title: Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats.
abstract: A number of human hereditary diseases have been associated with the instability of DNA repeats in the genome. Recently, spinocerebellar ataxia type 10 has been associated with expansion of the pentanucleotide repeat (ATTCT)(n).(AGAAT)(n) from a normal range of ten to 22 to as many as 4500 copies. The structural properties of this repeat cloned in circular plasmids were studied by a variety of methods. Two-dimensional gel electrophoresis and atomic force microscopy detected local DNA unpairing in supercoiled plasmids. Chemical probing analysis indicated that, at moderate superhelical densities, the (ATTCT)(n).(AGAAT)(n) repeat forms an unpaired region, which further extends into adjacent A+T-rich flanking sequences at higher superhelical densities. The superhelical energy required to initiate duplex unpairing is essentially length-independent from eight to 46 repeats. In plasmids containing five repeats, minimal unpairing of (ATTCT)(5).(AGAAT)(5) occurred while 2D gel analysis and chemical probing indicate greater unpairing in A+T-rich sequences in other regions of the plasmid. The observed experimental results are consistent with a statistical mechanical, computational analysis of these supercoiled plasmids. For plasmids containing 29 repeats, which is just above the normal human size range, flanked by an A+T-rich sequence, atomic force microscopy detected the formation of a locally condensed structure at high superhelical densities. However, even at high superhelical densities, DNA strands within the presumably compact A+T-rich region were accessible to small chemicals and oligonucleotide hybridization. Thus, DNA strands in this "collapsed structure" remain unpaired and accessible for interaction with other molecules. The unpaired DNA structure functioned as an aberrant replication origin, in that it supported complete plasmid replication in a HeLa cell extract. A model is proposed in which unscheduled or aberrant DNA replication is a critical step in the expansion mutation.
authors.affiliation: Laboratory of DNA Structure and Function, Center for Genome Research, Institute of Biosciences and Technology, Texas A and M University System Health Sciences Center, Houston, TX 77030-3303, USA.
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Potaman
authors.forename: John J
authors.initials: JJ
authors.lastname: Bissler
authors.forename: Vera I
authors.initials: VI
authors.lastname: Hashem
authors.forename: Elena A
authors.initials: EA
authors.lastname: Oussatcheva
authors.forename: Lu
authors.initials: L
authors.lastname: Lu
authors.forename: Luda S
authors.initials: LS
authors.lastname: Shlyakhtenko
authors.forename: Yuri L
authors.initials: YL
authors.lastname: Lyubchenko
authors.forename: Tohru
authors.initials: T
authors.lastname: Matsuura
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Ashizawa
authors.forename: Michael
authors.initials: M
authors.lastname: Leffak
authors.forename: Craig J
authors.initials: CJ
authors.lastname: Benham
authors.forename: Richard R
authors.initials: RR
authors.lastname: Sinden
mesh_terms: D001482:Base Composition; D020029:Base Pairing; D004261:DNA Replication; D004278:DNA, Superhelical / Q000737:chemistry* / Q000235:genetics / Q000648:ultrastructure; D015180:Electrophoresis, Gel, Two-Dimensional; D006367:HeLa Cells; D006801:Humans; D018895:Microsatellite Repeats; D018625:Microscopy, Atomic Force; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000235:genetics / Q000378:metabolism; D010957:Plasmids / Q000235:genetics* / Q000378:metabolism; D020754:Spinocerebellar Ataxias / Q000235:genetics*
chemical_list: D004278:DNA, Superhelical; D009841:Oligonucleotides