1S23

Crystal Structure Analysis of the B-DNA Decamer CGCAATTGCG

Summary for 1S23

• Entry DOI: 10.2210/pdb1s23/pdb
• Descriptor: 5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3', COBALT (II) ION (3 entities in total)
• Functional Keywords: deoxyoligonucleotide, cobalt, variability, dna
• Total number of polymer chains: 1
• Total formula weight: 3103.94

Authors

Valls, N.,Wright, G.,Steiner, R.A.,Murshudov, G.N.,Subirana, J.A. (deposition date: 2004-01-08, release date: 2004-04-06, Last modification date: 2024-04-03)

Primary citation

Valls, N.,Wright, G.,Steiner, R.A.,Murshudov, G.N.,Subirana, J.A.
DNA variability in five crystal structures of d(CGCAATTGCG).
Acta Crystallogr.,Sect.D, 60:680-685, 2004

PubMed Abstract: The deoxyoligonucleotide d(CGCAATTGCG) has previously been crystallized in four different space groups. The crystals diffract to moderate resolution (2.3-2.9 A). Here, a fifth crystal form that diffracts to higher resolution (1.6 A) is presented which was obtained thanks to the use of Co2+ and cryogenic temperatures. The availability of five different crystal structures allows a thorough analysis of the conformational variability of this DNA sequence. It is concluded that the central hexamer sequence CAATTG has a practically constant conformation under all conditions, whilst the terminal base pairs at both ends vary considerably as a result of differing interactions in the crystals. The new crystal structure presented here is stabilized by guanine-Co2+-guanine interactions and the formation of C1+ -G8.C3 triplexes between neighbouring duplexes. As a result of the higher resolution of the crystal structure, a more regular structure was obtained and a clear definition of the spine of hydration was observed which was not visible in the four previous structures.

PubMed: 15039556
DOI: 10.1107/S0907444904002896

Experimental method

X-RAY DIFFRACTION (1.6 Å)