LOCUS       sequence-332708-        4975 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  Force-activating hairpin for 3'-to-5' helicase.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 4975)
  AUTHORS   Taylor AMK, Okoniewski SR, Uyetake L, Perkins TT
  TITLE     Force-Activated DNA Substrates for In Situ Generation of ssDNA and 
            Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay.
  JOURNAL   Methods Mol Biol. 2022;2478:273-312. doi: 
            10.1007/978-1-0716-2229-2_10.
  PUBMED    36063324
REFERENCE   2  (bases 1 to 4975)
  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: "Methods Mol
            Biol."; date: "2022"; volume: "2478:273-312. doi"; pages: " 
            10.1007/978-1-0716-2229-2_10"
COMMENT     Sequence Label: hp-50%GC-Left-half-120bp
FEATURES             Location/Qualifiers
     source          1..4975
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     primer_bind     16..38
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     primer_bind     30..47
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     31..47
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     54..73
                     /label=T7
                     /note="T7 promoter, forward primer"
     promoter        54..72
                     /label=T7 promoter
                     /note="promoter for bacteriophage T7 RNA polymerase"
     rep_origin      972..1352
                     /direction=RIGHT
                     /label=M13 ori
                     /note="M13 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(1059..1078)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     1269..1290
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(1715..1731)
                     /label=M13 rev
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1715..1731)
                     /label=M13 Reverse
                     /note="In lacZ gene. Also called M13-rev"
     primer_bind     complement(1728..1750)
                     /label=M13/pUC Reverse
                     /note="In lacZ gene"
     protein_bind    1739..1755
                     /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(1763..1769,1770..1787,1788..1793))
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    1808..1829
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     primer_bind     complement(1946..1963)
                     /label=L4440
                     /note="L4440 vector, forward primer"
     rep_origin      complement(2117..2705)
                     /direction=LEFT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     complement(2197..2216)
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     CDS             complement(2843..3217)
                     /codon_start=1
                     /gene="Sh ble from Streptoalloteichus hindustanus"
                     /product="antibiotic-binding protein"
                     /label=BleoR
                     /note="confers resistance to bleomycin, phleomycin, and 
                     Zeocin(TM)"
                     /translation="MAKLTSAVPVLTARDVAGAVEFWTDRLGFSRDFVEDDFAGVVRDD
                     VTLFISAVQDQVVPDNTLAWVWVRGLDELYAEWSEVVSTNFRDASGPAMTEIGEQPWGR
                     EFALRDPAGNCVHFVAEEQD"
     regulatory      3214..3223
                     /label=Kozak sequence
                     /note="vertebrate consensus sequence for strong initiation 
                     of translation (Kozak, 1987)"
                     /regulatory_class="other"
     CDS             complement(3423..4217)
                     /codon_start=1
                     /product="aminoglycoside phosphotransferase"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     CDS             complement(3423..4217)
                     /codon_start=1
                     /gene="aph(3')-II (or nptII)"
                     /product="aminoglycoside phosphotransferase from Tn5"
                     /label=NeoR/KanR
                     /note="confers resistance to neomycin, kanamycin, and G418 
                     (Geneticin(R))"
                     /translation="MIEQDGLHAGSPAAWVERLFGYDWAQQTIGCSDAAVFRLSAQGRP
                     VLFVKTDLSGALNELQDEAARLSWLATTGVPCAAVLDVVTEAGRDWLLLGEVPGQDLLS
                     SHLAPAEKVSIMADAMRRLHTLDPATCPFDHQAKHRIERARTRMEAGLVDQDDLDEEHQ
                     GLAPAELFARLKASMPDGEDLVVTHGDACLPNIMVENGRFSGFIDCGRLGVADRYQDIA
                     LATRDIAEELGGEWADRFLVLYGIAAPDSQRIAFYRLLDEFF"
     primer_bind     complement(3534..3553)
                     /label=Neo-F
                     /note="Neomycin resistance gene, forward primer"
     primer_bind     4144..4163
                     /label=Neo-R
                     /note="Neomycin resistance gene, reverse primer"
     CDS             complement(4566..4868)
                     /codon_start=1
                     /gene="ccdB"
                     /product="CcdB, a bacterial toxin that poisons DNA gyrase"
                     /label=ccdB
                     /note="Plasmids containing the ccdB gene cannot be 
                     propagated in standard E. coli strains."
                     /translation="QFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKV
                     SRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI"
     primer_bind     complement(4668..4687)
                     /label=ccdB-fwd
                     /note="ccdB gene, forward primer"
ORIGIN
        1 taacgccagg gttttcccag tcacgacgtt gtaaaacgac ggccagtgaa ttgtaatacg
       61 actcactata gggcgaattg ggccctctag atgcatgctc gagcggccgc cagtgtgatg
      121 gatatctgca gaattcgccc tttcaataat cggctgtctt tccttatcat tccttctaaa
      181 tcctcaaatg tattatctat tgacggctct aatctattag ttgttagtgc tcctaaagat
      241 attttagata accttcctca attcctttca actgttgatt tgccaactga ccagatattg
      301 attgagggtt tgatatttga ggttcagcaa ggtgatgctt tagatttttc atttgctgct
      361 ggctctcagc gtggcactgt tgcaggcggt gttaatactg accgcctcac ctctgtttta
      421 tcttctgctg gtggttcgtt cggtattttt aatggcgatg ttttagggct atcagttcgc
      481 gcattaaaga ctaatagcca ttcaaaaata ttgtctgtgc cacgtattct tacgctttca
      541 ggtcagaagg gttctatctc tgttggccag aatgtccctt ttattactgg tcgtgtgact
      601 ggtgaatctg ccaatgtaaa taatccattt cagacgattg agcgtcaaaa tgtaggtatt
      661 tccatgagcg tttttcctgt tgcaatggct ggcggtaata ttgttctgga tattaccagc
      721 aaggccgata gtttgagttc ttctactcag gcaagtgatg ttattactaa tcaaagaagt
      781 attgctacaa cggttaattt gcgtgatgga cagactcttt tactcggtgg cctcactgat
      841 tataaaaaca cttctcagga ttctggcgta ccgttcctgt ctaaaatccc tttaatcggc
      901 ctcctgttta gctcccgctc tgattctaac gaggaaagca cgttatacgt gctcgtcaaa
      961 gcaaccatag tacgcgccct gtagcggcgc attaagcgcg gcgggtgtgg tggttacgcg
     1021 cagcgtgacc gctacacttg ccagcgccct agcgcccgct cctttcgctt tcttcccttc
     1081 ctttctcgcc acgttcgccg gctttccccg tcaagctcta aatcgggggc tccctttagg
     1141 gttccgattt agtgctttac ggcacctcga ccccaaaaaa cttgatttgg gtgatggttc
     1201 acgtagtggg ccatcgccct gatagacggt ttttcgccct ttgacgttgg agtccacgtt
     1261 ctttaatagt ggactcttgt tccaaactgg aacaacactc aaccctatct cgggctattc
     1321 ttttgattta taagggattt tgccgatttc ggaaccacca tcaaacagga ttttcgcctg
     1381 ctggggcaaa ccagcgtgga ccgcttgctg caactctctc agcgggcacg gccaggctcc
     1441 cgccctcagc atttactctg gtcacaggta tgcagctaca gtcaagcagt gaagcaagat
     1501 gtcactcttg atgagagtcg accagctcat gctcgtctag atcgactgac gtacgagtca
     1561 acgtctggat ccatttttat ggatcgatga agggcgaatt ctgcagatat ccatcacact
     1621 ggcggccgtt actagtggat ccgagctcgg taccaagctt gatgcatagc ttgagtattc
     1681 taacgcgtca cctaaatagc ttggcgtaat catggtcata gctgtttcct gtgtgaaatt
     1741 gttatccgct cacaattcca cacaacatac gagccggaag cataaagtgt aaagcctggg
     1801 gtgcctaatg agtgagctaa ctcacattaa ttgcgttgcg ctcactgccc gctttccagt
     1861 cgggaaacct gtcgtgccag ctgcattaat gaatcggcca acgcgcgggg agaggcggtt
     1921 tgcgtattgg gcgctcttcc gcttcctcgc tcactgactc gctgcgctcg gtcgttcggc
     1981 tgcggcgagc ggtatcagct cactcaaagg cggtaatacg gttatccaca gaatcagggg
     2041 ataacgcagg aaagaacatg tgagcaaaag gccagcaaaa ggccaggaac cgtaaaaagg
     2101 ccgcgttgct ggcgtttttc cataggctcc gcccccctga cgagcatcac aaaaatcgac
     2161 gctcaagtca gaggtggcga aacccgacag gactataaag ataccaggcg tttccccctg
     2221 gaagctccct cgtgcgctct cctgttccga ccctgccgct taccggatac ctgtccgcct
     2281 ttctcccttc gggaagcgtg gcgctttctc atagctcacg ctgtaggtat ctcagttcgg
     2341 tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc ccccgttcag cccgaccgct
     2401 gcgccttatc cggtaactat cgtcttgagt ccaacccggt aagacacgac ttatcgccac
     2461 tggcagcagc cactggtaac aggattagca gagcgaggta tgtaggcggt gctacagagt
     2521 tcttgaagtg gtggcctaac tacggctaca ctagaagaac agtatttggt atctgcgctc
     2581 tgctgaagcc agttaccttc ggaaaaagag ttggtagctc ttgatccggc aaacaaacca
     2641 ccgctggtag cggtggtttt tttgtttgca agcagcagat tacgcgcaga aaaaaaggat
     2701 ctcaagaaga tcctttgatc ttttctacgg ggtctgacgc tcagtggaac gaaaactcac
     2761 gttaagggat tttggtcatg agattatcaa aaaggatctt cacctagatc cttttaaatt
     2821 aaaaatgaag ttttagcacg tgtcagtcct gctcctcggc cacgaagtgc acgcagttgc
     2881 cggccgggtc gcgcagggcg aactcccgcc cccacggctg ctcgccgatc tcggtcatgg
     2941 ccggcccgga ggcgtcccgg aagttcgtgg acacgacctc cgaccactcg gcgtacagct
     3001 cgtccaggcc gcgcacccac acccaggcca gggtgttgtc cggcaccacc tggtcctgga
     3061 ccgcgctgat gaacagggtc acgtcgtccc ggaccacacc ggcgaagtcg tcctccacga
     3121 agtcccggga gaacccgagc cggtcggtcc agaactcgac cgctccggcg acgtcgcgcg
     3181 cggtgagcac cggaacggca ctggtcaact tggccatggt ggccctcctc acgtgctatt
     3241 attgaagcat ttatcagggt tattgtctca tgagcggata catatttgaa tgtatttaga
     3301 aaaataaaca aataggggtt ccgcgcacat ttccccgaaa agtgccacct gatgcggtgt
     3361 gaaataccgc acagatgcgt aaggagaaaa taccgcatca ggaaattgta agcgttaata
     3421 attcagaaga actcgtcaag aaggcgatag aaggcgatgc gctgcgaatc gggagcggcg
     3481 ataccgtaaa gcacgaggaa gcggtcagcc cattcgccgc caagctcttc agcaatatca
     3541 cgggtagcca acgctatgtc ctgatagcgg tccgccacac ccagccggcc acagtcgatg
     3601 aatccagaaa agcggccatt ttccaccatg atattcggca agcaggcatc gccatgggtc
     3661 acgacgagat cctcgccgtc gggcatgctc gccttgagcc tggcgaacag ttcggctggc
     3721 gcgagcccct gatgctcttc gtccagatca tcctgatcga caagaccggc ttccatccga
     3781 gtacgtgctc gctcgatgcg atgtttcgct tggtggtcga atgggcaggt agccggatca
     3841 agcgtatgca gccgccgcat tgcatcagcc atgatggata ctttctcggc aggagcaagg
     3901 tgagatgaca ggagatcctg ccccggcact tcgcccaata gcagccagtc ccttcccgct
     3961 tcagtgacaa cgtcgagcac agctgcgcaa ggaacgcccg tcgtggccag ccacgatagc
     4021 cgcgctgcct cgtcttgcag ttcattcagg gcaccggaca ggtcggtctt gacaaaaaga
     4081 accgggcgcc cctgcgctga cagccggaac acggcggcat cagagcagcc gattgtctgt
     4141 tgtgcccagt catagccgaa tagcctctcc acccaagcgg ccggagaacc tgcgtgcaat
     4201 ccatcttgtt caatcatgcg aaacgatcct catcctgtct cttgatcaga gcttgatccc
     4261 ctgcgccatc agatccttgg cggcaagaaa gccatccagt ttactttgca gggcttccca
     4321 accttaccag agggcgcccc agctggcaat tccggttcgc ttgctgtcca taaaaccgcc
     4381 cagtctagct atcgccatgt aagcccactg caagctacct gctttctctt tgcgcttgcg
     4441 ttttcccttg tccagatagc ccagtagctg acattcatcc ggggtcagca ccgtttctgc
     4501 ggactggctt tctacgtgaa aaggatctag gtgaagatcc tttttgataa tctcatgcct
     4561 gacatttata ttccccagaa catcaggtta atggcgtttt tgatgtcatt ttcgcggtgg
     4621 ctgagatcag ccacttcttc cccgataacg gagaccggca cactggccat atcggtggtc
     4681 atcatgcgcc agctttcatc cccgatatgc accaccgggt aaagttcacg ggagacttta
     4741 tctgacagca gacgtgcact ggccaggggg atcaccatcc gtcgccccgg cgtgtcaata
     4801 atatcactct gtacatccac aaacagacga taacggctct ctcttttata ggtgtaaacc
     4861 ttaaactgcc gtacgtatag gctgcgcaac tgttgggaag ggcgatcggt gcgggcctct
     4921 tcgctattac gccagctggc gaaaggggga tgtgctgcaa ggcgattaag ttggg
//
