1NDN

MOLECULAR STRUCTURE OF NICKED DNA. MODEL T4

Summary for 1NDN

• Entry DOI: 10.2210/pdb1ndn/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3'), DNA (5'-D(*CP*GP*CP*GP*TP*T)-3'), DNA (5'-D(*TP*TP*CP*GP*CP*G)-3'), ... (4 entities in total)
• Functional Keywords: b-dna, double helix, nicked, dna
• Total number of polymer chains: 3
• Total formula weight: 7281.83

Authors

Aymani, J.,Coll, M.,Van Der Marel, G.A.,Van Boom, J.H.,Wang, A.H.-J.,Rich, A. (deposition date: 1992-01-15, release date: 1992-07-14, Last modification date: 2024-02-14)

Primary citation

Aymami, J.,Coll, M.,van der Marel, G.A.,van Boom, J.H.,Wang, A.H.,Rich, A.
Molecular structure of nicked DNA: a substrate for DNA repair enzymes.
Proc.Natl.Acad.Sci.USA, 87:2526-2530, 1990

PubMed Abstract: The molecular structure of a nicked dodecamer DNA double helix, made of a ternary system containing d(CGCGAAAACGCG) + d(CGCGTT) + d(TTCGCG) oligonucleotides, has been determined by x-ray diffraction analysis at 3 A resolution. The molecule adopts a B-DNA conformation, not unlike those found in intact dodecamer DNA molecules crystallized in a somewhat different crystal lattice, despite a gap due to the absence of a phosphate group in the molecule. The helix has a distinct narrow minor groove near the center of the molecule at the AAAA region. This suggests that the internal stabilizing forces due to base stacking and hydrogen-bonding interactions are sufficient to overcome the loss of connectivity associated with the disruption of the covalent backbone of DNA.

PubMed: 2320572
DOI: 10.1073/pnas.87.7.2526

Experimental method

X-RAY DIFFRACTION (3 Å)