2QS6: Structure Of A Hoogsteen Antiparallel Duplex With Extra-helical Thymines

We present the crystal structure of the DNA duplex formed by d(ATATATCT). The crystals contain seven stacked antiparallel duplexes in the asymmetric unit with A.T Hoogsteen base pairs. The terminal CT sequences bend over so that the thymines enter the minor groove and form a hydrogen bond with thymine 2 of the complementary strand in the Hoogsteen duplex. Cytosines occupy extra-helical positions; they contribute to the crystal lattice through various kinds of interactions, including a unique CAA triplet. The presence of thymine in the minor groove apparently contributes to the stability of the DNA duplex in the Hoogsteen conformation. These observations open the way toward finding under what conditions the Hoogsteen duplex may be stabilized in vivo. The present crystal structure also confirms the tendency of A.T-rich oligonucleotides to crystallize as long helical stacks of duplexes.
PDB ID: 2QS6Download
MMDB ID: 63236
PDB Deposition Date: 2007/7/30
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 3.08  Å
Biological Unit for 2QS6: dimeric; determined by author and by software (PISA)
Molecular Components in 2QS6
Label Count Molecule
Nucleotide(1 molecule)
DNA (5'-d(*dap*dtp*dap*dtp*dap*dtp*dcp*dt)-3')
Molecule annotation
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