O., Smirnov, S.L.

(2018) Nucleic Acids Res 46: 10827-10839

• PubMed: 30289469 
• DOI: https://doi.org/10.1093/nar/gky893
• Primary Citation of Related Structures:  
  5L06, 5L2G, 5TRN, 5UZ1, 5UZ2, 5UZ3, 6ALS, 6ALT, 6ALU


• PubMed Abstract: 
  

DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI→BII transition in the backbone 3' to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.

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Organizational Affiliation: 

Chemistry Department, Western Washington University, 516 High St., Bellingham, WA 98225-9150, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.35 kDa 
• Atom Count: 488 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3')	A, B	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 18 
• Conformers Submitted: 9 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Miears, H.L., Hoppins, J.J., Gruber, D.R., Kasymov, R.D., Johnson, E.C., Zharkov, D.O., Smirnov, S.L.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1244641

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Structure summary
• Version 1.2: 2018-12-19
  Changes: Data collection, Database references
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence, Data collection