Stabilization by extra-helical thymines of a DNA duplex with Hoogsteen base pairs.
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.
Pous
Joan
J
Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, E-08028 Barcelona, Spain.
Urpí
Lourdes
L
Subirana
Juan A
JA
Gouyette
Catherine
C
Navaza
Jorge
J
Campos
J Lourdes
JL
D020029:Base Pairing; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D013941:Thymine / Q000031:analogs & derivatives / Q000737:chemistry*
D009841:Oligonucleotides; D003596:Cytosine; D004247:DNA; D013941:Thymine