LOCUS       sequence-160570-        3406 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  One of four plasmids needed to create the mismatched double Holliday
            junction substrate (MM-DHJS)..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 3406)
  AUTHORS   Plank JL, Hsieh TS
  TITLE     A novel, topologically constrained DNA molecule containing a double 
            Holliday junction: design, synthesis, and initial biochemical 
            characterization.
  JOURNAL   J Biol Chem. 2006 Jun 23;281(25):17510-6. Epub 2006 Apr 11.
  PUBMED    16608853
REFERENCE   2  (bases 1 to 3406)
  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: "J Biol 
            Chem."; date: "2006-06-23"; volume: "281(25)"; pages: "17510-6. Epub
            2006 Apr 11"
COMMENT     Sequence Label: pDHJS3 AN-
FEATURES             Location/Qualifiers
     source          1..3406
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     rep_origin      7..462
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(94..113)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     304..325
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     588..610
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     602..619
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     603..619
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     626..645
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        626..644
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     primer_bind     669..685
                     /label=pBluescriptKS
                     /note="For pBluescript vector"
     primer_bind     670..686
                     /label=KS primer
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     protein_bind    complement(700..733)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     protein_bind    complement(1164..1197)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     promoter        complement(1221..1239)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(1260..1276)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1260..1276)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(1273..1295)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    1284..1300
                     /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(1308..1314,1315..1332,1333..1338))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1353..1374
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(1491..1508)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(1662..2250)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(1742..1761)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2421..3212,3213..3281))
                     /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     3044..3063
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(3282..3386)
                     /gene="bla"
                     /label=AmpR promoter
ORIGIN
        1 cacctgacgc gccctgtagc ggcgcattaa gcgcggcggg tgtggtggtt acgcgcagcg
       61 tgaccgctac acttgccagc gccctagcgc ccgctccttt cgctttcttc ccttcctttc
      121 tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg ggggctccct ttagggttcc
      181 gatttagtgc tttacggcac ctcgacccca aaaaacttga ttagggtgat ggttcacgta
      241 gtgggccatc gccctgatag acggtttttc gccctttgac gttggagtcc acgttcttta
      301 atagtggact cttgttccaa actggaacaa cactcaaccc tatctcggtc tattcttttg
      361 atttataagg gattttgccg atttcggcct attggttaaa aaatgagctg atttaacaaa
      421 aatttaacgc gaattttaac aaaatattaa cgcttacaat ttccattcgc cattcaggct
      481 gcgcaactgt tgggaagggc gatcggtgcg ggcctcttcg ctattacgcc agctggcgaa
      541 agggggatgt gctgcaaggc gattaagttg ggtaacgcca gggttttccc agtcacgacg
      601 ttgtaaaacg acggccagtg aattgtaata cgactcacta tagggcgaat tgggtaccgg
      661 gccccccctc gaggtcgacg gtatcgataa gctagatcta taacttcgta tagcatacat
      721 tatacgaagt tatgaattca ggaccttgaa cgcgaggtgc gcggctgtca ggattacgcg
      781 tgattatctg gccgggctac tcggtgtaca acaaggtctt cgatttcgag gcccctgtgc
      841 gcggtcagaa tgccaaaatg gttatgacct ccgtatccgg ccacatgatg cagctggcat
      901 tccaggtgtc ttacaaaaat tggagaacgg tggatccgcg ctctttattc gacgcgccgg
      961 tggaaaaggg cgtgggctcg gattatgagc ctatcaaaag gaccttggaa cgcgaggtgc
     1021 gcggctgtca gggattgatt atctggacgg attgcgatcg cgagggcgag aacattggct
     1081 acgagattat tgatgtgcgg ccgcatccga gccattggaa gattaggttc tgctagcgca
     1141 cacaattgat gacttgatct agaataactt cgtatagcat acattatacg aagttatcat
     1201 atgagctcca gcttttgttc cctttagtga gggttaattt cgagcttggc gtaatcatgg
     1261 tcatagctgt ttcctgtgtg aaattgttat ccgctcacaa ttccacacaa catacgagcc
     1321 ggaagcataa agtgtaaagc ctggggtgcc taatgagtga gctaactcac attaattgcg
     1381 ttgcgctcac tgcccgcttt ccagtcggga aacctgtcgt gccagctgca ttaatgaatc
     1441 ggccaacgcg cggggagagg cggtttgcgt attgggcgct cttccgcttc ctcgctcact
     1501 gactcgctgc gctcggtcgt tcggctgcgg cgagcggtat cagctcactc aaaggcggta
     1561 atacggttat ccacagaatc aggggataac gcaggaaaga acatgtgagc aaaaggccag
     1621 caaaaggcca ggaaccgtaa aaaggccgcg ttgctggcgt ttttccatag gctccgcccc
     1681 cctgacgagc atcacaaaaa tcgacgctca agtcagaggt ggcgaaaccc gacaggacta
     1741 taaagatacc aggcgtttcc ccctggaagc tccctcgtgc gctctcctgt tccgaccctg
     1801 ccgcttaccg gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc
     1861 tcacgctgta ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac
     1921 gaaccccccg ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac
     1981 ccggtaagac acgacttatc gccactggca gcagccactg gtaacaggat tagcagagcg
     2041 aggtatgtag gcggtgctac agagttcttg aagtggtggc ctaactacgg ctacactaga
     2101 aggacagtat ttggtatctg cgctctgctg aagccagtta ccttcggaaa aagagttggt
     2161 agctcttgat ccggcaaaca aaccaccgct ggtagcggtg gtttttttgt ttgcaagcag
     2221 cagattacgc gcagaaaaaa aggatctcaa gaagatcctt tgatcttttc tacggggtct
     2281 gacgctcagt ggaacgaaaa ctcacgttaa gggattttgg tcatgagatt atcaaaaagg
     2341 atcttcacct agatcctttt aaattaaaaa tgaagtttta aatcaatcta aagtatatat
     2401 gagtaaactt ggtctgacag ttaccaatgc ttaatcagtg aggcacctat ctcagcgatc
     2461 tgtctatttc gttcatccat agttgcctga ctccccgtcg tgtagataac tacgatacgg
     2521 gagggcttac catctggccc cagtgctgca atgataccgc gagacccacg ctcaccggct
     2581 ccagatttat cagcaataaa ccagccagcc ggaagggccg agcgcagaag tggtcctgca
     2641 actttatccg cctccatcca gtctattaat tgttgccggg aagctagagt aagtagttcg
     2701 ccagttaata gtttgcgcaa cgttgttgcc attgctacag gcatcgtggt gtcacgctcg
     2761 tcgtttggta tggcttcatt cagctccggt tcccaacgat caaggcgagt tacatgatcc
     2821 cccatgttgt gcaaaaaagc ggttagctcc ttcggtcctc cgatcgttgt cagaagtaag
     2881 ttggccgcag tgttatcact catggttatg gcagcactgc ataattctct tactgtcatg
     2941 ccatccgtaa gatgcttttc tgtgactggt gagtactcaa ccaagtcatt ctgagaatag
     3001 tgtatgcggc gaccgagttg ctcttgcccg gcgtcaatac gggataatac cgcgccacat
     3061 agcagaactt taaaagtgct catcattgga aaacgttctt cggggcgaaa actctcaagg
     3121 atcttaccgc tgttgagatc cagttcgatg taacccactc gtgcacccaa ctgatcttca
     3181 gcatctttta ctttcaccag cgtttctggg tgagcaaaaa caggaaggca aaatgccgca
     3241 aaaaagggaa taagggcgac acggaaatgt tgaatactca tactcttcct ttttcaatat
     3301 tattgaagca tttatcaggg ttattgtctc atgagcggat acatatttga atgtatttag
     3361 aaaaataaac aaataggggt tccgcgcaca tttccccgaa aagtgc
//
