LOCUS       sequence-160572-        3407 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  One of four plasmids needed to create the double Holliday junction 
            substrate (DHJS)..
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 3407)
  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 3407)
  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 AS-
FEATURES             Location/Qualifiers
     source          1..3407
                     /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(1165..1198)
                     /label=loxP
                     /bound_moiety="Cre recombinase"
                     /note="Cre-mediated recombination occurs in the 8-bp core 
                     sequence (ATGTATGC) (Shaw et al., 2021)."
     promoter        complement(1222..1240)
                     /label=T3 promoter
                     /note="promoter for bacteriophage T3 RNA polymerase"
     primer_bind     complement(1261..1277)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1261..1277)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(1274..1296)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    1285..1301
                     /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(1309..1315,1316..1333,1334..1339))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1354..1375
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(1492..1509)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(1663..2251)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(1743..1762)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(join(2422..3213,3214..3282))
                     /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     3045..3064
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     promoter        complement(3283..3387)
                     /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 gcccgggcta ctcggtgtac aacaaggtct tcgatttcga ggcccctgtg
      841 cgcggtcaga atgccaaaat ggttatgacc tccgtatccg gccacatgat gcagctggca
      901 ttccaggtgt cttacaaaaa ttggagaacg gtggatccgc gctctttatt cgacgcgccg
      961 gtggaaaagg gcgtgggctc ggattatgag cctatcaaaa ggaccttgga acgcgaggtg
     1021 cgcggctgtc agggattgat tatctggacg gattgcgatc gcgagggcga gaacattggc
     1081 tacgagatta ttgatgtgcg gccgcatccg agccattgga agattaggtt ctgcatgcgc
     1141 acacaattga tgacttgatc tagaataact tcgtatagca tacattatac gaagttatca
     1201 tatgagctcc agcttttgtt ccctttagtg agggttaatt tcgagcttgg cgtaatcatg
     1261 gtcatagctg tttcctgtgt gaaattgtta tccgctcaca attccacaca acatacgagc
     1321 cggaagcata aagtgtaaag cctggggtgc ctaatgagtg agctaactca cattaattgc
     1381 gttgcgctca ctgcccgctt tccagtcggg aaacctgtcg tgccagctgc attaatgaat
     1441 cggccaacgc gcggggagag gcggtttgcg tattgggcgc tcttccgctt cctcgctcac
     1501 tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta tcagctcact caaaggcggt
     1561 aatacggtta tccacagaat caggggataa cgcaggaaag aacatgtgag caaaaggcca
     1621 gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg tttttccata ggctccgccc
     1681 ccctgacgag catcacaaaa atcgacgctc aagtcagagg tggcgaaacc cgacaggact
     1741 ataaagatac caggcgtttc cccctggaag ctccctcgtg cgctctcctg ttccgaccct
     1801 gccgcttacc ggatacctgt ccgcctttct cccttcggga agcgtggcgc tttctcatag
     1861 ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc tccaagctgg gctgtgtgca
     1921 cgaacccccc gttcagcccg accgctgcgc cttatccggt aactatcgtc ttgagtccaa
     1981 cccggtaaga cacgacttat cgccactggc agcagccact ggtaacagga ttagcagagc
     2041 gaggtatgta ggcggtgcta cagagttctt gaagtggtgg cctaactacg gctacactag
     2101 aaggacagta tttggtatct gcgctctgct gaagccagtt accttcggaa aaagagttgg
     2161 tagctcttga tccggcaaac aaaccaccgc tggtagcggt ggtttttttg tttgcaagca
     2221 gcagattacg cgcagaaaaa aaggatctca agaagatcct ttgatctttt ctacggggtc
     2281 tgacgctcag tggaacgaaa actcacgtta agggattttg gtcatgagat tatcaaaaag
     2341 gatcttcacc tagatccttt taaattaaaa atgaagtttt aaatcaatct aaagtatata
     2401 tgagtaaact tggtctgaca gttaccaatg cttaatcagt gaggcaccta tctcagcgat
     2461 ctgtctattt cgttcatcca tagttgcctg actccccgtc gtgtagataa ctacgatacg
     2521 ggagggctta ccatctggcc ccagtgctgc aatgataccg cgagacccac gctcaccggc
     2581 tccagattta tcagcaataa accagccagc cggaagggcc gagcgcagaa gtggtcctgc
     2641 aactttatcc gcctccatcc agtctattaa ttgttgccgg gaagctagag taagtagttc
     2701 gccagttaat agtttgcgca acgttgttgc cattgctaca ggcatcgtgg tgtcacgctc
     2761 gtcgtttggt atggcttcat tcagctccgg ttcccaacga tcaaggcgag ttacatgatc
     2821 ccccatgttg tgcaaaaaag cggttagctc cttcggtcct ccgatcgttg tcagaagtaa
     2881 gttggccgca gtgttatcac tcatggttat ggcagcactg cataattctc ttactgtcat
     2941 gccatccgta agatgctttt ctgtgactgg tgagtactca accaagtcat tctgagaata
     3001 gtgtatgcgg cgaccgagtt gctcttgccc ggcgtcaata cgggataata ccgcgccaca
     3061 tagcagaact ttaaaagtgc tcatcattgg aaaacgttct tcggggcgaa aactctcaag
     3121 gatcttaccg ctgttgagat ccagttcgat gtaacccact cgtgcaccca actgatcttc
     3181 agcatctttt actttcacca gcgtttctgg gtgagcaaaa acaggaaggc aaaatgccgc
     3241 aaaaaaggga ataagggcga cacggaaatg ttgaatactc atactcttcc tttttcaata
     3301 ttattgaagc atttatcagg gttattgtct catgagcgga tacatatttg aatgtattta
     3361 gaaaaataaa caaatagggg ttccgcgcac atttccccga aaagtgc
//
