7NBK | pdb_00007nbk

Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification

• PDB DOI: https://doi.org/10.2210/pdb7NBK/pdb
• BMRB: 34594
• NAKB: 7NBK

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


• Deposited: 2021-01-27 Released: 2021-04-07 
• Deposition Author(s): Cabrero, C., Martin-Pintado, N., Mazzini, S., Gargallo, R., Eritja, R., Avino, A., Gonzalez, C.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Literature

Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.

Cabrero, C., Martin-Pintado, N., Mazzini, S., Gargallo, R., Eritja, R., Avino, A., Gonzalez, C.

(2021) Chemistry 

• PubMed: 33772916 
• DOI: https://doi.org/10.1002/chem.202100503
• Primary Citation Related Structures: 
  7NBK, 7NBL, 7NEJ


• PubMed Abstract: 
  

  We report the structural effect of 2'-deoxy-2',2'-difluorocytidine (dFdC) insertions in the DNA strand of a DNA : RNA hybrid duplex and in a self-complementary DNA : DNA duplex. In both cases, the modification slightly destabilizes the duplex and provokes minor local distortions that are more pronounced in the case of the DNA : RNA hybrid. Analysis of the solution structures determined by NMR methods show that dFdC is an adaptable derivative that adopts North type sugar conformation when inserted in pure DNA, or a South sugar conformation in the context of DNA : RNA hybrids. In this latter context, South sugar pucker favors the formation of a 2'F⋅⋅H8 attractive interaction with a neighboring purine, which compensates the destabilizing effect of base pair distortions. These interactions share some features with pseudohydrogen bonds described previously in other nucleic acids structures with fluorine modified sugars.

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Organizational Affiliation: 
• Instituto de Química Física Rocasolano, CSIC, Serrano, 119, 28006, Madrid, Spain.
Department of Food, Environmental and Nutritional Sciences (DEFENS), Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy.
Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1, 08028, Barcelona, Spain.
BIOESTRAN associated unit UB-CSIC, 08028, Barcelona, Spain.
Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) CIBER-BBN, Jordi, Girona 18-26, 08034, Barcelona, Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 3.69 kDa 
• Atom Count: 244 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3')	A, B	6	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: all calculated structures submitted 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Cabrero, C., Martin-Pintado, N., Mazzini, S., Gargallo, R., Eritja, R., Avino, A., Gonzalez, C.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	BFU2017-89707-P
Spanish Ministry of Science, Innovation, and Universities	Spain	PRE2018-083173

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references