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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.

SUBMITTER: Kim D

PROVIDER: S-EPMC2715235 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA.

Kim Doyoun D Reddy Sanjith S Kim Dong Young DY Rich Alexander A Lee Sangho S Kim Kyeong Kyu KK Kim Yang-Gyun YG

Nucleic acids research 20090521 13

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 monitor ...[more]

PMID: 19465399

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