ABNOH-Linked Nucleotides and DNA for Bioconjugation and Cross-linking with Tryptophan-Containing Peptides and Proteins
Language English Country Germany Media print-electronic
Document type Journal Article
Grant support
20-00885X
Grantová Agentura České Republiky
CZ.02.01.01/00/22_008/0004575
Ministerstvo Školství, Mládeže a Tělovýchovy
LM2023042
Ministerstvo Školství, Mládeže a Tělovýchovy
CZ.02.1.01/0.0/0.0/18_046/0015974
Ministerstvo Školství, Mládeže a Tělovýchovy
- Keywords
- Bioconjugations, N-oxyl radicals, Nucleotides, Oligonucleotides, Peptides,
- MeSH
- DNA-Directed DNA Polymerase metabolism chemistry MeSH
- DNA * chemistry MeSH
- Nucleotides * chemistry MeSH
- Peptides * chemistry MeSH
- Proteins chemistry MeSH
- Cross-Linking Reagents chemistry MeSH
- Tryptophan * chemistry MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- DNA-Directed DNA Polymerase MeSH
- DNA * MeSH
- Nucleotides * MeSH
- Peptides * MeSH
- Proteins MeSH
- Cross-Linking Reagents MeSH
- Tryptophan * MeSH
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.
See more in 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.