7QA9 | pdb_00007qa9

10bp DNA/DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb7QA9/pdb
• NAKB: 7QA9
• BMRB: 34679

• Classification: DNA
• Organism(s): Octodon degus
• Mutation(s): No 


• Deposited: 2021-11-16 Released: 2022-11-16 
• Deposition Author(s): Li, Q., Trajkovski, M., Fan, C., Chen, J., Zhou, Y., Lu, K., Li, H., Su, X., Xi, Z., Plavec, J., Zhou, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Slovenian Research Agency

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

4'-SCF 3 -Labeling Constitutes a Sensitive 19 F NMR Probe for Characterization of Interactions in the Minor Groove of DNA.

Li, Q., Trajkovski, M., Fan, C., Chen, J., Zhou, Y., Lu, K., Li, H., Su, X., Xi, Z., Plavec, J., Zhou, C.

(2022) Angew Chem Int Ed Engl 61: e202201848-e202201848

• PubMed: 36163470 
• DOI: https://doi.org/10.1002/anie.202201848
• Primary Citation Related Structures: 
  7QA9, 7W0V


• PubMed Abstract: 
  

  Fluorinated nucleotides are invaluable for ¹⁹ F NMR studies of nucleic acid structure and function. Here, we synthesized 4'-SCF ₃ -thymidine (T $4^{}$ ' - SCF 3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ ) and incorporated it into DNA by means of solid-phase DNA synthesis. NMR studies showed that the 4'-SCF ₃ group exhibited a flexible orientation in the minor groove of DNA duplexes and was well accommodated by various higher order DNA structures. The three magnetically equivalent fluorine atoms in 4'-SCF ₃ -DNA constitute an isolated spin system, offering high ¹⁹ F NMR sensitivity and excellent resolution of the positioning of T $4^{}$ ' - SCF 3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ within various secondary and tertiary DNA structures. The high structural adaptability and high sensitivity of T $4^{}$ ' - SCF 3 ${{^{4{^\prime}\hbox{-}{\rm SCF}{_{3}}}}}$ make it a valuable ¹⁹ F NMR probe for quantitatively distinguishing diverse DNA structures with single-nucleotide resolution and for monitoring the dynamics of interactions in the minor groove of double-stranded DNA.

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Organizational Affiliation: 
• State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin, 300071, China.
Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.09 kDa 
• Atom Count: 404 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3')	A	10	Octodon degus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3')	B	10	Octodon degus

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Li, Q., Trajkovski, M., Fan, C., Chen, J., Zhou, Y., Lu, K., Li, H., Su, X., Xi, Z., Plavec, J., Zhou, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	Slovenia	91953115
National Natural Science Foundation of China (NSFC)	Slovenia	21877064
Slovenian Research Agency	Slovenia	P1-0242
Slovenian Research Agency	Slovenia	J1-1704

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2022-11-23
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Data collection, Database references