title: Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA.
abstract: Base extrusion is a major structural feature at the junction between B- and Z-DNA (the B-Z junction) where a base pair is broken, and the two bases are extruded from the double helix. Despite the demonstration of base extrusion at the B-Z junction, it is not clear whether a similar base extrusion occurs at other types of junctions involving the left-handed Z conformation. Here, we investigate structural changes of bases at three Z-form junctions: DNA B-Z and Z-Z and RNA A-Z junctions. By monitoring fluorescently labeled duplex nucleic acids using 2-aminopurines at various positions relative to the junction point, we show that base extrusion occurs not only at the DNA B-Z junction, but also at the RNA A-Z and DNA Z-Z junctions. Our data suggest that base extrusion is a general feature of Z-form nucleic-acid junctions.
authors.affiliation: Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.
authors.forename: Doyoun
authors.initials: D
authors.lastname: Kim
authors.forename: Sanjith
authors.initials: S
authors.lastname: Reddy
authors.forename: Dong Young
authors.initials: DY
authors.lastname: Kim
authors.forename: Alexander
authors.initials: A
authors.lastname: Rich
authors.forename: Sangho
authors.initials: S
authors.lastname: Lee
authors.forename: Kyeong Kyu
authors.initials: KK
authors.lastname: Kim
authors.forename: Yang-Gyun
authors.initials: YG
authors.lastname: Kim
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry; D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D043542:DNA, Z-Form / Q000737:chemistry*; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D043542:DNA, Z-Form; D015075:2-Aminopurine; D012313:RNA; D004247:DNA