Forget, A.L., Dombrowski, C.C., Amitani, I., and Kowalczykowski, S.C. (2013).
Exploring protein-DNA interactions in 3D using in situ construction, manipulation, and visualization of individual DNA dumbbells with optical traps, microfluidics, and fluorescence microscopy.
Nature Protocols, 8, 525-538. PMID: 23411634 [Abstract]  [Full Text]  [PDF]

Jensen, R.B., Ozes, A., Kim, T., Estep, A., and Kowalczykowski, S.C. (2013).
BRCA2 is epistatic to the RAD51 paralogs in response to DNA damage.
DNA Repair, 12, 306-311. PMID: 23384538; PMCID: PMC3602134. [Abstract] [Full Text] [PDF]

Cannavo, E., Cejka, P., and Kowalczykowski, S.C. (2013).
Relationship of DNA degradation by Saccharomyces cerevisiae Exonuclease 1 and its stimulation by RPA and Mre11-Rad50-Xrs2 to DNA end resection.
Proc. Natl. Acad. Sci. U.S.A., 109 (published online April 15, 2013 as doi: 10.1073/pnas.1305166110). PMID: 23589858. [Abstract] [Full Text] [PDF]

Bell, J.C., Plank, J.L., Dombrowski, C.C., and Kowalczykowski, S.C. (2012).
Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA.
Nature, 491, 274-278 (published online 24 October 2012 as doi: 10.1038/nature11598). PMID: 23103864. [Abstract] [Full Text] [PDF] [Supplementary Information]

Handa, N., Yang, L., Dillingham, M. S., Kobayashi, I., Wigley, D.B., and Kowalczykowski, S.C. (2012).
Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, c, by RecBCD enzyme.
Proc. Natl. Acad. Sci. U.S.A., 109, 8901-8906 (published online 17 May 2012, 10.1073/pnas.1206076109). PMID: 22603794; PMCID: PMC3384139 [Abstract] [Full Text] [PDF]

Yang, L., Handa, N., Liu, B., Dillingham, M. S., Wigley, D.B., and Kowalczykowski, S.C. (2012).
Alteration of c recognition by RecBCD reveals a regulated molecular latch and suggests a channel-bypass mechanism for biological control.
Proc. Natl. Acad. Sci. U.S.A., 109, 8907-8912 (published online 17 May 2012, 10.1073/pnas.1206081109). PMID: 22603793; PMCID: PMC3384165  [Abstract] [Full Text] [PDF]

Cejka, P., Plank, J.L., Dombrowski, C.C., and Kowalczykowski, S.C. (2012).
Decatenation of DNA by the S. cerevisiae Sgs1–Top3–Rmi1 and RPA complex: A mechanism for disentangling chromosomes.
Mol. Cell, 47, 886-896 (published online August 15, 2012). PMID: 22885009; PMCID: PMC3462259 [Abstract] [Full Text] [PDF] [Supplemental Information]

Forget, A.L. and Kowalczykowski, S.C. (2012).
Single-molecule imaging of DNA pairing by RecA reveals a three-dimensional homology search.
Nature, 482, 423–427 (published online February 8, 2012, doi:10.1038/nature10782). PMID: 22318518; PMCID: PMC3288143 [Abstract] [Full Text] [PDF]

Nimonkar, A.V., Genschel, J., Kinoshita, E., Polaczek, P., Campbell, J.L., Wyman, C., Modrich, P., and Kowalczykowski, S.C. (2011).
BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair.
Genes & Dev., 25,350-362. PMID: 21325134; PMCID: PMC3042158. [Abstract] [Full Text] [PDF]

Carreira, A. and Kowalczykowski, S.C. (2011).
Two classes of BRC repeats in BRCA2 promote RAD51 nucleoprotein filament function by distinct mechanisms.
Proc. Natl. Acad. Sci. U.S.A., 108, 10448-10453 (published online June 13, 2011, doi: 10.1073/pnas.1106971108). PMID: 21670257; PMCID: PMC3127913 [Abstract] [Full Text] [PDF]

Cejka, P., Plank, J.L., Bachrati, C.Z., Hickson, I.D., and Kowalczykowski, S.C. (2010).
Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1-Top3.
Nature Struct. Mol. Biol., 17, 1377-1382 (published online October 10, 2010; doi: 10.1038/nsmb.1919). PMID: 20935631; PMCID: PMC2988882  [Abstract] [Full Text] [PDF]

Jensen, R.B., Carreira, A., and Kowalczykowski, S.C. (2010).
Purified human BRCA2 stimulates RAD51-mediated recombination.
Nature, 467, 678-683 (published online: August 22, 2010, doi: 10.1038/nature09399). PMID: 20729832; PMCID: PMC2952063  [Abstract] [Full Text] [PDF]

Cejka, P., Cannavo, E., Polaczek, P., Masuda-Sasa, T., Pokharel, S., Campbell, J.L., and Kowalczykowski, S.C. (2010).
DNA end resection by Dna2-Sgs1-RPA and its stimulation by Top3-Rmi1 and Mre11-Rad50-Xrs2.
Nature, 467, 112-116 (doi: 10.1038/nature09355). PMID: 20811461; PMCID: PMC3089589  [Abstract] [Full Text] [PDF]

Amitani, I., Liu, B., Dombrowski, C.C., Baskin, R.J., and Kowalczykowski, S.C. (2010).
Watching individual proteins acting on single molecules of DNA.
In: Single Molecule Tools: Fluorescence Based Approaches, Part A, Methods Enzymol., 472, Nils G. Walters, editor, Burlington: Academic Press, 261-291 ISBN: 978-0-12-374954-3; doi: 10.1016/S0076-6879(10)72007-3. PMID: 20580968; PMCID: PMC3119597  [Abstract] [Full Text] [PDF]

Hilario, J., Amitani, I., Baskin, R.J., and Kowalczykowski, S.C. (2009).
Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules.
Proc. Natl. Acad. Sci. U.S.A., 106, 361-368 (published online January 2, 2009, doi: 10.1073/pnas.0811965106. PMID: 19122145; PMCID: PMC2613362 [Abstract]  [Full Text]  [PDF]

Nimonkar, A.V., Sica, R.A., and Kowalczykowski, S.C. (2009).
Rad52 promotes second-end DNA capture in double-stranded break repair to form complement-stabilized joint molecules.
Proc. Natl. Acad. Sci. U.S.A., 106, 3077-3082 (published online February 9, 2009, doi:10.1073/pnas.0813247106).  PMID: 19204284; PMCID: PMC2651264 [Abstract]  [Full Text]  [PDF]

Carreira, A., Hilario, J., Amitani, I., Baskin, R.J., Shivji, M.K.K., Venkitaraman, A.R., and Kowalczykowski, S.C. (2009).
The BRC repeats of BRCA2 modulate the DNA-binding selectivity of RAD51.
Cell, 136, 1032-1043, (doi:10.1016/j.cell.2009.02.019). PMID: 19303847; PMCID: PMC2669112  [Abstract]  [Full Text]  [PDF] [Supplemental Data]

Handa, N., Morimatsu, K., Lovett, S.T., and Kowalczykowski, S.C. (2009).
Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli.
Genes & Dev., 23, 1234-1245. PMID: 19451222; PMCID: PMC2685532  [Abstract]  [Full Text]  [PDF] [Supplemental Information]

Nimonkar, A.V., Özsoy, A.Z., Genschel, J., Modrich, P., and Kowalczykowski, S.C. (2008).
Human exonuclease 1 and BLM helicase interact to resect DNA and initiate DNA repair.
Proc. Natl. Acad. Sci. U.S.A., 105, 16906-16911 (published online October 29, 2008, as doi: 10.1073/pnas.0809380105). PMID: 18971343; PMCID: PMC2579351 [Abstract] [Full Text] [PDF] [Supporting Information] [Supplemental Material]

Kowalczykowski, S.C. (2008).
Structural biology: Snapshots of DNA repair.
Nature, 453, 463-466 (published online May 21, 2008 as doi:10.1038/453463a. PMID: 18497811. [Full Text] [PDF]

Spies, M., Amitani, I., Baskin, R.J., and Kowalczykowski, S.C. (2007).
RecBCD enzyme switches lead motor subunits in response to c-recognition.
Cell, 131, 16, 694-705 (doi:10.1016/j.cell.2007.9.023). PMID: 18022364. PMCID: PMC2151923.  [Abstract]  [Full Text]  [PDF]  [Supplementary Information]
(see Cell  "RecBCD: The Supercar of DNA Repair"  [PDF]

Spies, M. and Kowalczykowski, S.C. (2006).
The RecA-binding locus of RecBCD enzyme defines a generalized domain for recruitment of DNA strand exchange proteins.
Mol. Cell, 21, 573-580. PMID: 16483938. [Abstract] [Full Text] [PDF] [Supplemental Data]

Galletto, R., Amitani, I., Baskin, R.J., and Kowalczykowski, S.C. (2006).
Direct observation of individual RecA filaments assembling on single DNA molecules.
Nature, 443, 875-878. PMID: 16988658.  [Abstract] [Full Text] [PDF]  [Supplemental Data]
    (see ACS Chemical Biology Spotlight  [PDF])
    (see Bio.com  [PDF])
    (see MedicalNewsToday.com  [PDF])
    (see News-Medical.net  [PDF])
    (see PhysOrg.com  [PDF])
    (see nnseek.com  [PDF])
    (see ScienceDaily.com  [PDF])
    (see UC Davis News and Information  [PDF] [HTML]

Some classics:                                  (top)

Handa, N., Bianco, P.R., Baskin, R.J., and Kowalczykowski, S.C. (2005).
Direct visualization of RecBCD movement reveals co-translocation of the RecD motor after c-recognition.
Mol. Cell, 17, 745-750. PMID: 15749023. [Abstract] [Full Text] [PDF] [Supplemental Data] [Movie 1 - Chi⁰] [Movie 2 - Chi⁺]

Singleton, M. R., Dillingham, M.S., Gaudier, M., Kowalczykowski, S.C., and Wigley, D. B. (2004).
Crystal structure of RecBCD reveals a machine for processing DNA breaks.
Nature, 432, 187-193. PMID: 15538360.  [Abstract] [Full Text] [PDF]
(see News & Views  [Full Text] [PDF]
(see Nature "Highlights"  [Full Text]

Veaute, X., Jeusset, J., Soustelle, C., Kowalczykowski, S.C. , Le Cam, E., and Fabre, F. (2003).
The Srs2 helicase prevents homologous recombination by disrupting Rad51 nucleofilaments.
Nature, 423, 309-312. PMID: 12748645.  [Abstract] [Full Text] [PDF]
(see News & Views in Nature 423, 234 - 235 (2003); doi:10.1038/423234a  [Full Text] [PDF]
(Recommended paper by the Faculty of 1000:  #1  [Abstract] [PDF];  #2 [Abstract] [PDF]

Morimatsu, K. and Kowalczykowski, S.C.  (2003).
RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: A universal step of recombinational repair.
Mol. Cell, 11, 1337-1347. PMID: 12769856.  [Abstract] [Full Text] [PDF]

Alexeev, A., Mazin, A.V., and Kowalczykowski, S.C. (2003).
Rad54 protein possesses chromatin remodeling activity stimulated by the Rad51-ssDNA nucleoprotein filament.
Nature Struct. Biol., 10, 182-186 (published 10 February 2003 as doi.10.1038/nsb901). PMID: 12577053. [Abstract] [Full Text] [PDF] [Online cover]
(see Highlight in Nature Reviews Molecular Cell Biology 4, 261 (2003); doi:10.1038/nrm1089.  [Full Text]  [PDF]
(twice Recommended paper by the Faculty of 1000  [Full Text]

(see News & Information at UC Davis News Service  [Full Text] [Printable Version]
(see International Rett Syndrome Foundation Newsletter [PDF]

Spies, M., Bianco, P.R., Dillingham, M.S., Handa, N., Baskin, R.J., and Kowalczykowski, S.C.  (2003).
A molecular throttle: The recombination hotspot c controls DNA translocation by the RecBCD helicase.
Cell, 114, 647-654. PMID: 13678587. [Abstract] [Full Text] [PDF] [Featured Article]
(see News & Features at Bio.com  [Full Text] [PDF]
(see News & Information at UC Davis News Service  [Full Text] [Printable Version]
(see News & Information at UC Davis News Service  [Full Text] [Printable Version]

Dillingham, M.S., Spies, M., and Kowalczykowski, S.C. (2003).
RecBCD enzyme is a bipolar DNA helicase.
Nature, 423, 893 - 897. PMID: 12815438. [Abstract] [Full Text] [PDF]
(see News & Views in Nature Structural Biology 10, 499 - 500 (2003)  [Full Text]  [PDF]
(see Highlight in Nature Reviews Molecular Cell Biology 4, 513 (2003); doi:10.1038/nrm1162. [Full Text] [PDF]
(Must Read paper by Faculty of 1000 [Full Text]
(see News & Information at UC Davis News Service  [Full Text] [Printable Version]

Kantake, N., Madiraju, M.V.V.M., Sugiyama, T., and Kowalczykowski, S.C. (2002).
Escherichia coli RecO protein anneals ssDNA complexed with its cognate ssDNA-binding protein: A common step in genetic recombination.
Proc. Natl. Acad. Sci. USA, 99, 15327-15332 (published November 18, 2002, as 10.1073/pnas.252633399). PMID: 12438681; PMCID: PMC137716. [Abstract] [Full Text] [PDF]
(Recommended paper by Faculty of 1000 [Full Text])

Bianco, P.R., Brewer, L.R., Corzett, M., Balhorn, R., Yeh, Y., Kowalczykowski, S.C., and Baskin, R.J. (2001).
Processive translocation and DNA unwinding by individual RecBCD enzyme molecules.
Nature, 409, 374-378. PMID: 11201750. [Abstract] [Full Text] [PDF]
Movies!   37°C:  1 mM ATP        23°C:   1 mM ATP;    250 µM ATP #1;    250 µM ATP #2;    no ATP
(see coverage in Biophotonics (2001) 8, 48-49   [TOC] [PDF]
(see UC Davis Division of Biological Sciences Newsletter [PDF])

Press coverage:
Capitol Public Radio - January 17, 2001 - Full transcript
San Francisco Chronicle - January 20, 2001 - excerpt
Full article - "Watch DNA Unzip in Micromovie-Molecular action film highlights potential of nanotechnology"
San Francisco Chronicle - January 24, 2001 - excerpt
Full article: "A Little Spark Of Inspiration"
San Francisco Chronicle - January 26, 2001 - excerpt
Full article: "Never Metatag We Didn't Like"
News & Information at UC Davis News Service  [Full Text]
Nanotech Dreams - The Scientist 16[5]:34, Mar. 4, 2002 - Excerpt Full article
Davis  Community  Television - February 8, 2001 7:00 PM  - "Get The Word Out." Double helix unwinds on camera. Stephen Kowalczykowski interviewed by Jon Price. (Rerun on Tues Feb 13, 2001 at 7:30 PM). [VIDEO]

Mazin, A.V., Bornarth, C.J., Solinger, J.A., Heyer, W.-D., and Kowalczykowski, S.C. (2000).
Rad54 Protein is targeted to pairing loci by the Rad51 nucleoprotein filament.
Mol. Cell, 6, 583–592. PMID: 11030338. [Abstract] [Full Text] [PDF]

Mazin, A.V., Zaitseva, E., Sung, P., and Kowalczykowski, S.C. (2000).
Tailed duplex DNA is the preferred substrate for Rad51 protein-mediated homologous pairing.
EMBO J., 19, 1148-1156. PMID: 10698955; PMCID: PMC305653. [Abstract] [Full Text] [PDF]
(see commentary in CHEMTRACTS-Biochemistry and Molecular Biology, 13, 415-423, 2000:  [Full Text] [PDF]

Bianco, P.R. and Kowalczykowski, S.C.  (2000).
The translocation step size and mechanism of the RecBC helicase.
Nature, 405, 368-372. PMID: 10830968. [Abstract] [Full Text] [PDF]
(see Dispatch in Current Biology: [Abstract] [Full Text] [PDF])
(see News & Information at UC Davis News Service  [Full Text] [Printable Version])
(see Science Blog [PDF])

New, J.H., Sugiyama, T., Zaitseva, E., and Kowalczykowski, S.C. (1998).
Rad52 protein stimulates DNA strand exchange by Rad51 and replication protein A.
Nature, 391, 407-410. PMID: 9450760. [Abstract] [Full Text] [PDF]
(see Nature News & Views: [News&Views] [N&V PDF])

Sugiyama, T., New, J.H., and Kowalczykowski, S.C. (1998).
DNA Annealing by Rad52 protein is stimulated by specific interaction with the complex of replication protein A and single-stranded DNA.
Proc. Natl. Acad. Sci. USA, 95, 6049-6054. PMID: 9600915; PMCID: PMC27583. [Abstract] [Full Text] [PDF]

Seitz, E.M., Brockman, J.P., Sandler, S.J., Clark, A.J., and Kowalczykowski, S.C. (1998).
RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange.
Genes & Dev., 12, 1248-1253. PMID: 9573041; PMCID: PMC316774. [Abstract] [Full Text] [PDF]
[Genes & Dev. cover] [Genes & Dev. cover.jpeg]

Sugiyama, T., Zaitseva, E.M., and Kowalczykowski, S.C. (1997).
A single-stranded DNA-binding protein is needed for efficient presynaptic complex formation by the Saccharomyces cerevisiae Rad51 protein.
J. Biol. Chem., 272, 7940-7945. PMID: 9065463. [Abstract] [Full Text] [PDF]

Anderson, D.G. and Kowalczykowski, S.C. (1997).
The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a c-regulated manner.
Cell, 90, 77-86. PMID: 9230304. [Abstract] [Full Text] [PDF]
(see Dispatch in Current Biology:  [Full Text] [PDF])

Anderson, D.G. and Kowalczykowski, S.C. (1997).
The recombination hot spot chi is a regulatory element that switches the polarity of DNA degradation by the RecBCD enzyme.
Genes & Dev., 11, 571-581. PMID: 9119222. [Abstract] [Full Text] [PDF]

Dixon, D.A. and Kowalczykowski, S.C.(1993).
The recombination hotspot χ is a regulatory sequence that acts by attenuating the nuclease activity of the E. coli RecBCD enzyme.
Cell, 73, 87-96. PMID: 8384931. [Abstract] [Full Text] [PDF]

Dixon, D.A. and Kowalczykowski, S.C. (1991).
Homologous pairing in vitro stimulated by the recombination hotspot, Chi.
Cell, 66 361-371. PMID: 1855256. [Abstract] [Full Text] [PDF]

Menetski, J.P., Bear, D.G., and Kowalczykowski, S.C. (1990).
Stable DNA heteroduplex formation by the Escherichia coli RecA protein in the absence of ATP hydrolysis.
Proc. Natl. Acad. Sci. U.S.A. 87, 21-25. PMID: 2404275; PMCID: PMC53191. [Abstract] [Full Text] [PDF]

Kowalczykowski, S.C. and Krupp, R.A. (1987).
Effects of the Escherichia coli SSB protein on the single-stranded DNA-dependent ATPase activity of Escherichia coli RecA protein: Evidence that SSB protein facilitates the binding of RecA protein to regions of secondary structure within single-stranded DNA.
J. Mol. Biol. 193, 97-113. PMID: 2953903. [Abstract] [PDF]