Probing the structure of a putative intermediate in homologous recombination: the third strand in the parallel DNA triplex is in contact with the major groove of the duplex.
A three-stranded DNA that is a putative intermediate of homologous recombination is a novel DNA triplex, R-form DNA. In R-form DNA the third strand includes both purines and pyrimidines and is parallel to the identical strand of the duplex. To test and refine our previously proposed R-form base triplets we have used two approaches: (1) dimethyl sulfate protection of R-form DNA; and (2) thermal dissociation of R-form DNAs in which the duplex strands were substituted in a strand-specific manner with either 7-deaza-guanine or 7-deaza-adenine. Together, the footprinting and isosteric substitution results demonstrate that the third strand in R-form DNA is in contact with the purines in the N7 position in the major groove of the Watson-Crick duplex in three ((GC):G, (AT):A and (TA):T) out of the four possible triplets. Furthermore, these results suggest that the N7 positions of the duplex play a significant role in stabilizing the DNA-DNA contacts during the homology recognition process.
Kim
M G
MG
Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-1810, USA.
Zhurkin
V B
VB
Jernigan
R L
RL
Camerini-Otero
R D
RD
D017104:Bacteriophage M13 / Q000235:genetics*; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics; D004268:DNA-Binding Proteins; D006358:Hot Temperature; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011687:Purines / Q000737:chemistry; D011938:Rec A Recombinases; D011995:Recombination, Genetic / Q000235:genetics*; D013463:Sulfuric Acid Esters
D004279:DNA, Viral; D004268:DNA-Binding Proteins; D011687:Purines; D013463:Sulfuric Acid Esters; C051802:triplex DNA; D004247:DNA; D011938:Rec A Recombinases; C007482:dimethyl sulfate