DNA Oligomers

Cloning Primer

polA*

upstream: 5'- CGC ATC ATG CCA TGG GC AGC AGC CAT CAT CAT CAT CAT CAC AGC AGC GAA CGC GAA CAC GCG CAG ACC CCC GAG GAG–3´

NcoI site, 6xHis-Tag

downstream: 5'- CGG GAA TTC CAT ATG TCA CTT CGT GTC AAA CCA GTT CGG CCC CGT CCC -3' NdeI site

DNA / RNA Template Dependent Polymerase Activity:

Template MS2 DNA Sequence 50mer:

5’-ATC GCT CGA GAA CGC AAG TTC TTC AGC GAA AAG CAC GAC AGT GGT CGC TA

Primer MS2 3’-Primer: 5’-TAG CGA CCA CTG TCG TGC TT

Single Nucleotide Incorporation:

P F20H 3´ TA GGA GGA AGT CCT GGT TGC

T F33 5´ AAA TCA ACC XAT CCT CCT TCA GGA CCA ACG TAC

Modifications with DNA Lesions:

- abasic site

P F20H 3´ TA GGA GGA AGT CCT GGT TGC

7. Appendix

P F23 3´ GG ATA GGA GGA AGT CCT GGT TGC

T F33as 5´ AAA TCA aCC TAT CCT CCT TCA GGA CCA ACG TAC

- 8-oxoG/8-oxoA

P: F20H 3´ TA GGA GGA AGT CCT GGT TGC

T: F33O 5´ AAA TOA ACC TAT CCT CCT TCA GGA CCA ACG TAC

P: F25 3´ T TGG ATA GGA GGA AGT CCT GGT TGC

T: F33O 5´ AAA TOA ACC TAT CCT CCT TCA GGA CCA ACG TAC

Remote Mismatch

+1

P F20H 3´ TA GGA GGA AGT CCT GGT TGC

T F33 5´ AAA TCA ACC AXT CCT CCT TCA GGA CCA ACG TAC

+2

P F20H 3´ TA GGA GGA AGT CCT GGT TGC

T F33 5´ AAA TCA ACC AAX CCT CCT TCA GGA CCA ACG TAC

+3

P F20H 3´ TA GGA GGA AGT CCT GGT TGC

T F33 5´ AAA TCA ACC AAT XCT CCT TCA GGA CCA ACG TAC

+4

P F20H 3´ TA GGA GGA AGT CCT GGT TGC

T F33 5´ AAA TCA ACC AAT CXT CCT TCA GGA CCA ACG TAC

+5

P F20H 3´ TA GGA GGA AGT CCT GGT TGC

T F33 5´ AAA TCA ACC AAT CCX CCT TCA GGA CCA ACG TAC

7. Appendix

M13 Processivity

Primer: 5´ CCT TAG AAT CCT TGA AAA CAT AGC GA

Sequence 7249 bp

aatgctacta ctattagtag aattgatgcc accttttcag ctcgcgcccc aaatgaaaat tagctaaac aggttattga ccatttgcga aatgtatcta atggtcaaac taaatctact cgttcgcaga attgggaatc aactgttaca tggaatgaaa cttccagaca ccgtacttta gttgcatatt taaaacatgt tgagctacag caccagattc agcaattaag ctctaagcca tccgcaaaaa tgacctctta tcaaaaggag caattaaagg tactctctaa tcctgacctg ttggagtttg cttccggtct ggttcgcttt gaagctcgaa ttaaaacgcg atatttgaag tctttcgggc ttcctcttaa tctttttgat gcaatccgct ttgcttctga ctataatagt cagggtaaag acctgatttt tgatttatgg tcattctcgt tttctgaact gtttaaagca tttgaggggg attcaatgaa tatttatgac gattccgcag tattggacgc tatccagtct aaacatttta ctattacccc ctctggcaaa acttcttttg caaaagcctc tcgctatttt ggtttttatc gtcgtctggt aaacgagggt tatgatagtg ttgctcttac tatgcctcgt aattcctttt ggcgttatgt atctgcatta gttgaatgtg gtattcctaa atctcaactg atgaatcttt ctacctgtaa taatgttgtt ccgttagttc gttttattaa cgtagatttt tcttcccaac gtcctgactg gtataatgag ccagttctta aaatcgcata aggtaattca caatgattaa agttgaaatt aaaccatctc aagcccaatt tactactcgt tctggtgttc tcgtcagggc aagccttatt cactgaatga gcagctttgt tacgttgatt tgggtaatga atatccggtt cttgtcaaga ttactcttga tgaaggtcag ccagcctatg cgcctggtct gtacaccgtt catctgtcct ctttcaaagt tggtcagttc ggttccctta tgattgaccg tctgcgcctc gttccggcta agtaacatgg agcaggtcgc ggatttcgac acaatttatc aggcgatgat acaaatctcc gttgtacttt gtttcgcgct tggtataatc gctgggggtc aaagatgagt gttttagtgt attctttcgc ctctttcgtt ttaggttggt gccttcgtag tggcattacg tattttaccc gtttaatgga aacttcctca tgaaaaagtc tttagtcctc aaagcctctg tagccgttgc taccctcgtt ccgatgctgt ctttcgctgc tgagggtgac gatcccgcaa aagcggcctt taactccctg caagcctcag cgaccgaata tatcggttat gcgtgggcga tggttgttgt cattgtcggc gcaactatcg gtatcaagct gtttaagaaa ttcacctcga aagcaagctg ataaaccgat acaattaaag gctccttttg gagccttttt ttttggagat tttcaacgtg aaaaaattat tattcgcaat tcctttagtt gttcctttct attctcactc cgctgaaact gttgaaagtt gtttagcaaa accccataca gaaaattcat ttactaacgt ctggaaagac gacaaaactt tagatcgtta cgctaactat gagggttgtc tgtggaatgc tacaggcgtt gtagtttgta ctggtgacga aactcagtgt tacggtacat gggttcctat tgggcttgct atccctgaaa atgagggtgg tggctctgag ggtggcggtt ctgagggtgg cggttctgag ggtggcggta ctaaacctcc tgagtacggt gatacaccta ttccgggcta tacttatatc aaccctctcg acggcactta tccgcctggt actgagcaaa accccgctaa tcctaatcct tctcttgagg agtctcagcc tcttaatact ttcatgtttc agaataatag gttccgaaat aggcaggggg cattaactgt ttatacgggc actgttactc aaggcactga ccccgttaaa acttattacc agtacactcc tgtatcatca aaagccatgt atgacgctta ctggaacggt aaattcagag actgcgcttt ccattctggc tttaatgaag atccattcgt ttgtgaatat caaggccaat cgtctgacct gcctcaacct cctgtcaatg ctggcggcgg ctctggtggt ggttctggtg gcggctctga gggtggtggc tctgagggtg gcggttctga gggtggcggc tctgagggag gcggttccgg tggtggctct ggttccggtg attttgatta tgaaaagatg gcaaacgcta ataagggggc tatgaccgaa aatgccgatg aaaacgcgct acagtctgac gctaaaggca aacttgattc tgtcgctact gattacggtg ctgctatcga tggtttcatt ggtgacgttt ccggccttgc taatggtaat ggtgctactg gtgattttgc tggctctaat tcccaaatgg ctcaagtcgg tgacggtgat aattcacctt taatgaataa tttccgtcaa tatttacctt ccctccctca atcggttgaa tgtcgccctt ttgtctttag cgctggtaaa ccatatgaat tttctattga ttgtgacaaa ataaacttat tccgtggtgt ctttgcgttt cttttatatg ttgccacctt tatgtatgta ttttctacgt ttgctaacat actgcgtaat aaggagtctt aatcatgcca gttcttttgg gtattccgtt attattgcgt ttcctcggtt tccttctggt aactttgttc ggctatctgc ttacttttct taaaaagggc ttcggtaaga tagctattgc tatttcattg tttcttgctc ttattattgg gcttaactca attcttgtgg gttatctctc tgatattagc gctcaattac cctctgactt tgttcagggt gttcagttaa ttctcccgtc taatgcgctt ccctgttttt atgttattct ctctgtaaag gctgctattt tcatttttga cgttaaacaa aaaatcgttt cttatttgga ttgggataaa taatatggct gtttattttg taactggcaa attaggctct ggaaagacgc tcgttagcgt tggtaagatt caggataaaa ttgtagctgg gtgcaaaata gcaactaatc

7. Appendix

cctacgatga aaataaaaac ggcttgcttg ttctcgatga gtgcggtact tggtttaata cccgttcttg gaatgataag gaaagacagc cgattattga ttggtttcta catgctcgta aattaggatg ggatattatt tttcttgttc aggacttatc tattgttgat aaacaggcgc gttctgcatt agctgaacat gttgtttatt gtcgtcgtct ggacagaatt actttacctt ttgtcggtac tttatattct cttattactg gctcgaaaat gcctctgcct aaattacatg ttggcgttgt taaatatggc gattctcaat taagccctac tgttgagcgt tggctttata ctggtaagaa tttgtataac gcatatgata ctaaacaggc tttttctagt aattatgatt ccggtgttta ttcttattta acgccttatt tatcacacgg tcggtatttc aaaccattaa atttaggtca gaagatgaaa ttaactaaaa tatatttgaa aaagttttct cgcgttcttt gtcttgcgat tggatttgca tcagcattta catatagtta tataacccaa cctaagccgg aggttaaaaa ggtagtctct cagacctatg attttgataa attcactatt gactcttctc agcgtcttaa tctaagctat cgctatgttt tcaaggattc taagggaaaa ttaattaata gcgacgattt acagaagcaa ggttattcac tcacatatat tgatttatgt actgtttcca ttaaaaaagg taattcaaat gaaattgtta aatgtaatta attttgtttt cttgatgttt gtttcatcat cttcttttgc tcaggtaatt gaaatgaata attcgcctct gcgcgatttt gtaacttggt attcaaagca atcaggcgaa tccgttattg tttctcccga tgtaaaaggt actgttactg tatattcatc tgacgttaaa cctgaaaatc tacgcaattt ctttatttct gttttacgtg ctaataattt tgatatggtt ggttcaattc cttccataat tcagaagtat aatccaaaca atcaggatta tattgatgaa ttgccatcat ctgataatca ggaatatgat gataattccg ctccttctgg tggtttcttt gttccgcaaa atgataatgt tactcaaact tttaaaatta ataacgttcg ggcaaaggat ttaatacgag ttgtcgaatt gtttgtaaag tctaatactt ctaaatcctc aaatgtatta tctattgacg gctctaatct attagttgtt agtgcaccta aagatatttt agataacctt cctcaattcc tttctactgt tgatttgcca actgaccaga tattgattga gggtttgata tttgaggttc agcaaggtga tgctttagat ttttcatttg ctgctggctc tcagcgtggc actgttgcag gcggtgttaa tactgaccgc ctcacctctg ttttatcttc tgctggtggt tcgttcggta tttttaatgg cgatgtttta gggctatcag ttcgcgcatt aaagactaat agccattcaa aaatattgtc tgtgccacgt attcttacgc tttcaggtca gaagggttct atctctgttg gccagaatgt cccttttatt actggtcgtg tgactggtga atctgccaat gtaaataatc catttcagac gattgagcgt caaaatgtag gtatttccat gagcgttttt cctgttgcaa tggctggcgg taatattgtt ctggatatta ccagcaaggc cgatagtttg agttcttcta ctcaggcaag tgatgttatt actaatcaaa gaagtattgc tacaacggtt aatttgcgtg atggacagac tcttttactc ggtggcctca ctgattataa aaacacttct caagattctg gcgtaccgtt cctgtctaaa atccctttaa tcggcctcct gtttagctcc cgctctgatt ccaacgagga aagcacgtta tacgtgctcg tcaaagcaac catagtacgc gccctgtagc ggcgcattaa gcgcggcggg tgtggtggtt acgcgcagcg tgaccgctac acttgccagc gccctagcgc ccgctccttt cgctttcttc ccttcctttc tcgccacgtt cgccggcttt ccccgtcaag ctctaaatcg ggggctccct ttagggttcc gatttagtgc tttacggcac ctcgacccca aaaaacttga tttgggtgat ggttcacgta gtgggccatc gccctgatag acggtttttc gccctttgac gttggagtcc acgttcttta atagtggact cttgttccaa actggaacaa cactcaaccc tatctcgggc tattcttttg atttataagg gattttgccg atttcggaac caccatcaaa caggattttc gcctgctggg gcaaaccagc gtggaccgct tgctgcaact ctctcagggc caggcggtga agggcaatca gctgttgccc gtctcgctgg tgaaaagaaa aaccaccctg gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca cgacaggttt cccgactgga aagcgggcag tgagcgcaac gcaattaatg tgagttagct cactcattag gcaccccagg ctttacactt tatgcttccg gctcgtatgt tgtgtggaat tgtgagcgga taacaatttc acacaggaaa cagctatgac catgattacg aattcgagct cggtacccgg ggatcctcta gagtcgacct gcaggcatgc aagcttggca ctggccgtcg ttttacaacg tcgtgactgg gaaaaccctg gcgttaccca acttaatcgc cttgcagcac atcccccttt cgccagctgg cgtaatagcg aagaggcccg caccgatcgc ccttcccaac agttgcgcag cctgaatggc gaatggcgct ttgcctggtt tccggcacca gaagcggtgc cggaaagctg gctggagtgc gatcttcctg aggccgatac ggtcgtcgtc ccctcaaact ggcagatgca cggttacgat gcgcccatct acaccaacgt aacctatccc attacggtca atccgccgtt tgttcccacg gagaatccga cgggttgtta ctcgctcaca tttaatgttg atgaaagctg gctacaggaa ggccagacgc gaattatttt tgatggcgtt cctattggtt aaaaaatgag ctgatttaac aaaaatttaa cgcgaatttt aacaaaatat taacgtttac aatttaaata tttgcttata caatcttcct gtttttgggg cttttctgat tatcaaccgg ggtacatatg attgacatgc tagttttacg attaccgttc atcgattctc ttgtttgctc cagactctca ggcaatgacc tgatagcctt tgtagatctc tcaaaaatag ctaccctctc cggcattaat ttatcagcta gaacggttga atatcatatt gatggtgatt tgactgtctc cggcctttct cacccttttg aatctttacc tacacattac tcaggcattg catttaaaat atatgagggt tctaaaaatt tttatccttg cgttgaaata aaggcttctc ccgcaaaagt attacagggt cataatgttt ttggtacaac cgatttagct ttatgctctg aggctttatt gcttaatttt gctaattctt tgccttgcct gtatgattta ttggatgtt

7. Appendix

Strand Displacement Synthesis:

Template F90: 5’- CCG TCA GCT GTG CCG TCG CGC AGC ACG CGC CGC CGT GGA CAG AGG ACT GCA GAA AAT CAA CCT ATC CTC CTT CAG GAC CAA CGT ACA GAG

Primer:

Fgap16: 5´ CTC TGT ACG TTG GTC C

Fgap24: 5´ G GAT AGG TTG ATT TTC TGC AGT CC

Chemically Modified DNA [277]:

7. Appendix

7.2.2. Protein Sequences