2P8D

The Structure of the Dickerson Sequence with an Incorporated CeNA Residue

Summary for 2P8D

• Entry DOI: 10.2210/pdb2p8d/pdb
• Related: 2H0N
• Descriptor: 5'-D(*DCP*DGP*DCP*DGP*DAP*(XAR)P*DTP*DTP*DCP*DGP*DCP*DG)-3', COBALT HEXAMMINE(III) (3 entities in total)
• Functional Keywords: cena, sugar modification, dna
• Total number of polymer chains: 2
• Total formula weight: 7830.21

Authors

Robeyns, K.,Van Meervelt, L. (deposition date: 2007-03-22, release date: 2008-02-05, Last modification date: 2023-08-30)

Primary citation

Robeyns, K.,Herdewijn, P.,Van Meervelt, L.
Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG).
Nucleic Acids Res., 36:1407-1414, 2008

PubMed Abstract: Cyclohexene nucleic acids (CeNA), which are characterized by the presence of a cyclohexene moiety instead of a natural (deoxy)ribose sugar, are known to increase the thermal and enzymatic stability when incorporated in RNA oligonucleotides. As it has been demonstrated that even a single cyclohexenyl nucleoside, when incorporated in an oligonucleotide, can have a profound effect on the biological activity of the oligonucleotide, further research is warranted to study the complex of such oligonucleotides with target proteins. In order to analyse the influence of CeNA residues onto the helix conformation and hydration of natural nucleic acid structures, a cyclohexenyl-adenine building block (xAr) was incorporated into the Dickerson sequence CGCGA(xAr)TTCGCG. The crystal structure of this sequence determined to a resolution of 1.90 A. The global helix belongs to the B-type family and shows a water spine, which is partially broken up by the apolar cyclohexene residue. The cyclohexene ring adopts the (2)E-conformation allowing a better incorporation of the residue in the dodecamer sequence. The crystal packing is stabilized by cobalt hexamine residues and belongs to space group P222(1), never before reported for nucleic acids.

PubMed: 18160414
DOI: 10.1093/nar/gkm1132

Experimental method

X-RAY DIFFRACTION (1.9 Å)