title: Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2at 1.7 Å resolution.
abstract: We present here a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)2all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of zinc, magnesium, and in the absence of any metal ion, it does not take up the junction structure, but forms an A-type double helix. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Upon addition of the zinc ion, there is a change in the space group from P41212 to P41. The overall conformation of the duplex remains the same. There are small changes in the interaction of the metal ions with the DNA. In the zinc-bound structure, there are two zinc ions that show direct interaction with the N7 atoms of terminal G13bases at either end of the molecule. There are small changes in the interhelical contacts. The consequence of these differences is to break some of the symmetry and change the space group.
authors.affiliation: a CAS in Crystallography and Biophysics , University of Madras , Guindy Campus, Chennai , Tamil Nadu , India.
authors.forename: S
authors.initials: S
authors.lastname: Karthik
authors.affiliation: a CAS in Crystallography and Biophysics , University of Madras , Guindy Campus, Chennai , Tamil Nadu , India.
authors.forename: A
authors.initials: A
authors.lastname: Thirugnanasambandam
authors.affiliation: a CAS in Crystallography and Biophysics , University of Madras , Guindy Campus, Chennai , Tamil Nadu , India.
authors.forename: P K
authors.initials: PK
authors.lastname: Mandal
authors.affiliation: a CAS in Crystallography and Biophysics , University of Madras , Guindy Campus, Chennai , Tamil Nadu , India.
authors.forename: N
authors.initials: N
authors.lastname: Gautham
mesh_terms: D001483:Base Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D044704:DNA, A-Form / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D015032:Zinc / Q000737:chemistry
chemical_list: D044704:DNA, A-Form; D009838:Oligodeoxyribonucleotides; D004247:DNA; D008274:Magnesium; D015032:Zinc
keywords: A-DNA duplex; X-ray crystallography; two tetragonal space groups; zinc interactions