Homologous Pairing and Strand Exchange in Genetic Recombination

Radding, Charles M.

doi:10.1146/annurev.ge.16.120182.002201

Cited by 443 publications

(194 citation statements)

References 70 publications

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“…For 15 N-labeled J1 and J2, all seven oligonucleotides were synthesized by Keystone Laboratories (Menlo Park, CA). For the one strand common to both J1 and J2, [1,[3][4][5][6][7][8][9][10][11][12][13][14][15] N]thymidine phosphoramidite (synthesized by the National Stable Isotope Resource, Los Alamos, NM) was used for the thymidine at position 9. Purification by anion-exchange chromatography was carried out using HQ POROS resin in an 8-ml column on a Biocad Sprint (PerCeptives Biosystems, Cambridge, MA).…”

Section: Methodsmentioning

confidence: 99%

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Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions

Miick

Fee

Millar

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

109

101

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Recombination of genes is essential to the evolution of genetic diversity, the segregation of chromosomes during cell division, and certain DNA repair processes. The Holliday junction, a four-arm, four-strand branched DNA crossover structure, is formed as a transient intermediate during genetic recombination and repair processes in the cell. The recognition and subsequent resolution of Holliday junctions into parental or recombined products appear to be critically dependent on their three-dimensional structure. Complementary NMR and time-resolved f luorescence resonance energy transfer experiments on immobilized four-arm DNA junctions reported here indicate that the Holliday junction cannot be viewed as a static structure but rather as an equilibrium mixture of two conformational isomers. Furthermore, the distribution between the two possible crossover isomers was found to depend on the sequence in a manner that was not anticipated on the basis of previous low-resolution experiments.Genetic recombination is a primary biological process that is critical to the continual evolution of all organisms, and the Holliday junction is a requisite intermediate in nearly all recombination events. Holliday (1) proposed the first and most basic mechanism of genetic recombination: homologous chromatids are nicked at identical sites, then the duplex DNA is partially unwound and the single strands are paired with the complementary strands of the homologs. The structure thus formed, termed the Holliday junction (HJ), may travel (branch-migrate) in either direction along the DNA. Eventually, the structure is cut endonucleolytically (resolved) to give two chromosomes with either a parental (patch) or a recombined (splice) configuration (Fig. 1). Although many postulated mechanisms for recombination exist, they differ only in how recombination is initiated and in how DNA strands are displaced (1-5). Most recombination mechanisms invoke formation of heteroduplex DNA molecules containing branched structures.It has been reported for more than 40 years that DNA sequence at or near a HJ influences how it is resolved and the corresponding ratio of parental to recombined molecules (6).Results from a variety of experiments suggest that resolution must be predetermined for certain sequences and that not all HJs are identical in structure (e.g., refs. 7-10). To gain an in-depth understanding of recognition and resolution of HJs, it is imperative to characterize their structure and dynamics at the atomic level and to establish how these properties vary with sequence.A consensus view of HJ structure has emerged from biophysical studies of immobilized four-arm DNA junctions in which the sequence is designed to eliminate the possibility of branch migration (for reviews see refs. 11 and 12). The four helical arms are seen to stack upon each other in a pairwise fashion, forming two duplex domains with an acute interhelical angle (Fig. 2). In this configuration, two contiguous strands run antiparallel to each other and the two crossover stra...

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Section: Methodsmentioning

confidence: 99%

“…1). Although many postulated mechanisms for recombination exist, they differ only in how recombination is initiated and in how DNA strands are displaced (1)(2)(3)(4)(5). Most recombination mechanisms invoke formation of heteroduplex DNA molecules containing branched structures.…”

mentioning

confidence: 99%

Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions

Miick

Fee

Millar

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

109

101

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“…Its abilities to bind DNA, form synapses among a rapid rate at which workable genetic syste, being variety of combinations of DNA molecules, promote the developed for several cyanobacteria. These s take assimilation of a single strand of DNA into a DNA duplex, advantage of the ability of a number of cyai tetia to and mediate polarized branch migration have all been demundergo DNA-mediated transformation (35) oi Sserve as onstrated in vitro (38). Its regulatory and direct biochemical recipients in conjugation involving E. coli do lls (49).…”

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confidence: 99%

Molecular cloning and characterization of the recA gene from the cyanobacterium Synechococcus sp. strain PCC 7002

Murphy¹,

Bryant²,

Porter³

et al. 1987

J Bacteriol

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The recA gene of Synechococcus sp. strain PCC 7002 was detected and cloned from a lambda gtwes genomic library by heterologous hybridization by using a gene-internal fragment of the Escherichia coli recA gene as the probe. The gene encodes a 38-kilodalton polypeptide which is antigenically related to the RecA protein of E. coli. The nucleotide sequence of a portion of the gene was determined. The translation of this region was 55% homologous to the E. coli protein; allowances for conservative amino acid replacements yield a homology value of about 74%. The cyanobacterial recA gene product was proficient in restoring homologous recombination and partial resistance to UV irradiation to recA mutants of E. coli. Heterologous hybridization experiments, in which the Synechococcus sp. strain PCC 7002 recA gene was used as the probe, indicate that a homologous gene is probably present in all cyanobacterial strains.

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“…The ability to invert its orientation was lost once the plasmid was transformed into a recA-strain, such as HB101. This result suggested that long inverted repeats of Tc4 are recognized by the bacterial system (28) usual oligonucleotide-labeling procedure, which requires the presence of a single-stranded template (20). Only when Tc4 was first cleaved in the middle with an appropriate restriction enzyme-e.g., Bgi II-could it be labeled.…”

Section: Resultsmentioning

confidence: 99%

Tc4, a Caenorhabditis elegans transposable element with an unusual fold-back structure.

Yuan

Finney

Tsung

et al. 1991

Proc. Natl. Acad. Sci. U.S.A.

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We have identified and characterized a family of transposable elements in the nematode Caenorhabdits ekgans. The Tc4 transposable element family is present at about 20 copies per haploid genome in the C. elegans Bristol and Bergerac strains. Although Tc4 transposition events have not been observed in these wild-type strains, we have identified Tc4 transposition events in the mut-2 mutant strain TR679, in which the elements Tcl and Tc3 also transpose at a higher frequency than in the wild type. We determined the sequence of one Tc4 element. This 1.6-kilobase element contains almost perfect inverted terminal repeats of 774 base pairs (bp) with a 57-bp unique internal sequence. Tc4 is a fold-back element, but its long inverted terminal repeats, unlike those of the fold-back elements of other organisms, do not consist of multiple short repeats. In the two cases studied, Tc4 insertion resulted in duplication of a TNA trinucleotide target site. The family of Tc4 elements differs from other C. ekgans transposable element families in structure, degree of structural heterogeneity, and target-site specificity. that consists mainly of two long inverted repeats (2-4). These transposable elements are called fold-back elements because when denatured and allowed to reanneal, the inverted repeat sequences fold back rapidly, yielding a hairpin structure. The mechanism of transposition of fold-back elements is largely unknown.Three families of Caenorhabditis elegans transposable elements, Tcl, Tc2, and Tc3, have been reported (5-9). Transposable elements of the Tcl and Tc3 families are structurally similar to the P elements of Drosophila. Tcl has been shown to transpose in the germ line of certain wild-type strains at low frequency, causing insertional mutations (5-7). Tcl is 1.6 kilobases (kb) long, contains inverted terminal repeats of 54 base pairs (bp), and has a long internal open reading frame (10). Tc3 is 2.5 kb long and contains inverted terminal repeats that are similar to those of Tcl (9). Collins et al. (9, 11) isolated mutant strains with increased frequencies of Tcl and Tc3 insertion events. These strains have greatly facilitated the use of Tcl and Tc3 for gene cloning in C. elegans. Nevertheless, not all mutations isolated from these mutator strains are caused by insertion of Tcl or Tc3. In this manuscript, we describe a study of two non-Tcl and non-Tc3 insertion mutations. These studies have led us to the identification of an additional C. elegans transposable element family, Tc4, characterized by long inverted terminal repeats ¶ and, in this way, structurally similar to the fold-back elements of Drosophila and sea urchins. MATERIALS AND METHODSStrains and Nomenclature. Methods for the culturing of C. elegans and for genetic analysis were as described by Brenner (12). All strains were grown at 200C. The C. elegans wild-type strains studied were the Bristol N2 strain and the Bergerac RW7000 strain (12, 13). The marker genes used have been described (12,14). The mutator mut-2 strain TR679 was provided by J. C...

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Homologous Pairing and Strand Exchange in Genetic Recombination

Cited by 443 publications

References 70 publications

Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions

Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions

Molecular cloning and characterization of the recA gene from the cyanobacterium Synechococcus sp. strain PCC 7002

Tc4, a Caenorhabditis elegans transposable element with an unusual fold-back structure.

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