title: The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences.
abstract: The structure of the decadeoxyribonucleotide d(GCATGCATGC) is presented at a resolution of 1.8 Å. The decamer adopts a novel double-folded structure in which the direction of progression of the backbone changes at the two thymine residues. Intra-strand stacking interactions (including an interaction between the endocylic O atom of a ribose moiety and the adjacent purine base), hydrogen bonds and cobalt-ion interactions stabilize the double-folded structure of the single strand. Two such double-folded strands come together in the crystal to form a dimer. Inter-strand Watson-Crick hydrogen bonds form four base pairs. This portion of the decamer structure is similar to that observed in other previously reported oligonucleotide structures and has been dubbed a `bi-loop'. Both the double-folded single-strand structure, as well as the dimeric bi-loop structure, serve as starting points to construct models for triplet-repeat DNA sequences, which have been implicated in many human diseases.
authors.affiliation: CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India.
authors.forename: Arunachalam
authors.initials: A
authors.lastname: Thirugnanasambandam
authors.affiliation: CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India.
authors.forename: Selvam
authors.initials: S
authors.lastname: Karthik
authors.affiliation: CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India.
authors.forename: Pradeep Kumar
authors.initials: PK
authors.lastname: Mandal
authors.affiliation: CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India.
authors.forename: Namasivayam
authors.initials: N
authors.lastname: Gautham
mesh_terms: D001483:Base Sequence; D003035:Cobalt / Q000737:chemistry; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D003854:Deoxyribonucleotides / Q000737:chemistry*; D019281:Dimerization; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D016415:Sequence Alignment; D013941:Thymine / Q000737:chemistry
chemical_list: D003854:Deoxyribonucleotides; D009841:Oligonucleotides; D003035:Cobalt; D004247:DNA; D013941:Thymine
keywords: DNA; bi-loop; double-folded structure; minor-groove tetrad; triplet repeat