[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [1] Aihara H., Ito Y., Kurumizaka H., Terada T., Yokoyama S., Shibata T., 1997, An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing., J Mol Biol 274(2):213-21

 [2] Al Mamun AA., Lombardo MJ., Shee C., Lisewski AM., Gonzalez C., Lin D., Nehring RB., Saint-Ruf C., Gibson JL., Frisch RL., Lichtarge O., Hastings PJ., Rosenberg SM., 2012, Identity and function of a large gene network underlying mutagenic repair of DNA breaks., Science 338(6112):1344-8

 [3] Alexseyev AA., Baitin DM., Kuramitsu S., Ogawa T., Ogawa H., Lanzov VA., 1997, A recombinational defect in the C-terminal domain of Escherichia coli RecA2278-5 protein is compensated by protein binding to ATP., Mol Microbiol 23(2):255-65

 [4] Alexseyev AA., Bakhlanova IV., Zaitsev EN., Lanzov VA., 1996, Genetic characteristics of new recA mutants of Escherichia coli K-12., J Bacteriol 178(7):2018-24

 [5] Amarh V., White MA., Leach DRF., 2018, Dynamics of RecA-mediated repair of replication-dependent DNA breaks., J Cell Biol 217(7):2299-2307

 [6] Baitin DM., Bakhlanova IV., Chervyakova DV., Kil YV., Lanzov VA., Cox MM., 2008, Two RecA protein types that mediate different modes of hyperrecombination., J Bacteriol 190(8):3036-45

 [7] Bakhlanova IV., Dudkina AV., Baitin DM., Knight KL., Cox MM., Lanzov VA., 2010, Modulating cellular recombination potential through alterations in RecA structure and regulation., Mol Microbiol 78(6):1523-38

 [8] Bakhlanova IV., Dudkina AV., Wood EA., Lanzov VA., Cox MM., Baitin DM., 2016, DNA Metabolism in Balance: Rapid Loss of a RecA-Based Hyperrec Phenotype., PLoS One 11(4):e0154137

 [9] Bakhlanova IV., Ogawa T., Lanzov VA., 2001, Recombinogenic activity of chimeric recA genes (Pseudomonas aeruginosa/Escherichia coli): a search for RecA protein regions responsible for this activity., Genetics 159(1):7-15

 [10] Banda S., Tiwari PB., Darici Y., Tse-Dinh YC., 2016, Investigating direct interaction between Escherichia coli topoisomerase I and RecA., Gene 585(1):65-70

 [11] Bar-Ziv R., Libchaber A., 2001, Effects of DNA sequence and structure on binding of RecA to single-stranded DNA., Proc Natl Acad Sci U S A 98(16):9068-73

 [12] Bedale WA., Cox M., 1996, Evidence for the coupling of ATP hydrolysis to the final (extension) phase of RecA protein-mediated DNA strand exchange., J Biol Chem 271(10):5725-32

 [13] Bell JC., Plank JL., Dombrowski CC., Kowalczykowski SC., 2012, Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA., Nature 491(7423):274-8

 [14] Bianchi M., DasGupta C., Radding CM., 1983, Synapsis and the formation of paranemic joints by E. coli RecA protein., Cell 34(3):931-9

 [15] Boyer B., Danilowicz C., Prentiss M., Prevost C., 2019, Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination., Nucleic Acids Res 47(15):7798-7808

 [16] Boyer B., Ezelin J., Poulain P., Saladin A., Zacharias M., Robert CH., Prevost C., 2015, An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA., PLoS One 10(3):e0116414

 [17] Brenner SL., Mitchell RS., Morrical SW., Neuendorf SK., Schutte BC., Cox MM., 1987, recA protein-promoted ATP hydrolysis occurs throughout recA nucleoprotein filaments., J Biol Chem 262(9):4011-6

 [18] Britt RL., Chitteni-Pattu S., Page AN., Cox MM., 2011, RecA K72R filament formation defects reveal an oligomeric RecA species involved in filament extension., J Biol Chem 286(10):7830-40

 [19] Britt RL., Haruta N., Lusetti SL., Chitteni-Pattu S., Inman RB., Cox MM., 2010, Disassembly of Escherichia coli RecA E38K/DeltaC17 nucleoprotein filaments is required to complete DNA strand exchange., J Biol Chem 285(5):3211-26

 [20] Butler BC., Hanchett RH., Rafailov H., MacDonald G., 2002, Investigating structural changes induced by nucleotide binding to RecA using difference FTIR., Biophys J 82(4):2198-210

 [21] Calsou P., Villaverde A., Defais M., 1987, Activated RecA protein may induce expression of a gene that is not controlled by the LexA repressor and whose function is required for mutagenesis and repair of UV-irradiated bacteriophage lambda., J Bacteriol 169(10):4816-21

 [22] Campbell MJ., Davis RW., 1999, Toxic mutations in the recA gene of E. coli prevent proper chromosome segregation., J Mol Biol 286(2):417-35

 [23] Campbell MJ., Davis RW., 1999, On the in vivo function of the RecA ATPase., J Mol Biol 286(2):437-45

 [24] Cazaux C., Larminat F., Defais M., null, Site-directed mutagenesis in the Escherichia coli recA gene., Biochimie 73(2-3):281-4

 [25] Cazaux C., Larminat F., Villani G., Johnson NP., Schnarr M., Defais M., 1994, Purification and biochemical characterization of Escherichia coli RecA proteins mutated in the putative DNA binding site., J Biol Chem 269(11):8246-54

 [26] Cazaux C., Mazard AM., Defais M., 1993, Inducibility of the SOS response in a recA730 or recA441 strain is restored by transformation with a new recA allele., Mol Gen Genet 240(2):296-301

 [27] Chandran AV., Jayanthi S., Vijayan M., 2018, Structure and interactions of RecA: plasticity revealed by molecular dynamics simulations., J Biomol Struct Dyn 36(1):98-111

 [28] Chen Z., Yang H., Pavletich NP., 2008, Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures., Nature 453(7194):489-4

 [29] Chervyakova D., Kagansky A., Petukhov M., Lanzov V., 2001, [L29M] substitution in the interface of subunit-subunit interactions enhances Escherichia coli RecA protein properties important for its recombinogenic activity., J Mol Biol 314(4):923-35

 [30] Chiu SK., Wong BC., Chow SA., 1990, Homologous pairing in duplex DNA regions and the formation of four-stranded paranemic joints promoted by RecA protein. Effects of gap length and negative superhelicity., J Biol Chem 265(34):21262-8

 [31] Chow SA., Chiu SK., Wong BC., null, RecA protein-promoted homologous pairing between duplex molecules: functional role of duplex regions of gapped duplex DNA., Biochimie 73(2-3):157-61

 [32] Chow SA., Honigberg SM., Bainton RJ., Radding CM., 1986, Patterns of nuclease protection during strand exchange. recA protein forms heteroduplex DNA by binding to strands of the same polarity., J Biol Chem 261(15):6961-71

 [33] Chow SA., Honigberg SM., Radding CM., 1988, DNase protection by recA protein during strand exchange. Asymmetric protection of the Holliday structure., J Biol Chem 263(7):3335-47

 [34] Clark AJ., 1973, Recombination deficient mutants of E. coli and other bacteria., Annu Rev Genet 7:67-86

 [35] Cockram CA., Filatenkova M., Danos V., El Karoui M., Leach DR., 2015, Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo., Proc Natl Acad Sci U S A 112(34):E4735-42

 [36] Conover AJ., Danilowicz C., Gunaratne R., Coljee VW., Kleckner N., Prentiss M., 2011, Changes in the tension in dsDNA alter the conformation of RecA bound to dsDNA-RecA filaments., Nucleic Acids Res 39(20):8833-43

 [37] Cox JM., Li H., Wood EA., Chitteni-Pattu S., Inman RB., Cox MM., 2008, Defective dissociation of a "slow" RecA mutant protein imparts an Escherichia coli growth defect., J Biol Chem 283(36):24909-21

 [38] Cox JM., Tsodikov OV., Cox MM., 2005, Organized unidirectional waves of ATP hydrolysis within a RecA filament., PLoS Biol 3(2):e52

 [39] Craig NL., Roberts JW., 1980, E. coli recA protein-directed cleavage of phage lambda repressor requires polynucleotide., Nature 283(5742):26-30

 [40] Craig NL., Roberts JW., 1981, Function of nucleoside triphosphate and polynucleotide in Escherichia coli recA protein-directed cleavage of phage lambda repressor., J Biol Chem 256(15):8039-44

 [41] Cunningham RP., Wu AM., Shibata T., DasGupta C., Radding CM., 1981, Homologous pairing and topological linkage of DNA molecules by combined action of E. coli RecA protein and topoisomerase I., Cell 24(1):213-23

 [42] Danilowicz C., Hermans L., Coljee V., Prevost C., Prentiss M., 2017, ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences., Nucleic Acids Res 45(14):8448-8462

 [43] DasGupta C., Wu AM., Kahn R., Cunningham RP., Radding CM., 1981, Concerted strand exchange and formation of Holliday structures by E. coli RecA protein., Cell 25(2):507-16

 [44] Defais M., Phez E., Johnson NP., 2003, Kinetic mechanism for the formation of the presynaptic complex of the bacterial recombinase RecA., J Biol Chem 278(6):3545-51

 [45] Devoret R., Pierre M., Moreau PL., 1983, Prophage phi 80 is induced in Escherichia coli K12 recA430., Mol Gen Genet 189(2):199-206

 [46] Dri AM., Moreau PL., 1991, Properties of RecA441 protein reveal a possible role for RecF and SSB proteins in Escherichia coli., Mol Gen Genet 227(3):488-92

 [47] Dudkina AV., Bakhlanova IV., Baitin DM., null, The new mechanism of the frequency of recombination exchanges increase by improving the synaptase activity of the RecA protein from Escherichia coli., Dokl Biochem Biophys 432:120-2

 [48] Dutreix M., Moreau PL., Bailone A., Galibert F., Battista JR., Walker GC., Devoret R., 1989, New recA mutations that dissociate the various RecA protein activities in Escherichia coli provide evidence for an additional role for RecA protein in UV mutagenesis., J Bacteriol 171(5):2415-23

 [49] Eggler AL., Lusetti SL., Cox MM., 2003, The C terminus of the Escherichia coli RecA protein modulates the DNA binding competition with single-stranded DNA-binding protein., J Biol Chem 278(18):16389-96

 [50] Eguchi Y., Ogawa T., Ogawa H., 1988, Two forms of RecA-single-stranded DNA-adenosine 5'-O-(3-thiotriphosphate) complexes with different activities for cleavage of phage phi 80 cI repressor., J Mol Biol 204(1):61-7

 [51] Eguchi Y., Ogawa T., Ogawa H., 1988, Stimulation of RecA-mediated cleavage of phage phi 80 cI repressor by deoxydinucleotides., J Mol Biol 204(1):69-77

 [52] Eguchi Y., Ogawa T., Ogawa H., 1988, Cleavage of bacteriophage phi 80 CI repressor by RecA protein., J Mol Biol 202(3):565-73

 [53] Ennis DG., Fisher B., Edmiston S., Mount DW., 1985, Dual role for Escherichia coli RecA protein in SOS mutagenesis., Proc Natl Acad Sci U S A 82(10):3325-9

 [54] Ennis DG., Levine AS., Koch WH., Woodgate R., 1995, Analysis of recA mutants with altered SOS functions., Mutat Res 336(1):39-48

 [55] Ennis DG., Little JW., Mount DW., 1993, Novel mechanism for UV sensitivity and apparent UV nonmutability of recA432 mutants: persistent LexA cleavage following SOS induction., J Bacteriol 175(22):7373-82

 [56] Ferrin LJ., 2001, Flexible genetic engineering using RecA protein., Mol Biotechnol 18(3):233-41

 [57] Ferrin LJ., Camerini-Otero RD., 1991, Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage., Science 254(5037):1494-7

 [58] Forget AL., Kowalczykowski SC., 2012, Single-molecule imaging of DNA pairing by RecA reveals a three-dimensional homology search., Nature 482(7385):423-7

 [59] Frank EG., Cheng N., Do CC., Cerritelli ME., Bruck I., Goodman MF., Egelman EH., Woodgate R., Steven AC., 2000, Visualization of two binding sites for the Escherichia coli UmuD'(2)C complex (DNA pol V) on RecA-ssDNA filaments., J Mol Biol 297(3):585-97

 [60] Frank EG., Gonzalez M., Ennis DG., Levine AS., Woodgate R., 1996, In vivo stability of the Umu mutagenesis proteins: a major role for RecA., J Bacteriol 178(12):3550-6

 [61] Frank EG., Hauser J., Levine AS., Woodgate R., 1993, Targeting of the UmuD, UmuD', and MucA' mutagenesis proteins to DNA by RecA protein., Proc Natl Acad Sci U S A 90(17):8169-73

 [62] Freitag N., McEntee K., 1989, "Activated"-RecA protein affinity chromatography of LexA repressor and other SOS-regulated proteins., Proc Natl Acad Sci U S A 86(21):8363-7

 [63] Fu H., Le S., Muniyappa K., Yan J., 2013, Dynamics and Regulation of RecA Polymerization and De-Polymerization on Double-Stranded DNA., PLoS One 8(6):e66712

 [64] Fulconis R., Bancaud A., Allemand JF., Croquette V., Dutreix M., Viovy JL., 2004, Twisting and untwisting a single DNA molecule covered by RecA protein., Biophys J 87(4):2552-63

 [65] Fulconis R., Mine J., Bancaud A., Dutreix M., Viovy JL., 2006, Mechanism of RecA-mediated homologous recombination revisited by single molecule nanomanipulation., EMBO J 25(18):4293-304

 [66] Galkin VE., Britt RL., Bane LB., Yu X., Cox MM., Egelman EH., 2011, Two modes of binding of DinI to RecA filament provide a new insight into the regulation of SOS response by DinI protein., J Mol Biol 408(5):815-24

 [67] Galletto R., Amitani I., Baskin RJ., Kowalczykowski SC., 2006, Direct observation of individual RecA filaments assembling on single DNA molecules., Nature 443(7113):875-8

 [68] Gardner RV., Voloshin ON., Camerini-Otero RD., 1995, The identification of the single-stranded DNA-binding domain of the Escherichia coli RecA protein., Eur J Biochem 233(2):419-25

 [69] Gataulin DV., Carey JN., Li J., Shah P., Grubb JT., Bishop DK., 2018, The ATPase activity of E. coli RecA prevents accumulation of toxic complexes formed by erroneous binding to undamaged double stranded DNA., Nucleic Acids Res 46(18):9510-9523

 [70] Ghodke H., Paudel BP., Lewis JS., Jergic S., Gopal K., Romero ZJ., Wood EA., Woodgate R., Cox MM., van Oijen AM., 2019, Spatial and temporal organization of RecA in the Escherichia coli DNA-damage response., Elife 8

 [71] Goswami M., Narayana Rao AVSS., 2018, Transcriptome Profiling Reveals Interplay of Multifaceted Stress Response in Escherichia coli on Exposure to Glutathione and Ciprofloxacin., mSystems 3(1)

 [72] Gruenig MC., Renzette N., Long E., Chitteni-Pattu S., Inman RB., Cox MM., Sandler SJ., 2008, RecA-mediated SOS induction requires an extended filament conformation but no ATP hydrolysis., Mol Microbiol 69(5):1165-79

 [73] Gumbs OH., Shaner SL., 1998, Three mechanistic steps detected by FRET after presynaptic filament formation in homologous recombination. ATP hydrolysis required for release of oligonucleotide heteroduplex product from RecA., Biochemistry 37(33):11692-706

 [74] Guo C., Li G., Liu Z., Sun L., Sun Y., Xu F., Zhang Y., Yang T., Li Z., 2009, Influence of polyelectrolyte on DNA-RecA nucleoprotein filaments: poly-L-lysine used as a model., Chemphyschem 10(9-10):1624-9

 [75] Guo C., Song Y., Wang L., Sun L., Sun Y., Peng C., Liu Z., Yang T., Li Z., 2008, Atomic force microscopic study of low temperature induced disassembly of RecA-dsDNA filaments., J Phys Chem B 112(3):1022-7

 [76] Handa N., Kowalczykowski SC., 2007, A RecA mutant, RecA(730), suppresses the recombination deficiency of the RecBC(1004)D-chi* interaction in vitro and in vivo., J Mol Biol 365(5):1314-25

 [77] Harmon FG., Rehrauer WM., Kowalczykowski SC., 1996, Interaction of Escherichia coli RecA protein with LexA repressor. II. Inhibition of DNA strand exchange by the uncleavable LexA S119A repressor argues that recombination and SOS induction are competitive processes., J Biol Chem 271(39):23874-83

 [78] Haruta N., Yu X., Yang S., Egelman EH., Cox MM., 2003, A DNA pairing-enhanced conformation of bacterial RecA proteins., J Biol Chem 278(52):52710-23

 [79] Hortnagel K., Voloshin ON., Kinal HH., Ma N., Schaffer-Judge C., Camerini-Otero RD., 1999, Saturation mutagenesis of the E. coli RecA loop L2 homologous DNA pairing region reveals residues essential for recombination and recombinational repair., J Mol Biol 286(4):1097-106

 [80] Ishimori K., Sommer S., Bailone A., Takahashi M., Cox MM., Devoret R., 1996, Characterization of a mutant RecA protein that facilitates homologous genetic recombination but not recombinational DNA repair: RecA423., J Mol Biol 264(4):696-712

 [81] Iwabuchi M., Shibata T., Ohtani T., Natori M., Ando T., 1983, ATP-dependent unwinding of the double helix and extensive supercoiling by Escherichia coli recA protein in the presence of topoisomerase., J Biol Chem 258(20):12394-404

 [82] Jain SK., Cox MM., Inman RB., 1994, On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. III. Unidirectional branch migration and extensive hybrid DNA formation., J Biol Chem 269(32):20653-61

 [83] Jaszczur M., Bertram JG., Robinson A., van Oijen AM., Woodgate R., Cox MM., Goodman MF., 2016, Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword., Biochemistry 55(16):2309-18

 [84] Julin DA., Riddles PW., Lehman IR., 1986, On the mechanism of pairing of single- and double-stranded DNA molecules by the recA and single-stranded DNA-binding proteins of Escherichia coli., J Biol Chem 261(3):1025-30

 [85] Karu AE., Belk ED., 1982, Induction of E. coli recA protein via recBC and alternate pathways: quantitation by enzyme-linked immunosorbent assay (ELISA)., Mol Gen Genet 185(2):275-82

 [86] Kates-Harbeck J., Tilloy A., Prentiss M., 2013, Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites., Phys Rev E Stat Nonlin Soft Matter Phys 88(1):012702

 [87] Katz FS., Bryant FR., 2003, Three-strand exchange by the Escherichia coli RecA protein using ITP as a nucleotide cofactor: mechanistic parallels with the ATP-dependent reaction of the RecA protein from Streptococcus pneumoniae., J Biol Chem 278(38):35889-96

 [88] Kim JI., Cox MM., Inman RB., 1992, On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. I. Bypassing a short heterologous insert in one DNA substrate., J Biol Chem 267(23):16438-43

 [89] Kim JI., Cox MM., Inman RB., 1992, On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. II. Four-strand exchanges., J Biol Chem 267(23):16444-9

 [90] Kim T., Chitteni-Pattu S., Cox BL., Wood EA., Sandler SJ., Cox MM., 2015, Directed Evolution of RecA Variants with Enhanced Capacity for Conjugational Recombination., PLoS Genet 11(6):e1005278

 [91] Klitgaard RN., Jana B., Guardabassi L., Nielsen KL., Lobner-Olesen A., 2018, DNA Damage Repair and Drug Efflux as Potential Targets for Reversing Low or Intermediate Ciprofloxacin Resistance in E. coli K-12., Front Microbiol 9:1438

 [92] Konola JT., Guzzo A., Gow JB., Walker GC., Knight KL., 1998, Differential cleavage of LexA and UmuD mediated by recA Pro67 mutants: implications for common LexA and UmuD binding sites on RecA., J Mol Biol 276(2):405-15

 [93] Konola JT., Logan KM., Knight KL., 1994, Functional characterization of residues in the P-loop motif of the RecA protein ATP binding site., J Mol Biol 237(1):20-34

 [94] Kovacic L., Paulic N., Leonardi A., Hodnik V., Anderluh G., Podlesek Z., Zgur-Bertok D., Krizaj I., Butala M., 2013, Structural insight into LexA-RecA* interaction., Nucleic Acids Res 41(21):9901-10

 [95] Kowalczykowski SC., Clow J., Somani R., Varghese A., 1987, Effects of the Escherichia coli SSB protein on the binding of Escherichia coli RecA protein to single-stranded DNA. Demonstration of competitive binding and the lack of a specific protein-protein interaction., J Mol Biol 193(1):81-95

 [96] Kowalczykowski SC., Krupp RA., 1987, Effects of 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(1):97-113

 [97] Krishna P., van de Sande JH., 1990, Interaction of RecA protein with acidic phospholipids inhibits DNA-binding activity of RecA., J Bacteriol 172(11):6452-8

 [98] Larminat F., Cazaux C., Germanier M., Defais M., 1992, New mutations in and around the L2 disordered loop of the RecA protein modulate recombination and/or coprotease activity., J Bacteriol 174(19):6264-9

 [99] Lavery PE., Kowalczykowski SC., 1992, Biochemical basis of the constitutive repressor cleavage activity of recA730 protein. A comparison to recA441 and recA803 proteins., J Biol Chem 267(29):20648-58

 [100] Lavery PE., Kowalczykowski SC., 1990, Properties of recA441 protein-catalyzed DNA strand exchange can be attributed to an enhanced ability to compete with SSB protein., J Biol Chem 265(7):4004-10

 [101] Lee AJ., Sharma R., Hobbs JK., Walti C., 2017, Cooperative RecA clustering: the key to efficient homology searching., Nucleic Acids Res 45(20):11743-11751

 [102] Lee AM., Xiao J., Singleton SF., 2006, Origins of sequence selectivity in homologous genetic recombination: insights from rapid kinetic probing of RecA-mediated DNA strand exchange., J Mol Biol 360(2):343-59

 [103] Lee CD., Wang TF., 2009, The N-terminal domain of Escherichia coli RecA have multiple functions in promoting homologous recombination., J Biomed Sci 16:37

 [104] Lee JY., Qi Z., Greene EC., 2016, ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex., J Biol Chem 291(42):22218-22230

 [105] Lee JY., Steinfeld JB., Qi Z., Kwon Y., Sung P., Greene EC., 2017, Sequence imperfections and base triplet recognition by the Rad51/RecA family of recombinases., J Biol Chem 292(26):11125-11135

 [106] Lee JY., Terakawa T., Qi Z., Steinfeld JB., Redding S., Kwon Y., Gaines WA., Zhao W., Sung P., Greene EC., 2015, DNA RECOMBINATION. Base triplet stepping by the Rad51/RecA family of recombinases., Science 349(6251):977-81

 [107] Lesterlin C., Ball G., Schermelleh L., Sherratt DJ., 2014, RecA bundles mediate homology pairing between distant sisters during DNA break repair., Nature 506(7487):249-53

 [108] Levin-Zaidman S., Frenkiel-Krispin D., Shimoni E., Sabanay I., Wolf SG., Minsky A., 2000, Ordered intracellular RecA-DNA assemblies: a potential site of in vivo RecA-mediated activities., Proc Natl Acad Sci U S A 97(12):6791-6

 [109] Li BS., Sattin BD., Goh MC., 2006, Direct and real-time visualization of the disassembly of a single RecA-DNA-ATPgammaS complex using AFM imaging in fluid., Nano Lett 6(7):1474-8

 [110] Li BS., Wei B., Goh MC., 2012, Direct visualization of the formation of RecA/dsDNA complexes at the single-molecule level., Micron 43(10):1073-5

 [111] Lin LL., Little JW., 1989, Autodigestion and RecA-dependent cleavage of Ind- mutant LexA proteins., J Mol Biol 210(3):439-52

 [112] Lin YH., Chu CC., Fan HF., Wang PY., Cox MM., Li HW., 2019, A 5'-to-3' strand exchange polarity is intrinsic to RecA nucleoprotein filaments in the absence of ATP hydrolysis., Nucleic Acids Res 47(10):5126-5140

 [113] Lindsley JE., Cox MM., 1990, On RecA protein-mediated homologous alignment of two DNA molecules. Three strands versus four strands., J Biol Chem 265(17):10164-71

 [114] Lipfert J., Kerssemakers JW., Jager T., Dekker NH., 2010, Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments., Nat Methods 7(12):977-80

 [115] Little JW., 1991, Mechanism of specific LexA cleavage: autodigestion and the role of RecA coprotease., Biochimie 73(4):411-21

 [116] Little JW., 1984, Autodigestion of lexA and phage lambda repressors., Proc Natl Acad Sci U S A 81(5):1375-9

 [117] Little JW., Edmiston SH., Pacelli LZ., Mount DW., 1980, Cleavage of the Escherichia coli lexA protein by the recA protease., Proc Natl Acad Sci U S A 77(6):3225-9

 [118] Liu SK., Eisen JA., Hanawalt PC., Tessman I., 1993, recA mutations that reduce the constitutive coprotease activity of the RecA1202(Prtc) protein: possible involvement of interfilament association in proteolytic and recombination activities., J Bacteriol 175(20):6518-29

 [119] Logan KM., Knight KL., 1993, Mutagenesis of the P-loop motif in the ATP binding site of the RecA protein from Escherichia coli., J Mol Biol 232(4):1048-59

 [120] Long JE., Renzette N., Sandler SJ., 2009, Suppression of constitutive SOS expression by recA4162 (I298V) and recA4164 (L126V) requires UvrD and RecX in Escherichia coli K-12., Mol Microbiol 73(2):226-39

 [121] Lovett ST., 2012, Biochemistry: A glimpse of molecular competition., Nature 491(7423):198-200

 [122] Lu CH., Chang TT., Cho CC., Lin HC., Li HW., 2017, Stable Nuclei of Nucleoprotein Filament and High ssDNA Binding Affinity Contribute to Enhanced RecA E38K Recombinase Activity., Sci Rep 7(1):14964

 [123] Lu D., Danilowicz C., Tashjian TF., Prevost C., Godoy VG., Prentiss M., 2019, Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology., J Biol Chem 294(21):8606-8616

 [124] Lusetti SL., Voloshin ON., Inman RB., Camerini-Otero RD., Cox MM., 2004, The DinI protein stabilizes RecA protein filaments., J Biol Chem 279(29):30037-46

 [125] MacFarland KJ., Shan Q., Inman RB., Cox MM., 1997, RecA as a motor protein. Testing models for the role of ATP hydrolysis in DNA strand exchange., J Biol Chem 272(28):17675-85

 [126] Maeda T., Horinouchi T., Sakata N., Sakai A., Furusawa C., 2019, High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds., J Antibiot (Tokyo) 72(7):566-573

 [127] Malkov VA., Panyutin IG., Neumann RD., Zhurkin VB., Camerini-Otero RD., 2000, Radioprobing of a RecA-three-stranded DNA complex with iodine 125: evidence for recognition of homology in the major groove of the target duplex., J Mol Biol 299(3):629-40

 [128] Mani A., Braslavsky I., Arbel-Goren R., Stavans J., 2010, Caught in the act: the lifetime of synaptic intermediates during the search for homology on DNA., Nucleic Acids Res 38(6):2036-43

 [129] Mazin AV., Kowalczykowski SC., 1999, A novel property of the RecA nucleoprotein filament: activation of double- stranded DNA for strand exchange in trans., Genes Dev 13(15):2005-16

 [130] McEntee K., Hesse JE., Epstein W., 1976, Identification and radiochemical purification of the recA protein of Escherichia coli K-12., Proc Natl Acad Sci U S A 73(11):3979-83

 [131] McEntee K., Weinstock GM., Lehman IR., 1981, Binding of the recA protein of Escherichia coli to single- and double-stranded DNA., J Biol Chem 256(16):8835-44

 [132] Menetski JP., Kowalczykowski SC., 1990, Biochemical properties of the Escherichia coli recA430 protein. Analysis of a mutation that affects the interaction of the ATP-recA protein complex with single-stranded DNA., J Mol Biol 211(4):845-55

 [133] Menge KL., Bryant FR., 1992, Effect of nucleotide cofactor structure on recA protein-promoted DNA pairing. 1. Three-strand exchange reaction., Biochemistry 31(22):5151-7

 [134] Mikawa T., Masui R., Ogawa T., Ogawa H., Kuramitsu S., 1995, N-terminal 33 amino acid residues of Escherichia coli RecA protein contribute to its self-assembly., J Mol Biol 250(4):471-83

 [135] Mirshad JK., Kowalczykowski SC., 2003, Biochemical basis of the constitutive coprotease activity of RecA P67W protein., Biochemistry 42(19):5937-44

 [136] Mirshad JK., Kowalczykowski SC., 2003, Biochemical characterization of a mutant RecA protein altered in DNA-binding loop 1., Biochemistry 42(19):5945-54

 [137] Mishra S., Mazumdar PA., Dey J., Das AK., 2003, Molecular modeling of RecX reveals its mode of interaction with RecA., Biochem Biophys Res Commun 312(3):615-22

 [138] Moreau PL., 1988, Overproduction of single-stranded-DNA-binding protein specifically inhibits recombination of UV-irradiated bacteriophage DNA in Escherichia coli., J Bacteriol 170(6):2493-500

 [139] Moreau PL., 1987, Effects of overproduction of single-stranded DNA-binding protein on RecA protein-dependent processes in Escherichia coli., J Mol Biol 194(4):621-34

 [140] Moreau PL., Fanica M., Devoret R., 1980, Cleavage of lambda repressor and induction of recA protein synthesis elicited by aflatoxin B1 metabolites in Escherichia coli., Carcinogenesis 1(10):837-48

 [141] Moreau PL., Pelico JV., Devoret R., 1982, Cleavage of lambda repressor and synthesis of RecA protein induced by transferred UV-damaged F sex factor., Mol Gen Genet 186(2):170-9

 [142] Moreau PL., Roberts JW., 1984, RecA protein--promoted lambda repressor cleavage: complementation between RecA441 and RecA430 proteins in vitro., Mol Gen Genet 198(2):25-34

 [143] Morimatsu K., Horii T., 1995, Analysis of the DNA binding site of Escherichia coli RecA protein., Adv Biophys 31:23-48

 [144] Morrical SW., Cox MM., 1990, Stabilization of recA protein-ssDNA complexes by the single-stranded DNA binding protein of Escherichia coli., Biochemistry 29(3):837-43

 [145] Morrical SW., Lee J., Cox MM., 1986, Continuous association of Escherichia coli single-stranded DNA binding protein with stable complexes of recA protein and single-stranded DNA., Biochemistry 25(7):1482-94

 [146] Muniyappa K., Ramdas J., Mythili E., Galande S., null, Homologous pairing between nucleosome cores on a linear duplex DNA and nucleoprotein filaments of RecA protein-single stranded DNA., Biochimie 73(2-3):187-90

 [147] Mustard JA., Little JW., 2000, Analysis of Escherichia coli RecA interactions with LexA, lambda CI, and UmuD by site-directed mutagenesis of recA., J Bacteriol 182(6):1659-70

 [148] Ogawa H., Ogawa T., 1990, Regulation in repressor inactivation by RecA protein., Adv Biophys 26:33-49

 [149] Ohtani T., Shibata T., Iwabuchi M., Nakagawa K., Ando T., 1982, Hydrolysis of ATP dependent on homologous double-stranded DNA and single-stranded fragments promoted by RecA protein of Escherichia coli., J Biochem 91(5):1767-75

 [150] Paulus BF., Bryant FR., 1997, Time-dependent inhibition of recA protein-catalyzed ATP hydrolysis by ATPgammaS: evidence for a rate-determining isomerization of the recA-ssDNA complex., Biochemistry 36(25):7832-8

 [151] Peacock-Villada A., Yang D., Danilowicz C., Feinstein E., Pollock N., McShan S., Coljee V., Prentiss M., 2012, Complementary strand relocation may play vital roles in RecA-based homology recognition., Nucleic Acids Res 40(20):10441-51

 [152] Piechura JR., Tseng TL., Hsu HF., Byrne RT., Windgassen TA., Chitteni-Pattu S., Battista JR., Li HW., Cox MM., 2015, Biochemical characterization of RecA variants that contribute to extreme resistance to ionizing radiation., DNA Repair (Amst) 26:30-43

 [153] Pinsince JM., Muench KA., Bryant FR., Griffith JD., 1993, Two mutant RecA proteins possessing pH-dependent strand exchange activity exhibit pH-dependent presynaptic filament formation., J Mol Biol 233(1):59-66

 [154] Prevost C., Takahashi M., 2003, Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination., Q Rev Biophys 36(4):429-53

 [155] Pugh BF., Cox MM., 1987, recA protein binding to the heteroduplex product of DNA strand exchange., J Biol Chem 262(3):1337-43

 [156] Quillardet P., Moreau PL., Ginsburg H., Mount DW., Devoret R., 1982, Cell survival, UV-reactivation and induction of prophage lambda in Escherichia coli K12 overproducing RecA protein., Mol Gen Genet 188(1):37-43

 [157] Radman M., 1975, SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis., Basic Life Sci 5A:355-67

 [158] Rajagopalan M., Lu C., Woodgate R., O'Donnell M., Goodman MF., Echols H., 1992, Activity of the purified mutagenesis proteins UmuC, UmuD', and RecA in replicative bypass of an abasic DNA lesion by DNA polymerase III., Proc Natl Acad Sci U S A 89(22):10777-81

 [159] Rajendram M., Zhang L., Reynolds BJ., Auer GK., Tuson HH., Ngo KV., Cox MM., Yethiraj A., Cui Q., Weibel DB., 2015, Anionic Phospholipids Stabilize RecA Filament Bundles in Escherichia coli., Mol Cell 60(3):374-84

 [160] Ramdas J., Muniyappa K., 1995, Recognition and alignment of homologous DNA sequences between minichromosomes and single-stranded DNA promoted by RecA protein., Mol Gen Genet 249(3):336-48

 [161] Ramdas J., Mythili E., Muniyappa K., 1989, RecA protein promoted homologous pairing in vitro. Pairing between linear duplex DNA bound to HU Protein (nucleosome cores) and nucleoprotein filaments of recA protein-single-stranded DNA., J Biol Chem 264(29):17395-400

 [162] Ramirez BE., Voloshin ON., Camerini-Otero RD., Bax A., 2000, Solution structure of DinI provides insight into its mode of RecA inactivation., Protein Sci 9(11):2161-9

 [163] Ramreddy T., Sen S., Rao BJ., Krishnamoorthy G., 2003, DNA dynamics in RecA-DNA filaments: ATP hydrolysis-related flexibility in DNA., Biochemistry 42(41):12085-94

 [164] Rangarajan S., Woodgate R., Goodman MF., 2002, Replication restart in UV-irradiated Escherichia coli involving pols II, III, V, PriA, RecA and RecFOR proteins., Mol Microbiol 43(3):617-28

 [165] Rao BJ., Jwang B., Radding CM., 1990, RecA protein reinitiates strand exchange on isolated protein-free DNA intermediates. An ADP-resistant process., J Mol Biol 213(4):789-809

 [166] Rao BJ., Radding CM., 1995, RecA protein mediates homologous recognition via non-Watson-Crick bonds in base triplets., Philos Trans R Soc Lond B Biol Sci 347(1319):5-12

 [167] Raychaudhury P., Marians KJ., 2019, The recombination mediator proteins RecFOR maintain RecA* levels for maximal DNA polymerase V Mut activity., J Biol Chem 294(3):852-860

 [168] Rebollo JE., Moreau PL., Blanco M., Devoret R., 1984, Restoration of RecA protein activity by genetic complementation., Mol Gen Genet 195(1-2):83-9

 [169] Reckinger AR., Jeong KS., Khodursky AB., Hiasa H., 2007, RecA can stimulate the relaxation activity of topoisomerase I: Molecular basis of topoisomerase-mediated genome-wide transcriptional responses in Escherichia coli., Nucleic Acids Res 35(1):79-86

 [170] Rehrauer WM., Lavery PE., Palmer EL., Singh RN., Kowalczykowski SC., 1996, Interaction of Escherichia coli RecA protein with LexA repressor. I. LexA repressor cleavage is competitive with binding of a secondary DNA molecule., J Biol Chem 271(39):23865-73

 [171] Reuven NB., Arad G., Maor-Shoshani A., Livneh Z., 1999, The mutagenesis protein UmuC is a DNA polymerase activated by UmuD', RecA, and SSB and is specialized for translesion replication., J Biol Chem 274(45):31763-6

 [172] Reuven NB., Arad G., Stasiak AZ., Stasiak A., Livneh Z., 2001, Lesion bypass by the Escherichia coli DNA polymerase V requires assembly of a RecA nucleoprotein filament., J Biol Chem 276(8):5511-7

 [173] Reymer A., Babik S., Takahashi M., Norden B., Beke-Somfai T., 2015, ATP Hydrolysis in the RecA-DNA Filament Promotes Structural Changes at the Protein-DNA Interface., Biochemistry 54(30):4579-82

 [174] Rice KP., Eggler AL., Sung P., Cox MM., 2001, DNA pairing and strand exchange by the Escherichia coli RecA and yeast Rad51 proteins without ATP hydrolysis: on the importance of not getting stuck., J Biol Chem 276(42):38570-81

 [175] Riddles PW., Lehman IR., 1985, The formation of paranemic and plectonemic joints between DNA molecules by the recA and single-stranded DNA-binding proteins of Escherichia coli., J Biol Chem 260(1):165-9

 [176] Roberts JW., Roberts CW., 1981, Two mutations that alter the regulatory activity of E. coli recA protein., Nature 290(5805):422-4

 [177] Ronayne EA., Cox MM., 2014, RecA-dependent programmable endonuclease Ref cleaves DNA in two distinct steps., Nucleic Acids Res 42(6):3871-83

 [178] Roy R., Kozlov AG., Lohman TM., Ha T., 2009, SSB protein diffusion on single-stranded DNA stimulates RecA filament formation., Nature 461(7267):1092-7

 [179] Sagi D., Tlusty T., Stavans J., 2006, High fidelity of RecA-catalyzed recombination: a watchdog of genetic diversity., Nucleic Acids Res 34(18):5021-31

 [180] Saladin A., Amourda C., Poulain P., Ferey N., Baaden M., Zacharias M., Delalande O., Prevost C., 2010, Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments., Nucleic Acids Res 38(19):6313-23

 [181] Sassanfar M., Roberts J., 1991, Constitutive and UV-mediated activation of RecA protein: combined effects of recA441 and recF143 mutations and of addition of nucleosides and adenine., J Bacteriol 173(18):5869-75

 [182] Sattin BD., Goh MC., 2004, Direct observation of the assembly of RecA/DNA complexes by atomic force microscopy., Biophys J 87(5):3430-6

 [183] Sauer RT., Ross MJ., Ptashne M., 1982, Cleavage of the lambda and P22 repressors by recA protein., J Biol Chem 257(8):4458-62

 [184] Schutte BC., Cox MM., 1987, Homology-dependent changes in adenosine 5'-triphosphate hydrolysis during recA protein promoted DNA strand exchange: evidence for long paranemic complexes., Biochemistry 26(18):5616-25

 [185] Shan Q., Bork JM., Webb BL., Inman RB., Cox MM., 1997, RecA protein filaments: end-dependent dissociation from ssDNA and stabilization by RecO and RecR proteins., J Mol Biol 265(5):519-40

 [186] Shan Q., Cox MM., 1996, RecA protein dynamics in the interior of RecA nucleoprotein filaments., J Mol Biol 257(4):756-74

 [187] Shaner SL., Flory J., Radding CM., 1987, The distribution of Escherichia coli recA protein bound to duplex DNA with single-stranded ends., J Biol Chem 262(19):9220-30

 [188] Shaner SL., Radding CM., 1987, Translocation of Escherichia coli recA protein from a single-stranded tail to contiguous duplex DNA., J Biol Chem 262(19):9211-9

 [189] Shi WX., Larson RG., 2005, Atomic force microscopic study of aggregation of RecA-DNA nucleoprotein filaments into left-handed supercoiled bundles., Nano Lett 5(12):2476-81

 [190] Shi WX., Larson RG., 2007, RecA-ssDNA filaments supercoil in the presence of single-stranded DNA-binding protein., Biochem Biophys Res Commun 357(3):755-60

 [191] Shinagawa H., Iwasaki H., Kato T., Nakata A., 1988, RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis., Proc Natl Acad Sci U S A 85(6):1806-10

 [192] Shinohara T., Arai N., Iikura Y., Kasagi M., Masuda-Ozawa T., Yamaguchi Y., Suzuki-Nagata K., Shibata T., Mikawa T., 2018, Nonfilament-forming RecA dimer catalyzes homologous joint formation., Nucleic Acids Res 46(20):10855-10869

 [193] Shinohara T., Ikawa S., Iwasaki W., Hiraki T., Hikima T., Mikawa T., Arai N., Kamiya N., Shibata T., 2015, Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair., Nucleic Acids Res 43(2):973-86

 [194] Simatovic A., Mitrikeski PT., Vlasic I., Sopta M., Brcic-Kostic K., 2016, The Walker A motif mutation recA4159 abolishes the SOS response and recombination in a recA730 mutant of Escherichia coli., Res Microbiol 167(6):462-71

 [195] Skiba MC., Knight KL., 1994, Functionally important residues at a subunit interface site in the RecA protein from Escherichia coli., J Biol Chem 269(5):3823-8

 [196] Slilaty SN., Rupley JA., Little JW., 1986, Intramolecular cleavage of LexA and phage lambda repressors: dependence of kinetics on repressor concentration, pH, temperature, and solvent., Biochemistry 25(22):6866-75

 [197] Soltis DA., Lehman IR., 1983, recA protein promoted DNA strand exchange., J Biol Chem 258(10):6073-7

 [198] Stasiak AZ., Rosselli W., Stasiak A., null, RecA-DNA helical filaments in genetic recombination., Biochimie 73(2-3):199-208

 [199] Steffen SE., Bryant FR., 2012, Altered nucleotide cofactor-dependent properties of the mutant [S240K]RecA protein., Biochem Biophys Res Commun 421(3):527-31

 [200] Stole E., Bryant FR., 1995, Spectroscopic demonstration of a linkage between the kinetics of NTP hydrolysis and the conformational state of the recA-single-stranded DNA complex., J Biol Chem 270(35):20322-8

 [201] Stole E., Bryant FR., 1994, Introduction of a tryptophan reporter group into loop 1 of the recA protein. Examination of the conformational states of the recA-ssDNA complex by fluorescence spectroscopy., J Biol Chem 269(11):7919-25

 [202] Stole E., Bryant FR., 1996, Reengineering the nucleotide cofactor specificity of the RecA protein by mutation of aspartic acid 100., J Biol Chem 271(31):18326-8

 [203] Stole E., Bryant FR., 1997, The rate-determining step on the recA protein-catalyzed ssDNA-dependent ATP hydrolysis reaction pathway., Biochemistry 36(12):3483-90

 [204] Story RM., Bishop DK., Kleckner N., Steitz TA., 1993, Structural relationship of bacterial RecA proteins to recombination proteins from bacteriophage T4 and yeast., Science 259(5103):1892-6

 [205] Story RM., Steitz TA., 1992, Structure of the recA protein-ADP complex., Nature 355(6358):374-6

 [206] Sweasy JB., 2005, RecA kicks Pol V into gear., Nat Struct Mol Biol 12(3):215-6

 [207] Takahashi M., Norden B., 1994, Structure of RecA-DNA complex and mechanism of DNA strand exchange reaction in homologous recombination., Adv Biophys 30:1-35

 [208] Tessman ES., Peterson P., 1985, Plaque color method for rapid isolation of novel recA mutants of Escherichia coli K-12: new classes of protease-constitutive recA mutants., J Bacteriol 163(2):677-87

 [209] Tessman ES., Peterson PK., 1985, Isolation of protease-proficient, recombinase-deficient recA mutants of Escherichia coli K-12., J Bacteriol 163(2):688-95

 [210] Tessman ES., Tessman I., Peterson PK., Forestal JD., 1986, Roles of RecA protease and recombinase activities of Escherichia coli in spontaneous and UV-induced mutagenesis and in Weigle repair., J Bacteriol 168(3):1159-64

 [211] Thoms B., Wackernagel W., 1988, Suppression of the UV-sensitive phenotype of Escherichia coli recF mutants by recA(Srf) and recA(Tif) mutations requires recJ+., J Bacteriol 170(8):3675-81

 [212] Umemura K., Komatsu J., Uchihashi T., Choi N., Ikawa S., Nishinaka T., Shibata T., Nakayama Y., Katsura S., Mizuno A., Tokumoto H., Ishikawa M., Kuroda R., 2001, Atomic force microscopy of RecA--DNA complexes using a carbon nanotube tip., Biochem Biophys Res Commun 281(2):390-5

 [213] Umemura K., Komatsu J., Uchihashi T., Choi N., Ikawa S., Nishinaka T., Shibata T., Nakayama Y., Katsura S., Mizuno A., Tokumoto H., Ishikawa M., Kuroda R., 2000, RecA-double stranded DNA complexes studied by atomic force microscopy., Nucleic Acids Symp Ser (44):213-4

 [214] Umezu K., Kolodner RD., 1994, Protein interactions in genetic recombination in Escherichia coli. Interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA-binding protein., J Biol Chem 269(47):30005-13

 [215] Uranga LA., Balise VD., Benally CV., Grey A., Lusetti SL., 2011, The Escherichia coli DinD protein modulates RecA activity by inhibiting postsynaptic RecA filaments., J Biol Chem 286(34):29480-91

 [216] Urios A., Herrera G., Aleixandre V., Blanco M., 1990, Expression of the recA gene is reduced in Escherichia coli topoisomerase I mutants., Mutat Res 243(4):267-72

 [217] VanLoock MS., Yu X., Yang S., Galkin VE., Huang H., Rajan SS., Anderson WF., Stohl EA., Seifert HS., Egelman EH., 2003, Complexes of RecA with LexA and RecX differentiate between active and inactive RecA nucleoprotein filaments., J Mol Biol 333(2):345-54

 [218] Venkatesh R., Ganesh N., Guhan N., Reddy MS., Chandrasekhar T., Muniyappa K., 2002, RecX protein abrogates ATP hydrolysis and strand exchange promoted by RecA: insights into negative regulation of homologous recombination., Proc Natl Acad Sci U S A 99(19):12091-6

 [219] Vlasic I., Simatovic A., Brcic-Kostic K., 2011, Genetic requirements for high constitutive SOS expression in recA730 mutants of Escherichia coli., J Bacteriol 193(18):4643-51

 [220] Vlassakis J., Feinstein E., Yang D., Tilloy A., Weiller D., Kates-Harbeck J., Coljee V., Prentiss M., 2013, Tension on dsDNA bound to ssDNA-RecA filaments may play an important role in driving efficient and accurate homology recognition and strand exchange., Phys Rev E Stat Nonlin Soft Matter Phys 87(3)

 [221] Volodin AA., Bocharova TN., Smirnova EA., Camerini-Otero RD., 2009, Reversibility, equilibration, and fidelity of strand exchange reaction between short oligonucleotides promoted by RecA protein from escherichia coli and human Rad51 and Dmc1 proteins., J Biol Chem 284(3):1495-504

 [222] Voloshin ON., Ramirez BE., Bax A., Camerini-Otero RD., 2001, A model for the abrogation of the SOS response by an SOS protein: a negatively charged helix in DinI mimics DNA in its interaction with RecA., Genes Dev 15(4):415-27

 [223] Voloshin ON., Wang L., Camerini-Otero RD., 2000, The homologous pairing domain of RecA also mediates the allosteric regulation of DNA binding and ATP hydrolysis: a remarkable concentration of functional residues., J Mol Biol 303(5):709-20

 [224] Wang TC., Chang HY., Hung JL., 1993, Cosuppression of recF, recR and recO mutations by mutant recA alleles in Escherichia coli cells., Mutat Res 294(2):157-66

 [225] Wang WB., Tessman ES., 1986, Location of functional regions of the Escherichia coli RecA protein by DNA sequence analysis of RecA protease-constitutive mutants., J Bacteriol 168(2):901-10

 [226] Weinstock GM., McEntee K., Lehman IR., 1981, Hydrolysis of nucleoside triphosphates catalyzed by the recA protein of Escherichia coli. Steady state kinetic analysis of ATP hydrolysis., J Biol Chem 256(16):8845-9

 [227] Weinstock GM., McEntee K., Lehman IR., 1981, Interaction of the recA protein of Escherichia coli with adenosine 5'-O-(3-thiotriphosphate)., J Biol Chem 256(16):8850-5

 [228] Weinstock GM., McEntee K., Lehman IR., 1981, Hydrolysis of nucleoside triphosphates catalyzed by the recA protein of Escherichia coli. Characterization of ATP hydrolysis., J Biol Chem 256(16):8829-34

 [229] Weinstock GM., McEntee K., Lehman IR., 1981, Hydrolysis of nucleoside triphosphates catalyzed by the recA protein of Escherichia coli. Hydrolysis of UTP., J Biol Chem 256(16):8856-8

 [230] Witkin EM., 1974, Thermal enhancement of ultraviolet mutability in a tif-1 uvrA derivative of Escherichia coli B-r: evidence that ultraviolet mutagenesis depends upon an inducible function., Proc Natl Acad Sci U S A 71(5):1930-4

 [231] Woodgate R., Ennis DG., 1991, Levels of chromosomally encoded Umu proteins and requirements for in vivo UmuD cleavage., Mol Gen Genet 229(1):10-6

 [232] Wu AM., Bianchi M., DasGupta C., Radding CM., 1983, Unwinding associated with synapsis of DNA molecules by recA protein., Proc Natl Acad Sci U S A 80(5):1256-60

 [233] Wu AM., Kahn R., DasGupta C., Radding CM., 1982, Formation of nascent heteroduplex structures by RecA protein and DNA., Cell 30(1):37-44

 [234] Wu HY., Lu CH., Li HW., 2017, RecA-SSB Interaction Modulates RecA Nucleoprotein Filament Formation on SSB-Wrapped DNA., Sci Rep 7(1):11876

 [235] Xiao J., Lee AM., Singleton SF., 2006, Construction and evaluation of a kinetic scheme for RecA-mediated DNA strand exchange., Biopolymers 81(6):473-96

 [236] Xiao J., Lee AM., Singleton SF., 2006, Direct evaluation of a kinetic model for RecA-mediated DNA-strand exchange: the importance of nucleic acid dynamics and entropy during homologous genetic recombination., Chembiochem 7(8):1265-78

 [237] Xiao J., Singleton SF., 2002, Elucidating a key intermediate in homologous DNA strand exchange: structural characterization of the RecA-triple-stranded DNA complex using fluorescence resonance energy transfer., J Mol Biol 320(3):529-58

 [238] Xing X., Bell CE., 2004, Crystal structures of Escherichia coli RecA in a compressed helical filament., J Mol Biol 342(5):1471-85

 [239] Yakimov A., Pobegalov G., Bakhlanova I., Khodorkovskii M., Petukhov M., Baitin D., 2017, Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide., Nucleic Acids Res 45(16):9788-9796

 [240] Yang D., Boyer B., Prevost C., Danilowicz C., Prentiss M., 2015, Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure., Nucleic Acids Res 43(21):10251-63

 [241] Yasuda T., Morimatsu K., Horii T., Nagata T., Ohmori H., 1998, Inhibition of Escherichia coli RecA coprotease activities by DinI., EMBO J 17(11):3207-16

 [242] Yasuda T., Morimatsu K., Kato R., Usukura J., Takahashi M., Ohmori H., 2001, Physical interactions between DinI and RecA nucleoprotein filament for the regulation of SOS mutagenesis., EMBO J 20(5):1192-202

 [243] Yu X., Egelman EH., 1993, The LexA repressor binds within the deep helical groove of the activated RecA filament., J Mol Biol 231(1):29-40

 [244] Yu X., Jacobs SA., West SC., Ogawa T., Egelman EH., 2001, Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA., Proc Natl Acad Sci U S A 98(15):8419-24

 [245] Zaitsev EN., Kowalczykowski SC., 1999, The simultaneous binding of two double-stranded DNA molecules by Escherichia coli RecA protein., J Mol Biol 287(1):21-31

 [246] Zaitsev EN., Kowalczykowski SC., 2000, A novel pairing process promoted by Escherichia coli RecA protein: inverse DNA and RNA strand exchange., Genes Dev 14(6):740-9

 [247] Zhang Z., Yoon D., LaPorte JR., Chen J., 2001, Appropriate initiation of the strand exchange reaction promoted by RecA protein requires ATP hydrolysis., J Mol Biol 309(1):29-43

 [248] Zhao B., Zhang D., Li C., Yuan Z., Yu F., Zhong S., Jiang G., Yang YG., Le XC., Weinfeld M., Zhu P., Wang H., 2017, ATPase activity tightly regulates RecA nucleofilaments to promote homologous recombination., Cell Discov 3:16053

 [249] Zhao XC., Fu H., Song L., Yang YJ., Zhou EC., Liu GX., Chen XF., Li Z., Wu WQ., Zhang XH., 2019, S-DNA and RecA/RAD51-Mediated Strand Exchange in Vitro., Biochemistry 58(15):2009-2016

 [250] Zhou X., Adzuma K., 1997, DNA strand exchange mediated by the Escherichia coli RecA protein initiates in the minor groove of double-stranded DNA., Biochemistry 36(15):4650-61

 [251] van der Heijden T., van Noort J., van Leest H., Kanaar R., Wyman C., Dekker NH., Dekker N., Dekker C., 2005, Torque-limited RecA polymerization on dsDNA., Nucleic Acids Res 33(7):2099-105

 [252] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muńiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.