Reactive N-hydroxy-9-azabicyclo[3.3.1]nonane (ABNOH) linked 2'-deoxyuridine 5'-O-mono- and triphosphates were synthesized through a CuAAC reaction of ABNOH-PEG4-N3 with 5-ethynyl-dUMP or -dUTP. The modified triphosphate was used as substrate for enzymatic synthesis of modified DNA probes with KOD XL DNA polymerase. The keto-ABNO radical reacted with tryptophan (Trp) and Trp-containing peptides to form a stable tricyclic fused hexahydropyrrolo-indole conjugates. Similarly modified ABNOH-linked nucleotides reacted with Trp-containing peptides to form a stable conjugate in the presence but surprisingly even in the absence of NaNO2 (presumably through activation by O2). The reactive ABNOH-modified DNA probe was used for bioconjugations and crosslinking with Trp-containing peptides or proteins.

Department of Organic Chemistry Faculty of Science Charles University Prague Hlavova 8 CZ 12843 Prague 2 Czech Republic

Institute of Microbiology Czech Academy of Sciences Videnska 1083 14220 Prague 4 Czech Republic

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam 2 16610 Prague 6 Czech Republic

Zobrazit více v PubMed

R. Rohs, X. Jin, S. M. West, R. Joshi, B. Honig, R. S. Mann, Annu. Rev. Biochem. 2010, 79, 233–269.

S. A. Lambert, A. Jolma, L. F. Campitelli, P. K. Das, Y. Yin, M. Albu, X. Chen, J. Taipale, T. R. Hughes, M. T. Weirauch, Cell 2018, 172, 650–665.

T. S. Furey, Nat. Rev. Genet. 2012, 13, 840–852.

I. Dovgan, O. Koniev, S. Kolodych, A. Wagner, Bioconjug. Chem. 2019, 30, 2483–2501;

T. B. Nielsen, R. P. Thomsen, M. R. Mortensen, J. Kjems, P. F. Nielsen, T. E. Nielsen, A. L. B. Kodal, E. Cló, K. V. Gothelf, Angew. Chem. Int. Ed. 2019, 58, 9068–9072;

J. Balintová, M. Welter, A. Marx, Chem. Sci. 2018, 9, 7122–7125.

P. Shi, Y. Wang, Angew. Chem. Int. Ed. 2021, 60, 11580–11591.

C. M. Niemeyer, Angew. Chem. Int. Ed. 2010, 49, 1200–1216.

M. Winnacker, S. Breeger, R. Strasser, T. Carell, ChemBioChem 2009, 10, 109–118;

L. Lercher, J. F. McGouran, B. M. Kessler, C. J. Schofield, B. G. Davis, Angew. Chem. Int. Ed. 2013, 52, 10553–10558;

C. L. Norris, P. L. Meisenheimer, T. H. Koch, J. Am. Chem. Soc. 1996, 118, 5796–5803.

I. Ivancová, D.-L. Leone, M. Hocek, Curr. Opin. Chem. Biol. 2019, 52, 136–144;

N. Klöcker, F. P. Weissenboeck, A. Rentmeister, Chem. Soc. Rev. 2020, 49, 8749–8773;

K. Krell, D. Harijan, D. Ganz, L. Doll, H.-A. Wagenknecht, Bioconjug. Chem. 2020, 31, 990–1011;

D. Ganz, D. Harijan, H.-A. Wagenknecht, RSC Chem. Biol. 2020, 1, 86–97;

M. Jbara, J. Rodriguez, H. H. Dhanjee, A. Loas, S. L. Buchwald, B. L. Pentelute, Angew. Chem. Int. Ed. 2021, 60, 12109–12115;

J. Konč, L. Brown, D. R. Whiten, Y. Zuo, P. Ravn, D. Klenerman, G. J. L. Bernardes, Angew. Chem. Int. Ed. 2021, 60, 25905–25913.

P. M. E. Gramlich, S. Warncke, J. Gierlich, T. Carell, Angew. Chem. Int. Ed. 2008, 47, 3442–3444;

H. Busskamp, E. Batroff, A. Niederwieser, O. S. Abdel-Rahman, R. F. Winter, V. Wittmann, A. Marx, Chem. Commun. 2014, 50, 10827–10829;

U. Rieder, N. W. Luedtke, Angew. Chem. Int. Ed. 2014, 53, 9168–9172;

S. Arndt, H.-A. Wagenknecht, Angew. Chem. Int. Ed. Engl. 2014, 53, 14580–14582;

K. Wang, D. Wang, K. Ji, W. Chen, Y. Zheng, C. Dai, B. Wang, Org. Biomol. Chem. 2015, 13, 909–915;

X. Ren, A. H. El-Sagheer, T. Brown, Nucleic Acids Res. 2016, 44, e79;

U. Reisacher, D. Ploschik, F. Rönicke, G. B. Cserép, P. Kele, H.-A. Wagenknecht, Chem. Sci. 2019, 10, 4032–4037;

K. Krell, B. Pfeuffer, F. Rönicke, Z. S. Chinoy, C. Favre, F. Friscourt, H.-A. Wagenknecht, Chem. Eur. J. 2021, 27, 16093–16097;

A. Spampinato, E. Kužmová, R. Pohl, V. Sýkorová, M. Vrábel, T. Kraus, M. Hocek, Bioconjug. Chem. 2023, 34, 772–780;

B. Pfeuffer, P. Geng, H.-A. Wagenknecht, ChemBioChem 2024, 25, e202300739;

N. Seul, D. Lamade, P. Stoychev, M. Mijic, R. Michenfelder, L. Rieger, P. Geng, H.-A. Wagenknecht, Angew. Chem. Int. Ed. 2024, 63, e202403044.

J. Dadová, P. Orság, R. Pohl, M. Brázdová, M. Fojta, M. Hocek, Angew. Chem. Int. Ed. 2013, 52, 10515–10518.

K. Odaira, K. Yamada, S. Ishiyama, H. Okamura, F. Nagatsugi, Appl. Sci. 2020, 10, 7709.

Olszewska, R. Pohl, M. Brázdová, M. Fojta, M. Hocek, Bioconjug. Chem. 2016, 27, 2089–2094.

M. Brunderová, M. Krömer, M. Vlková, M. Hocek, Angew. Chem. Int. Ed. 2023, 62, e202213764.

D.-L. Leone, M. Hubálek, R. Pohl, V. Sýkorová, M. Hocek, Angew. Chem. Int. Ed. 2021, 60, 17383–17387.

D.-L. Leone, R. Pohl, M. Hubálek, M. Kadeřábková, M. Krömer, V. Sýkorová, M. Hocek, Chem. Eur. J 2022, 28, e202104208.

M. Fonvielle, N. Sakkas, L. Iannazzo, C. Le Fournis, D. Patin, D. Mengin-Lecreulx, A. El-Sagheer, E. Braud, S. Cardon, T. Brown, M. Arthur, M. Etheve-Quelquejeu, Angew. Chem. Int. Ed. 2016, 55, 13553–13557.

I. Ivancová, R. Pohl, M. Hubálek, M. Hocek, Angew. Chem. Int. Ed. 2019, 58, 13345–13348.

A.-D. Guo, K.-N. Yan, H. Hu, L. Zhai, T.-F. Hu, H. Su, Y. Chi, J. Zha, Y. Xu, D. Zhao, X. Lu, Y.-J. Xu, J. Zhang, M. Tan, X.-H. Chen, Nat. Chem. 2023, 15, 803–814.

P. Chauhan, R. V. M. Kumar, R. Molla, S. D. Mishra, S. Basa, V. Rai, Chem. Soc. Rev. 2024, 53, 380–449.

N. L. Kjaersgaard, T. B. Nielsen, K. V. Gothelf, ChemBioChem 2022, 23, e202200245;

N. H. Fischer, M. T. Oliveira, F. Diness, Biomater. Sci. 2023, 11, 719–748.

M. B. Hansen, F. Hubálek, T. Skrydstrup, T. Hoeg-Jensen, Chem. Eur. J. 2016, 22, 1572–1576;

K. Rahimidashaghoul, I. Klimánková, M. Hubálek, M. Korecký, M. Chvojka, D. Pokorný, V. Matoušek, L. Fojtík, D. Kavan, Z. Kukačka, P. Novák, P. Beier, Chem. Eur. J. 2019, 25, 15779–15785.

S. Sato, H. Nakamura, Molecules 2019, 24, 3980.

Y. Seki, T. Ishiyama, D. Sasaki, J. Abe, Y. Sohma, K. Oisaki, M. Kanai, J. Am. Chem. Soc. 2016, 138, 10798–10801.

K. Maruyama, K. J. Malawska, N. Konoue, K. Oisaki, M. Kanai, Synlett 2020, 31, 784–787.

K. J. Malawska, S. Takano, K. Oisaki, H. Yanagisawa, M. Kikkawa, T. Tsukuda, M. Kanai, Bioconjug. Chem. 2023, 34, 781–788.

M. Slavíčková, M. Janoušková, A. Šimonová, H. Cahová, M. Kambová, H. Šanderová, L. Krásný, M. Hocek, Chem. Eur. J. 2018, 24, 8311–8314.

Y. Fujita, T. Fujita, Y. Miwa, J. Nihashi, J. Biol. Chem. 1986, 261, 13744–13753.

Y. Miwa, Y. Fujita, J. Biol. Chem. 1988, 15, 263, 13252–13257.

S. Rigali, A. Derouaux, F. Giannotta, J. Dusart, J. Biol. Chem. 2002, 277, 12507–12515.

C. R. Horne, H. Venugopal, S. Panjikar, D. M. Wood, A. Henrickson, E. Brookes, R. A. North, J. M. Murphy, R. Friemann, M. D. W. Griffin, G. Ramm, B. Demeler, R. C. J. Dobson Nat. Commun. 2021, 12, 1988.

J. Jumper, R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, K. Tunyasuvunakool, R. Bates, A. Židek, A. Potapenko, A. Bridgland, C. Meyer, S. Kohl, J. A. Ballard, A. Cowie, B. Romera-Paredes, S. Nikolov, R. Jain, J. Adler, T. Back, S. Petersen, D. Reiman, E. Clancy, M. Zielinski, M. Steinegger, M. Pacholska, T. Berghammer, S. Bodenstein, D. Silver, O. Vinyals, A. W. Senior, K. Kavukcuoglu, P. Kohli, D. Hassabis Nature 2021, 596, 583–589.

J. Dadová, M. Vrábel, M. Adámik, M. Brázdová, R. Pohl, M. Fojta, M. Hocek, Chem. Eur. J. 2015, 21, 16091–16102.

P. M. E. Gramlich, C. T. Wirges, J. Gierlich, T. Carell, Org. Lett. 2008, 10, 249–251.

Hirschmann-Laborgeräte, Ringcaps 2021, https://hirschmann-laborgeraete.de/en/artikelgruppe/96001

Bruker, EPR Sofware/Xenone Software 2022, https://www.bruker.com/en/products-and-solutions/mr/epr-instruments/epr-software/xenon.html

N. Y. Buffalo, University Magnetic Resonance Center/EPR Spectrometer Guides 2022, http://www.nmrcenter.buffalo.edu/.

G. R. Eaton, S. S. Eaton, D. P. Barr, R. T. Weber, Quantitative EPR [online]. Springer Vienna 2010, DOI: https://doi.org/10.1007%2F978-3-211-92948-3.

J. Barton, M. Gulka, J. Tarabek, Y. Mindarava, Z. Wang, J. Schimer, H. Raabova, J. Bednar, M. Plenio, F. Jelezko, M. Nesladek, P. Cigler, ACS Nano 2020, 14, 12938–12950.

M. T. Marty, A. J. Baldwin, E. G. Marklund, G. K. A. Hochberg, J. L. P. Benesch, C. V. Robinson, Anal. Chem. 2015, 87, 4370–4376.

J. Písačková, K. Procházková, M. Fábry, P. Řezáčová, Cryst. Growth Des. 2013, 13, 844–848.

K. Procházková, K. Čermáková, P. Pachl, I. Sieglová, M. Fábry, Z. Otwinowski, P. Řezáčová, Acta Crystallogr. D Biol. Crystallogr. 2012, 68, 176–185.

U. B. Ericsson, B. M. Hallberg, G. T. Detitta, N. Dekker, P. Nordlund, Anal. Biochem. 2006, 357, 289–298.

H. Hernández, C. V. Robinson, Nat. Protoc. 2007, 2, 715–26.