Spontaneous DNA-DNA interaction of homologous duplexes and factors affecting the result of heteroduplex formation.
Mutation detection and mismatch repair investigations based on heteroduplex formation require a linear DNA structure. DNA branching, described previously under physiological conditions, has been analysed in the heteroduplex formation process. Symmetrical chi-structures were detected after heteroduplex formation by gel electrophoresis and electron microscopy. Buffer composition, DNA concentration and duplex end-sequences influence DNA branching. Duplexes with homologous central regions but non-complementary ends do not form hybrid heteroduplexes or hybrid Holliday junctions. Our results explain the requirements for efficient heteroduplex formation, which were previously determined empirically: special solution composition, optimal DNA concentration and GC clamps. This provides the theoretical background for further optimisation of the procedure.
Neschastnova
Anna A
AA
Institute of Carcinogenesis, Blokhin Cancer Research Centre, Russian Academy of Medical Sciences, Kashirskoye Shosse 24, Moscow 115478, Russia. myakubovskaya@crc.umos.ru
Gasanova
Victoria K
VK
Popenko
Vladimir I
VI
Lambrinakos
Andreana
A
Belitsky
Gennady A
GA
Cotton
Richard G H
RG
Yakubovskaya
Marianna G
MG
D000818:Animals; D020137:Base Pair Mismatch / Q000235:genetics; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D004587:Electrophoresis, Agar Gel; D051379:Mice; D008854:Microscopy, Electron; D009154:Mutation / Q000235:genetics; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure
D009692:Nucleic Acid Heteroduplexes; D004247:DNA