1QXB | pdb_00001qxb

NMR structure determination of the self complementary DNA Dodecamer CGCGAATT*CGCG in which a ribose is inserted between the 3'-OH of T8 and the 5'-phosphate group of C9

• PDB DOI: https://doi.org/10.2210/pdb1QXB/pdb
• NAKB: 1QXB

• Classification: DNA
• Mutation(s): No 


• Deposited: 2003-09-05 Released: 2004-02-03 
• Deposition Author(s): Nauwelaerts, K., Vastmans, K., Froeyen, M., Kempeneers, V., Rozenski, J., Rosemeyer, H., Van Aerschot, A., Busson, R., Efimtseva, E., Mikhailov, S., Lescrinier, E., Herdewijn, P.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Literature

Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside.

Nauwelaerts, K., Vastmans, K., Froeyen, M., Kempeneers, V., Rozenski, J., Rosemeyer, H., Van Aerschot, A., Busson, R., Lacey, J.C., Efimtseva, E., Mikhailov, S., Lescrinier, E., Herdewijn, P.

(2003) Nucleic Acids Res 31: 6758-6769

• PubMed: 14627809 
• DOI: https://doi.org/10.1093/nar/gkg911
• Primary Citation Related Structures: 
  1QXB


• PubMed Abstract: 
  

  A ribose residue inserted between the 3'-OH of one nucleotide and the 5'-phosphate group of the next nucleotide, functions as a site-specific cleavage site within DNA. This extra ribose does not interrupt helix formation and it protects duplex DNA against cleavage by restriction enzymes. Cleavage can be obtained with periodate and all ribose fragments can be removed with sodium hydroxide. As a result of this, an intact natural oligodeoxynucleotide is obtained after ligation reaction, which means that site-specific cleavage and recovering of intact DNA occurs without loss of genetic information.

---

Organizational Affiliation: 
• Rega Institute for Medical Research, Laboratory for Medicinal Chemistry, Minderbroedersstraat 10, B-3000 Leuven, Belgium.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.63 kDa 
• Atom Count: 504 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-d(CpGpCpGpApApTpTpCpGpCpG)-3'	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDR	C [auth A], D [auth B]	beta-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-TXICZTDVSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-03 
Deposition Author(s): Nauwelaerts, K., Vastmans, K., Froeyen, M., Kempeneers, V., Rozenski, J., Rosemeyer, H., Van Aerschot, A., Busson, R., Efimtseva, E., Mikhailov, S., Lescrinier, E., Herdewijn, P.

Revision History  

• Version 1.0: 2004-02-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-05-01
  Changes: Data collection, Database references, Structure summary