LOCUS       sequence-382394-        3070 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Generation and purification of R-loops for in vitro biochemistry.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 3070)
  AUTHORS   Hodson C, van Twest S, Dylewska M, O'Rourke JJ, Tan W, Murphy VJ, 
            Walia M, Abbouche L, Nieminuszczy J, Dunn E, Bythell-Douglas R, 
            Heierhorst J, Niedzwiedz W, Deans AJ
  TITLE     Branchpoint translocation by fork remodelers as a general mechanism 
            of R-loop removal.
  JOURNAL   Cell Rep. 2022 Dec 6;41(10):111749. doi: 
            10.1016/j.celrep.2022.111749.
  PUBMED    36476850
REFERENCE   2  (bases 1 to 3070)
  AUTHORS   .
  TITLE     Direct Submission
  JOURNAL   Exported Dec 15, 2025 from SnapGene Server 8.0.1
            https://www.snapgene.com
COMMENT     SGRef: number: 1; type: "Journal Article"; journalName: "Cell Rep.";
            date: "2022-12-6"; volume: "41(10):111749. doi"; pages: " 
            10.1016/j.celrep.2022.111749"
COMMENT     Sequence Label: pUC19-Mu-switch-R-loop
FEATURES             Location/Qualifiers
     source          1..3070
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(24..46)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     146..165
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     359..381
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     374..390
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     397..413
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     425..444
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        425..443
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(844..860)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(857..879)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    868..884
                     /label=lac operator
                     /bound_moiety="lac repressor encoded by lacI"
                     /note="The lac repressor binds to the lac operator to 
                     inhibit transcription in E. coli. This inhibition can be 
                     relieved by adding lactose or 
                     isopropyl-beta-D-thiogalactopyranoside (IPTG)."
     promoter        complement(join(892..898,899..916,917..922))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    937..958
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(1075..1092)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(1246..1834)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(1326..1345)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2005..2796,2797..2865))
                     /codon_start=1
                     /gene="bla"
                     /product="beta-lactamase"
                     /label=AmpR
                     /note="confers resistance to ampicillin, carbenicillin, and
                     related antibiotics"
                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI
                     ELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS
                     PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRW
                     EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSA
                     LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS
                     LIKHW"
     primer_bind     2628..2647
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(2866..2970)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     3038..3056
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
ORIGIN
        1 cgtttcggtg atgacggtga aaacctctga cacatgcagc tcccggagac ggtcacagct
       61 tgtctgtaag cggatgccgg gagcagacaa gcccgtcagg gcgcgtcagc gggtgttggc
      121 gggtgtcggg gctggcttaa ctatgcggca tcagagcaga ttgtactgag agtgcaccat
      181 atgcggtgtg aaataccgca cagatgcgta aggagaaaat accgcatcag gcgccattcg
      241 ccattcaggc tgcgcaactg ttgggaaggg cgatcggtgc gggcctcttc gctattacgc
      301 cagctggcga aagggggatg tgctgcaagg cgattaagtt gggtaacgcc agggttttcc
      361 cagtcacgac gttgtaaaac gacggccagt gaattcgtaa aacgacggcc agtgaattga
      421 gttctaatac gactcactat agggcgaaga atgcctcgag cttgcaatcg ctagctcaat
      481 atcctaacta tcatacctat cacataatca ctcgacctag gggggtgctg gggtaggtta
      541 gagcatggga accaggctgg acagctctgg aaggagctga gatatgtggg gttgtgggga
      601 acaggttgga cagctctggg gagctagggt agttgggggt gtggggacta ggctgggcag
      661 ctctactagt gctttcaacc ttggcgtaat catggtcata gctgtttcct ttccagtcgg
      721 gaaacctgtc gtgccagctg cattaatgaa tcggccaacg cgcgtctaga gtcgactgaa
      781 ccccttgggg cctctaaacg ggtcttgagg ggttttttgg tcgacaagct tggcgtaatc
      841 atggtcatag ctgtttcctg tgtgaaattg ttatccgctc acaattccac acaacatacg
      901 agccggaagc ataaagtgta aagcctgggg tgcctaatga gtgagctaac tcacattaat
      961 tgcgttgcgc tcactgcccg ctttccagtc gggaaacctg tcgtgccagc tgcattaatg
     1021 aatcggccaa cgcgcgggga gaggcggttt gcgtattggg cgctcttccg cttcctcgct
     1081 cactgactcg ctgcgctcgg tcgttcggct gcggcgagcg gtatcagctc actcaaaggc
     1141 ggtaatacgg ttatccacag aatcagggga taacgcagga aagaacatgt gagcaaaagg
     1201 ccagcaaaag gccaggaacc gtaaaaaggc cgcgttgctg gcgtttttcc ataggctccg
     1261 cccccctgac gagcatcaca aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg
     1321 actataaaga taccaggcgt ttccccctgg aagctccctc gtgcgctctc ctgttccgac
     1381 cctgccgctt accggatacc tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca
     1441 tagctcacgc tgtaggtatc tcagttcggt gtaggtcgtt cgctccaagc tgggctgtgt
     1501 gcacgaaccc cccgttcagc ccgaccgctg cgccttatcc ggtaactatc gtcttgagtc
     1561 caacccggta agacacgact tatcgccact ggcagcagcc actggtaaca ggattagcag
     1621 agcgaggtat gtaggcggtg ctacagagtt cttgaagtgg tggcctaact acggctacac
     1681 tagaagaaca gtatttggta tctgcgctct gctgaagcca gttaccttcg gaaaaagagt
     1741 tggtagctct tgatccggca aacaaaccac cgctggtagc ggtggttttt ttgtttgcaa
     1801 gcagcagatt acgcgcagaa aaaaaggatc tcaagaagat cctttgatct tttctacggg
     1861 gtctgacgct cagtggaacg aaaactcacg ttaagggatt ttggtcatga gattatcaaa
     1921 aaggatcttc acctagatcc ttttaaatta aaaatgaagt tttaaatcaa tctaaagtat
     1981 atatgagtaa acttggtctg acagttacca atgcttaatc agtgaggcac ctatctcagc
     2041 gatctgtcta tttcgttcat ccatagttgc ctgactcccc gtcgtgtaga taactacgat
     2101 acgggagggc ttaccatctg gccccagtgc tgcaatgata ccgcgagacc cacgctcacc
     2161 ggctccagat ttatcagcaa taaaccagcc agccggaagg gccgagcgca gaagtggtcc
     2221 tgcaacttta tccgcctcca tccagtctat taattgttgc cgggaagcta gagtaagtag
     2281 ttcgccagtt aatagtttgc gcaacgttgt tgccattgct acaggcatcg tggtgtcacg
     2341 ctcgtcgttt ggtatggctt cattcagctc cggttcccaa cgatcaaggc gagttacatg
     2401 atcccccatg ttgtgcaaaa aagcggttag ctccttcggt cctccgatcg ttgtcagaag
     2461 taagttggcc gcagtgttat cactcatggt tatggcagca ctgcataatt ctcttactgt
     2521 catgccatcc gtaagatgct tttctgtgac tggtgagtac tcaaccaagt cattctgaga
     2581 atagtgtatg cggcgaccga gttgctcttg cccggcgtca atacgggata ataccgcgcc
     2641 acatagcaga actttaaaag tgctcatcat tggaaaacgt tcttcggggc gaaaactctc
     2701 aaggatctta ccgctgttga gatccagttc gatgtaaccc actcgtgcac ccaactgatc
     2761 ttcagcatct tttactttca ccagcgtttc tgggtgagca aaaacaggaa ggcaaaatgc
     2821 cgcaaaaaag ggaataaggg cgacacggaa atgttgaata ctcatactct tcctttttca
     2881 atattattga agcatttatc agggttattg tctcatgagc ggatacatat ttgaatgtat
     2941 ttagaaaaat aaacaaatag gggttccgcg cacatttccc cgaaaagtgc cacctgacgt
     3001 ctaagaaacc attattatca tgacattaac ctataaaaat aggcgtatca cgaggccctt
     3061 tcgtctcgcg
//
