Interactions of three strands in joints made by RecA protein.
RecA protein from Escherichia coli has been used to form a triple-stranded DNA structure from either single-stranded M13 DNA or a single-stranded oligonucleotide plus a duplex oligonucleotide with a hairpin loop. The secondary structure of purified deproteinized triplex was examined by probing with DNase I, P1 nuclease, potassium permanganate, and diethyl pyrocarbonate. The two strands destined to form heteroduplex DNA showed the same patterns of chemical modification and enzymatic digestion as control duplex DNA, indicating that they formed a normal duplex substructure. However, the nascent outgoing strand showed properties consistent with a novel triplex structure: most of its purine residues, especially adenines, were hyperreactive to all probes. The patterns of digestion by DNase I and P1 nuclease indicated that the nascent outgoing strand was not a freely mobile or single-stranded branch but rather was still interacting with the newly formed heteroduplex DNA. On the basis of the planar base triads proposed previously (Rao et al., 1993) and energy minimization of a third strand in the major groove of B-form DNA, we derived a model that helps to rationalize the properties revealed by chemical and enzymatic probing.
Chiu
S K
SK
Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510.
Rao
B J
BJ
Story
R M
RM
Radding
C M
CM
D017104:Bacteriophage M13 / Q000737:chemistry; D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D004279:DNA, Viral / Q000737:chemistry; D004047:Diethyl Pyrocarbonate / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011196:Potassium Permanganate / Q000737:chemistry; D011938:Rec A Recombinases / Q000737:chemistry*; D013463:Sulfuric Acid Esters / Q000737:chemistry
D004279:DNA, Viral; D009838:Oligodeoxyribonucleotides; D013463:Sulfuric Acid Esters; D011196:Potassium Permanganate; D004247:DNA; D011938:Rec A Recombinases; C007482:dimethyl sulfate; D004047:Diethyl Pyrocarbonate