Abstract
The RecA protein ofEscherichia coli catalyzes homologous pairing and strand exchange between a wide range of molecules showing nucleotide sequence complementarity, including a linear duplex and a single-stranded DNA molecule. We demonstrate that RecA can promote formation of joint molecules when the duplex contains an RNA/DNA hairpin and a single-stranded circle serves as the pairing partner. A chimeric RNA/DNA hairpin can be used to form stable joint molecules with as little as 15 bases of shared homology as long as the RNA stretch contains complementarity to the circle. The joint molecule bears some resemblance to a triple helical structure composed of RNA residues surrounded by two DNA strands which are in a parallel orientation. Evidence is presented that supports the notion that short stretches of RNA can be used in homologous pairing reactions at lengths below that required for DNA-DNA heteroduplex formation.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Chase JW, Richardson CC (1974) Exonuclease VII ofEscherichia coli. J Biol Chem 249:4553–4561
Chiu SK, Rao BJ, Story RM, Radding CM (1993) Interactions of three strands in joints made by RecA protein. Biochemistry 32:13146–13155
Cox MM, Lehman IR (1987) Enzymes of general Recombination. Annu Rev Biochem 56:229–262
Egli M, Usman N, Rich A (1993) Conformational influence of the ribose 2′-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes. Biochemistry 32:3221–3327
Fedoroff OY, Salazar M, Reid BR (1993) Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA. J Mol Biol 233:509–523
Gonda DK, Radding CM (1983) By searching processively, RecA protein pairs DNA molecules that share a limited stretch of homology. Cell 34:647–654
Hsieh P, Camerini-Otero CS, Camerini-Otero RD (1990) Pairing of homologous DNA sequences by proteins: evidence for three-stranded DNA. Genes Dev 4:1951–1963
Hsieh P, Camerini-Otero CS, Camerini-Otero RD (1992) The synapsis event in the homologous pairing of DNAs: RecA recognizes and pairs less than one helical repeat of DNA. Proc Natl Acad Sci USA 89:6492–6496
Kotani H, Kmiec EB (1994a) Transcription activates RecA-promoted homologous pairing of nucleosomal DNA. Mol Cell Biol 14:1949–1955
Kotani H, Kmiec EB (1994b) A role for RNA synthesis in homologous pairing events. Mol Cell Biol 14:6097–6106
Kotani H, Kmiec EB (1994c) DNA cruciforms facilitate in vitro strand transfer on nucleosomal templates. Mol Gen Genet 244:410–419
Kowalczykowski SC (1991) Biochemical and biological function ofE scherichia coli RecA protein: behavior of mutant RecA proteins (Review) Biochimie 73:289–304
Lutzker S, Alt F (1988) Structure and expression of germ line immunoglobulin gamma 2b transcripts. Mol Cell Biol 8:1849–1852
Rao BJ, Chiu SK, Radding CM (1993) Homologous recognition and triplex formation promoted by RecA protein between duplex oligonucleotides and single-stranded DNA. J Mol Biol 229:328–343
Rao BJ, Chiu SK, Bazemore LR, Reddy G, Radding CM (1995) How specific is the first recognition step of homologous recombination? Trends Biochem Sci 20(3):109–113
Roberts RW, Crothers DM (1992) Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. Science 258:1463–1466
Roca AI, Cox MM (1990) The RecA protein: structure and function. Crit Rev Biochem Mol Biol 25:415–156
Stavnezer-Nordgren J, Sirlin S (1986) Specificity of immunoglobulin heavy chain switch correlates with activity of germline heavy chain genes prior to switching. EMBO J 5:95–102
Sung SC, Laskowski MS (1962) A nuclease from mung bean sprouts. J Biol Chem 237:506–511
Whoriskey SK, Ngheim V-H, Leong P-M, Masson J-M, Miller JH (1987) Genetic rearrangements and gene amplification inEscherichia coli: DNA sequences at the juncture of gene fusions. Genes Dev 1:227–237
Author information
Authors and Affiliations
Additional information
Communicated by M. Sekiguchi
Rights and permissions
About this article
Cite this article
Kotani, H., Germann, M.W., Andrus, A. et al. RNA facilitates RecA-mediated DNA pairing and strand transfer between molecules bearing limited regions of homology. Molec. Gen. Genet. 250, 626–634 (1996). https://doi.org/10.1007/BF02174450
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF02174450