LOCUS       sequence-260083-        4851 bp    DNA     circular SYN 15-DEC-2025
DEFINITION  pDX_init plasmid containing a loop Sybody for the generation of a 
            qPCR standard curve.
ACCESSION   .
VERSION     .
KEYWORDS    .
SOURCE      synthetic DNA construct
  ORGANISM  synthetic DNA construct
REFERENCE   1  (bases 1 to 4851)
  AUTHORS   Zimmermann I, Egloff P, Hutter CAJ, Kuhn BT, Brauer P, Newstead S, 
            Dawson RJP, Geertsma ER, Seeger MA
  TITLE     Generation of synthetic nanobodies against delicate proteins.
  JOURNAL   Nat Protoc. 2020 Apr 8. pii: 10.1038/s41596-020-0304-x. doi: 
            10.1038/s41596-020-0304-x.
  PUBMED    32269381
REFERENCE   2  (bases 1 to 4851)
  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: "Nat Protoc.
            2020 Apr 8. pii: 10.1038/s41596-020-0304-x. doi: 
            10.1038/s41596-020-0304-x."
COMMENT     Sequence Label: pDX_init containing Sb-loop
FEATURES             Location/Qualifiers
     source          1..4851
                     /mol_type="other DNA"
                     /organism="synthetic DNA construct"
     sig_peptide     21..86
                     /codon_start=1
                     /gene="pelB (fragment)"
                     /product="leader peptide for secretion"
                     /label=pelB signal sequence
                     /translation="MKYLLPTAAAGLLLLAAQPAMA"
     CDS             474..491
                     /codon_start=1
                     /product="6xHis affinity tag"
                     /label=6xHis
                     /translation="HHHHHH"
     primer_bind     complement(1776..1793)
                     /label=M13 Forward
                     /note="In lacZ gene. Also called M13-F20 or M13 (-21) 
                     Forward"
     primer_bind     complement(1776..1792)
                     /label=M13 fwd
                     /note="common sequencing primer, one of multiple similar 
                     variants"
     primer_bind     complement(1785..1807)
                     /label=M13/pUC Forward
                     /note="In lacZ gene"
     rep_origin      2005..2460
                     /direction=RIGHT
                     /label=f1 ori
                     /note="f1 bacteriophage origin of replication; arrow 
                     indicates direction of (+) strand synthesis"
     primer_bind     complement(2092..2111)
                     /label=F1ori-R
                     /note="F1 origin, reverse primer"
     primer_bind     2302..2323
                     /label=F1ori-F
                     /note="F1 origin, forward primer"
     primer_bind     complement(2477..2496)
                     /label=pRS-marker
                     /note="pRS vectors, use to sequence yeast selectable 
                     marker"
     primer_bind     2596..2618
                     /label=pGEX 3'
                     /note="pGEX vectors, reverse primer"
     primer_bind     complement(2656..2674)
                     /label=pBRforEco
                     /note="pBR322 vectors, upsteam of EcoRI site, forward 
                     primer"
     promoter        2742..2846
                     /gene="bla"
                     /label=AmpR promoter
     CDS             join(2847..2915,2916..3707)
                     /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     complement(3065..3084)
                     /label=Amp-R
                     /note="Ampicillin resistance gene, reverse primer"
     rep_origin      3878..4466
                     /direction=RIGHT
                     /label=ori
                     /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of 
                     replication"
     primer_bind     4367..4386
                     /label=pBR322ori-F
                     /note="pBR322 origin, forward primer"
     primer_bind     4620..4637
                     /label=L4440
                     /note="L4440 vector, forward primer"
     protein_bind    4754..4775
                     /label=CAP binding site
                     /bound_moiety="E. coli catabolite activator protein"
                     /note="CAP binding activates transcription in the presence 
                     of cAMP."
     promoter        join(4790..4795,4796..4813,4814..4820)
                     /label=lac promoter
                     /note="promoter for the E. coli lac operon"
     protein_bind    4828..4844
                     /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)."
ORIGIN
        1 agcttaagga gacagtacat atgaaatacc tattgcctac ggcagccgct ggattgttat
       61 tactcgcggc ccagccggcc atggcagccg gctcttcaag tcaggttcag ctggttgaga
      121 gcggtggtgg cctggtccaa gctggcggtt cgctgcgtct gagctgcgcc gcaagcggtt
      181 tcccggtgag cagcagcacg atgacctggt atcgtcaggc accgggcaaa gaacgtgagt
      241 gggtcgcggc gatttccagc tctggtagca ccacgaccta cgcagattct gttaagggcc
      301 gctttaccat cagccgcgac aacgcgaaga atacggtcta tttgcagatg aatagcctga
      361 aaccggaaga taccgcggtt tactactgta acgtgaaaga cagcggtagc tccagcagct
      421 cctacgacta ttggggccaa ggtacccaag tgactgtgag cgcaggaaga gctcaccacc
      481 atcaccatca cgaacctgaa gcccagtacc cgtacgacgt tccggactac ggttccactg
      541 ttgaaagttg tttagcaaaa cctcatacag aaaattcatt tactaacgtc tggaaagacg
      601 acaaaacttt agatcgttac gctaactatg agggctgtct gtggaatgct acaggcgttg
      661 tcgtttgtac tggtgacgaa actcagtgtt acggtacatg ggttcctatt gggcttgcta
      721 tccctgaaaa tgagggtggt ggctctgagg gtggcggttc tgagggtggc ggttctgagg
      781 gtggcggtac taaacctcct gagtacggtg atacacctat tccgggctat acttatatca
      841 accctctcga cggcacttat ccgcctggta ctgagcaaaa ccccgctaat cctaatcctt
      901 ctcttgagga gtctcagcct cttaatactt tcatgtttca gaataatagg ttccgaaata
      961 ggcagggtgc attaactgtt tatacgggca ctgttactca aggcactgac cccgttaaaa
     1021 cttattacca gtacactcct gtatcatcaa aagccatgta tgacgcttac tggaacggta
     1081 aattcagaga ctgcgctttc cattctggct ttaatgagga tccattcgtt tgtgaatatc
     1141 aaggccaatc gtctgacctg cctcaacctc ctgtcaatgc tggcggcggc tctggtggtg
     1201 gttctggtgg cggctctgag ggtggcggct ctgagggtgg cggctctgag ggtggcggtt
     1261 ctgagggtgg cggctctgag ggtggcggtt ccggtggcgg ctccggttcc ggtgattttg
     1321 attatgaaaa aatggcaaac gctaataagg gggctatgac cgaaaatgcc gatgaaaacg
     1381 cgctacagtc tgacgctaaa ggcaaacttg attctgtcgc tactgattac ggtgctgcta
     1441 tcgatggttt cattggtgac gtttccggcc ttgctaatgg taatggtgct actggtgatt
     1501 ttgctggctc taattcccaa atggctcaag tcggtgacgg tgataattca cctttaatga
     1561 ataatttccg tcaatattta ccttctttac ctcagtcggt tgaatgtcgc ccttatgtct
     1621 ttggcgctgg taaaccatat gaattttcta ttgattgtga caaaataaac ttattccgtg
     1681 gtgtctttgc gtttctttta tatgttgcca cctttatgta tgtattttcg acgtttgcta
     1741 acatactgcg taataaggag tcttaataag aattcactgg ccgtcgtttt acaacgtcgt
     1801 gactgggaaa accctggcgt tacccaactt aatcgccttg cagcacatcc ccctttcgcc
     1861 agctggcgta atagcgaaga ggcccgcacc gatcgccctt cccaacagtt gcgcagcctg
     1921 aatggcgaat ggcgcctgat gcggtatttt ctccttacgc atctgtgcgg tatttcacac
     1981 cgcatacgtc aaagcaacca tagtacgcgc cctgtagcgg cgcattaagc gcggcgggtg
     2041 tggtggttac gcgcagcgtg accgctacac ttgccagcgc cttagcgccc gctcctttcg
     2101 ctttcttccc ttcctttctc gccacgttcg ccggctttcc ccgtcaagct ctaaatcggg
     2161 ggctcccttt agggttccga tttagtgctt tacggcacct cgaccccaaa aaacttgatt
     2221 tgggtgatgg ttcacgtagt gggccatcgc cctgatagac ggtttttcgc cctttgacgt
     2281 tggagtccac gttctttaat agtggactct tgttccaaac tggaacaaca ctcaactcta
     2341 tctcgggcta ttcttttgat ttataaggga ttttgccgat ttcggtctat tggttaaaaa
     2401 atgagctgat ttaacaaaaa tttaacgcga attttaacaa aatattaacg tttacaattt
     2461 tatggtgcac tctcagtaca atctgctctg atgccgcata gttaagccag ccccgacacc
     2521 cgccaacacc cgctgacgcg ccctgacggg cttgtctgct cccggcatcc acttacagac
     2581 aagctgtgac cgtctccggg agctgcatgt gtcagaggtt ttcaccgtca tcaccgaaac
     2641 gcgcgagacg aaagggcctc gtgatacgcc tatttttata ggttaatgtc atgataataa
     2701 tggtttctta gacgtcaggt ggcacttttc ggggaaatgt gcgcggaacc cctatttgtt
     2761 tatttttcta aatacattca aatatgtatc cgctcatgag acaataaccc tgataaatgc
     2821 ttcaataata ttgaaaaagg aagagtatga gtattcaaca tttccgtgtc gcccttattc
     2881 ccttttttgc ggcattttgc cttcctgttt ttgctcaccc agaaacgctg gtgaaagtaa
     2941 aagatgctga agatcagttg ggtgcacgag tgggttacat cgaactggat ctcaacagcg
     3001 gtaagatcct tgagagtttt cgccccgaag aacgttttcc aatgatgagc acttttaaag
     3061 ttctgctatg tggcgcggta ttatcccgta ttgacgccgg gcaagagcaa ctcggtcgcc
     3121 gcatacacta ttctcagaat gacttggttg agtactcacc agtcacagaa aagcatctta
     3181 cggatggcat gacagtaaga gaattatgca gtgctgccat aaccatgagt gataacactg
     3241 cggccaactt acttctgaca acgatcggag gaccgaagga gctaaccgct tttttgcaca
     3301 acatggggga tcatgtaact cgccttgatc gttgggaacc ggagctgaat gaagccatac
     3361 caaacgacga gcgtgacacc acgatgcctg tagcaatggc aacaacgttg cgcaaactat
     3421 taactggcga actacttact ctagcttccc ggcaacaatt aatagactgg atggaggcgg
     3481 ataaagttgc aggaccactt ctgcgctcgg cccttccggc tggctggttt attgctgata
     3541 aatctggagc cggtgagcgt gggtctcgcg gtatcattgc agcactgggg ccagatggta
     3601 agccctcccg tatcgtagtt atctacacga cggggagtca ggcaactatg gatgaacgaa
     3661 atagacagat cgctgagata ggtgcctcac tgattaagca ttggtaactg tcagaccaag
     3721 tttactcata tatactttag attgatttaa aacttcattt ttaatttaaa aggatctagg
     3781 tgaagatcct ttttgataat ctcatgacca aaatccctta acgtgagttt tcgttccact
     3841 gagcgtcaga ccccgtagaa aagatcaaag gatcttcttg agatcctttt tttctgcgcg
     3901 taatctgctg cttgcaaaca aaaaaaccac cgctaccagc ggtggtttgt ttgccggatc
     3961 aagagctacc aactcttttt ccgaaggtaa ctggcttcag cagagcgcag ataccaaata
     4021 ctgttcttct agtgtagccg tagttaggcc actacttcaa gaactctgta gcaccgccta
     4081 catacctcgc actgctaatc ctgttaccag tggctgctgc cagtggcgat aagtcgtgtc
     4141 ttaccgggtt ggactcaaga cgatagttac cggataaggc gcagcggtcg ggctgaacgg
     4201 ggggttcgtg cacacagccc agcttggagc gaacgaccta caccgaactg agatacctac
     4261 agcgtgagct atgagaaagc gccacgcttc ccgaagggag aaaggcggac aggtatccgg
     4321 taagcggcag ggtcggaaca ggagagcgca cgagggagct tccaggggga aacgcctggt
     4381 atctttatag tcctgtcggg tttcgccacc tctgacttga gcgtcgattt ttgtgatgct
     4441 cgtcaggggg gcggagccta tggaaaaacg ccagcaacgc ggccttttta cggttcctgg
     4501 ccttttgctg gccttttgct cacatgttct ttcctgcgtt atcccctgat tctgtggata
     4561 accgtattac cgcctttgag tgagctgata ccgctcgccg cagccgaacg accgagcgca
     4621 gcgagtcagt gagcgaggaa gcggaagaga gcccaatacg caaaccgcct ctccccgcgc
     4681 gttggccgat tcattaatgc agctggcacg acaggtttcc cgactggaaa gcgggcagtg
     4741 agcgcaacgc aattaatgtg agttagctca ctcattaggc accccaggct ttacacttta
     4801 tgcttccggc tcgtatgttg tgtggaattg tgagcggata acaatttcac a
//
