LOCUS       sequence-382400-        3068 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 3068)
  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 3068)
  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-mAirn-R-loop
FEATURES             Location/Qualifiers
     source          1..3068
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     complement(36..58)
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     158..177
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     371..393
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     386..402
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     409..425
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     437..456
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        437..455
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     complement(854..870)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(867..889)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    878..894
                     /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(902..908,909..926,927..932))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    947..968
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(1085..1102)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(1256..1844)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(1336..1355)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2015..2806,2807..2875))
                     /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     2638..2657
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(2876..2980)
                     /gene="bla"
                     /label=AmpR promoter
     primer_bind     3048..3066
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
ORIGIN
        1 tttcgtctcg cgcgtttcgg tgatgacggt gaaaacctct gacacatgca gctcccggag
       61 acggtcacag cttgtctgta agcggatgcc gggagcagac aagcccgtca gggcgcgtca
      121 gcgggtgttg gcgggtgtcg gggctggctt aactatgcgg catcagagca gattgtactg
      181 agagtgcacc atatgcggtg tgaaataccg cacagatgcg taaggagaaa ataccgcatc
      241 aggcgccatt cgccattcag gctgcgcaac tgttgggaag ggcgatcggt gcgggcctct
      301 tcgctattac gccagctggc gaaaggggga tgtgctgcaa ggcgattaag ttgggtaacg
      361 ccagggtttt cccagtcacg acgttgtaaa acgacggcca gtgaattcgt aaaacgacgg
      421 ccagtgaatt gagttctaat acgactcact atagggcgaa gaatgcctcg agcttgcaat
      481 cgctagctca atatcctaac tatcatacct atcacataat cactcgacct aggggccggt
      541 agaaagccga aagccgcgct gccgccatgc cgcgtcagca agaggagaag ggaggggggc
      601 gtccagcgcg ggccgactgc tgcactgggg ggggggggtt tacgggcgat ttagagcacg
      661 agggtgccac gctgactagt gctttcaacc ttggcgtaat catggtcata gctgtttcct
      721 ttccagtcgg gaaacctgtc gtgccagctg cattaatgaa tcggccaacg cgcgtctaga
      781 gtcgactgaa ccccttgggg cctctaaacg ggtcttgagg ggttttttgg tcgacaagct
      841 tggcgtaatc atggtcatag ctgtttcctg tgtgaaattg ttatccgctc acaattccac
      901 acaacatacg agccggaagc ataaagtgta aagcctgggg tgcctaatga gtgagctaac
      961 tcacattaat tgcgttgcgc tcactgcccg ctttccagtc gggaaacctg tcgtgccagc
     1021 tgcattaatg aatcggccaa cgcgcgggga gaggcggttt gcgtattggg cgctcttccg
     1081 cttcctcgct cactgactcg ctgcgctcgg tcgttcggct gcggcgagcg gtatcagctc
     1141 actcaaaggc ggtaatacgg ttatccacag aatcagggga taacgcagga aagaacatgt
     1201 gagcaaaagg ccagcaaaag gccaggaacc gtaaaaaggc cgcgttgctg gcgtttttcc
     1261 ataggctccg cccccctgac gagcatcaca aaaatcgacg ctcaagtcag aggtggcgaa
     1321 acccgacagg actataaaga taccaggcgt ttccccctgg aagctccctc gtgcgctctc
     1381 ctgttccgac cctgccgctt accggatacc tgtccgcctt tctcccttcg ggaagcgtgg
     1441 cgctttctca tagctcacgc tgtaggtatc tcagttcggt gtaggtcgtt cgctccaagc
     1501 tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg cgccttatcc ggtaactatc
     1561 gtcttgagtc caacccggta agacacgact tatcgccact ggcagcagcc actggtaaca
     1621 ggattagcag agcgaggtat gtaggcggtg ctacagagtt cttgaagtgg tggcctaact
     1681 acggctacac tagaagaaca gtatttggta tctgcgctct gctgaagcca gttaccttcg
     1741 gaaaaagagt tggtagctct tgatccggca aacaaaccac cgctggtagc ggtggttttt
     1801 ttgtttgcaa gcagcagatt acgcgcagaa aaaaaggatc tcaagaagat cctttgatct
     1861 tttctacggg gtctgacgct cagtggaacg aaaactcacg ttaagggatt ttggtcatga
     1921 gattatcaaa aaggatcttc acctagatcc ttttaaatta aaaatgaagt tttaaatcaa
     1981 tctaaagtat atatgagtaa acttggtctg acagttacca atgcttaatc agtgaggcac
     2041 ctatctcagc gatctgtcta tttcgttcat ccatagttgc ctgactcccc gtcgtgtaga
     2101 taactacgat acgggagggc ttaccatctg gccccagtgc tgcaatgata ccgcgagacc
     2161 cacgctcacc ggctccagat ttatcagcaa taaaccagcc agccggaagg gccgagcgca
     2221 gaagtggtcc tgcaacttta tccgcctcca tccagtctat taattgttgc cgggaagcta
     2281 gagtaagtag ttcgccagtt aatagtttgc gcaacgttgt tgccattgct acaggcatcg
     2341 tggtgtcacg ctcgtcgttt ggtatggctt cattcagctc cggttcccaa cgatcaaggc
     2401 gagttacatg atcccccatg ttgtgcaaaa aagcggttag ctccttcggt cctccgatcg
     2461 ttgtcagaag taagttggcc gcagtgttat cactcatggt tatggcagca ctgcataatt
     2521 ctcttactgt catgccatcc gtaagatgct tttctgtgac tggtgagtac tcaaccaagt
     2581 cattctgaga atagtgtatg cggcgaccga gttgctcttg cccggcgtca atacgggata
     2641 ataccgcgcc acatagcaga actttaaaag tgctcatcat tggaaaacgt tcttcggggc
     2701 gaaaactctc aaggatctta ccgctgttga gatccagttc gatgtaaccc actcgtgcac
     2761 ccaactgatc ttcagcatct tttactttca ccagcgtttc tgggtgagca aaaacaggaa
     2821 ggcaaaatgc cgcaaaaaag ggaataaggg cgacacggaa atgttgaata ctcatactct
     2881 tcctttttca atattattga agcatttatc agggttattg tctcatgagc ggatacatat
     2941 ttgaatgtat ttagaaaaat aaacaaatag gggttccgcg cacatttccc cgaaaagtgc
     3001 cacctgacgt ctaagaaacc attattatca tgacattaac ctataaaaat aggcgtatca
     3061 cgaggccc
//
