[BioNEC-107]Huang, Ge; Dreisler, Marcus Winther; Kæstel-Hansen, Jacob; Nielsen, Annette Juma; Zhang, Min; Hatzakis, Nikos S. Defect-engineered metal-organic frameworks as nanocarriers for pharmacotherapy: Insights into intracellular dynamics at the single particle level.Advanced Materials (2024), 2405898.[]
[BioNEC-106]Møller, Delphine N; Kofoed, Christian; Thygesen, Mikkel B; Sørensen, Kasper K; Jensen, Knud J. Highly selective chemical modification of poly-His tagged peptides and proteins. Methods in Enzymology, Volume 698 (2024), 111-139. []
[BioNEC-105] Malle, Mette Galsgaard; Song, Ping; Löffler, Philipp M. G.; Kalisi, Nazmie; Yan, Yan; Valero, Julian; Vogel, Stefan; Kjems, Jørgen. Programmable RNA loading of extracellular vesicles with toehold-release purification. Journal of the American Chemical Society (2024), 146, 12410-12422. []
[BioNEC-104] Zhang, Xialin; Malle, Mette Galsgaard; Thomsen, Rasmus P.; Sørensen, Rasmus Schoeler; Sørensen, Emily Winther; Hatzakis, Nikos S.; Kjems, Jørgen. Deconvolutingthe effect of cell-penetrating peptidesfor enhancedand controlled insertion of large-scale DNA nanopores. ACS Applied Materials & Interfaces (2024), 16, 18422–18433. []
[BioNEC-103] Bender, Steen W. B.; Dreisler, Marcus W.; Zhang, Min; Kaestel-Hansen, Jacob; Hatzakis, Nikos S. SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis. Nature Communications (2024), 15, 1763. []
[BioNEC-102] Dinesen, Anders; Andersen, Veronica L.; Elkhashab, Marwa; Pilati, Diego; Bech, Pernille; Fuchs, Elisabeth; Samuelsen, Torbjørn R.; Winther, Alexander; Cai, Yunpeng; Marcher, Anders; Wall, Archie; Omer, Marjan; Nielsen, Jesper S.; Chudasama, Vijay; Baker, James R.; Gothelf, Kurt V.; Wengel, Jesper; Kjems, Jørgen; Howard, Kenneth A. An albumin-Holliday junction biomolecular modular design for programmable multifunctionality and prolonged circulation. Bioconjugate Chemistry (2024), 35, 214-222. []
[BioNEC-101] Danielsen, Mathias B.; Mao, Hanbin; Lou, Chenguang. Peptide-DNA conjugates as building blocks for de novo design of hybrid nanostructures. Cell Reports Physical Science (2023), 4, 101620. []
[BioNEC-100] Löffler, Philipp M. G.; Risgaard, Nikolaj Alexander; Svendsen, Bettina L.; Jepsen, Katrine A.; Rabe, Alexander; Vogel, Stefan. Label-free observation of DNA-encoded liposome fusion by surface plasmon resonance. Chem. Commun., (2023), 59, 10548–10551. []
[BioNEC-99] Tian, Xinwei; Risgaard, Nikolaj Alexander; Löffler, Philipp M. G.; Vogel, Stefan. DNA-Programmed lipid nanoreactors for synthesis of carbohydrate mimetics by fusion of aqueous sub-attoliter compartments. J. Am. Chem. Soc. (2023), 145, 19633–19641. []
[BioNEC-98] Ruck, Vanessa; Mishra, Narendra K.; Sørensen, Kasper K.; Liisberg, Mikkel B.; Sloth, Ane B.; Cerretani, Cecilia; Møllerup, Christian B.; Kjær, Andreas; Lou, Chenguang; Jensen, Knud J.; Vosch, Tom. Bioconjugation of a near-infrared DNA-stabilized silver nanocluster to peptides and human insulin by copper-free click chemistry. J. Am. Chem. Soc. (2023), 145, 16771–16777. []
[BioNEC-97] Zhang, Xialin; Galenkamp, Nicole Stephanie; van der Heide, Nieck Jordy; Moreno, Julian; Maglia, Giovanni; Kjems, Jørgen. Specific detection of proteins by a nanobody-functionalized nanopore sensor. ACS Nano (2023), 17, 9167-9177. []
[BioNEC-96] Benning, Nils A.; Kæstel-Hansen, Jacob; Rashid, Fahad; Park, Sangwoo; Merino Urteaga, Raquel; Liao, Ting-Wei; Hao, Jingzhou; Berger, James M.; Hatzakis, Nikos S.; Ha, Taekjip. Dimensional reduction for single-molecule imaging of DNA and nucleosome condensation by polyamines, HP1α and Ki-67. Journal of Physical Chemistry B. (2023), 127, 1922-1931. []
[BioNEC-95] Wu, Shunliang; Østergaard, Mads; Fredholt, Freja; Christensen, Niels Johan; Sørensen, Kasper K.; Mishra, Narendra K.; Nielsen, Hanne M.; and Jensen, Knud J. Ca2+-Responsive glyco-insulin. Bioconjugate Chem. (2023), 34, 3, 518–528. []
[BioNEC-94] Bohr, Freja; Bohr, Søren S-R; Mishra, Narendra Kumar; González-Foutel, Nicolás Sebastian; Pinholt, Henrik Dahl; Wu, Shunliang; Nielsen, Emilie Milan; Zhang, Min; Kjaergaard, Magnus; Jensen, Knud J.; and Hatzakis, Nikos S. Enhanced hexamerization of insulin via assembly pathway rerouting revealed by single particle studies. Communications Biology (2023), 6, 178. []
[BioNEC-93] Thorlaksen, Camilla; Schultz, Heidi S.; Gammelgaard, Simon K.; Jiskoot, Wim; Hatzakis, Nikos S.; Nielsen, Flemming S.; Solberg, Helene; Fodera, Vito; Bartholdy, Christina; Groenning, Minna. In vitro and in vivo immunogenicity assessment of protein aggregate characteristics. International Journal of Pharmaceutics (2023), 631, 122490. []
[BioNEC-92] Jensen, Knud J.; Thygesen, Mikkel B.; Sørensen, Kasper K.; Wu, Shunliang; Treiberg, Tuule; Schoffelen, Sanne. Selective Acylation of Proteins at Gly and Lys in His Tags.ChemBioChem (2022), 23, e202200359. []
[BioNEC-91] Jakobsen, Ulla; Rosholm, Kadla Røskva; Vogel, Stefan. Design, synthesis and membrane anchoring strength of lipidated polyaza crown ether DNA-conjugates (LiNAs) studied by DNA-controlled assembly of liposomes. Org. Biomol. Chem. (2022), 20, 9460-9468. []
[BioNEC-90] Bakowski, Kamil, Vogel, Stefan. Evolution of complexity in non-viral oligonucleotide delivery systems: from gymnotic delivery through bioconjugates to biomimetic nanoparticles. RNA Biology (2022), 19, 1256-1275. []
[BioNEC-89] Götz, Markus; Barth, Anders; Bohr, Søren S.-R.; Börner, Richard; Chen, Jixin; Cordes, Thorben; Erie, Dorothy A.; Gebhardt, Christian; Hadzic, Mélodie C. A. S.; Hamilton, George L; Hatzakis, Nikos S.; Hugel, Thorsten; Kisley, Lydia; Lamb, Don C.; de Lannoy, Carlos; Mahn, Chelsea; Dunukara, Dushani; de Ridder, Dick; Sanabria, Hugo; Schimpf, Julia; Seidel, Claus A. M.; Sigel, Roland K. O.; Sletfjerding, Magnus Berg; Thomsen, Johannes; Vollmar, Leonie; Wanninger, Simon; Weninger, Keith R.; Xu, Pengning; Schmid, Sonja. A blind benchmark of analysis tools to infer kinetic rate constants from single-molecule FRET trajectories. Nature Communications (2022), 13, 5402. []
[BioNEC-88] : Thorlaksen, Camilla; Stanciu, Adriana-Maria; Busch Neergaard, Martin; Hatzakis, Nikos; Foderà, Vito; Groenning, Minna. Morphological integrity of insulin amyloid-like aggregates depends on preparation methods and post-production treatments. European Journal of Pharmaceutics and Biopharmaceutics (2022), 179, 147–155. []
[BioNEC-87] Veit, Sarina; Paweletz, Laura Charlotte; Bohr, Søren S.-R.; Menon, Anant K.; Hatzakis, Nikos S.; Pomorski, Thomas Guenther. Single vesicle fluorescence-bleaching assay for multi-parameter analysis of proteoliposomes by total internal reflection fluorescence microscopy. ACS Applied Materials and Interfaces (2022) 14, 29659-29667. []
[BioNEC-86] Lisowiec-W膮chnicka, Jolanta; Danielsen, Mathias B.; Nader, Eugenie Abi; Jørgensen, Per T.; Wengel, Jesper; Pasternak, Anna. Evaluation of gene expression knock-down by chemically and structurally modified gapmer antisense oligonucleotides. ChemBioChem (2022), 23, e202200168. []
[BioNEC-85] Schmidt, Solveig G.; Malle, Mette Galsgaard; Nielsen, Anne Kathrine; Bohr, Søren S.-R.; Pugh, Ciara F.; Nielsen, Jeppe C.; Poulsen, Ida H.; Rand, Kasper D.; Hatzakis, Nikos S.; Loland, Claus J. The dopamine transporter antiports potassium to increase the uptake of dopamine. Nature Communications (2022), 13, 2446. []
[BioNEC-84] Di Giorgio, Eros; Ferino, Annalisa; Choudhary, Himanshi; Loffler, Phillip M. G.; D'Este, Francesca; Rapozzi, Valentina; Tikhomirov, Alexander; Shchekotikhin, Andrey; Vogel, Stefan; Xodo, Luigi E. Photosensitization of pancreatic cancer cells by cationic alkyl-porphyrins in free form or engrafted into POPC liposomes: The relationship between delivery mode and mechanism of cell death. Journal of Photochemistry and Photobiology, B: Biology (2022), 231, 112449. []
[BioNEC-83] Malle, Mette Galsgaard; Löffler, Philipp M. G.; Bohr, Søren S. R.; Sletfjerding, Magnus Berg; Risgaard, Nikolaj Alexander; Jensen, Simon Bo; Zhang, Min; Hedegård, Per; Vogel, Stefan; Hatzakis, Nikos S. Single-particle combinatorial multiplexed liposome fusion mediated by DNA. Nature Chemistry (2022), 14, 558-565. []
[BioNEC-82] Kofoed, Christian; Wu, Shunliang; Sørensen, Kasper K.; Treiberg, Tuule; Arnsdorf, Johnny; Bjørn, Sara P.; Jensen, Tanja L.; Voldborg, Bjørn G.; Thygesen, Mikkel B.; Jensen, Knud J.; Schoffelen, Sanne. Highly selective lysine acylation in proteins using a Lys-His tag sequence. Chemistry - A European Journal (2022), 28, e202200147. []
[BioNEC-81] Dinesen, Anders; Winther, Alexander; Wall, Archie; Marcher, Anders; Palmfeldt, Johan; Chudasama, Vijay; Wengel, Jesper; Gothelf, Kurt V.; Baker, James R.; Howard, Kenneth A. Albumin biomolecular drug designs stabilized through improved thiol conjugation and a modular locked nucleic acid functionalized assembly. Bioconjugate Chemistry (2022), 33, 333-342. []
[BioNEC-80] Pandey, Shankar; Mandal, Shankar; Danielsen, Mathias Bogetoft; Brown, Asha; Hu, Changpeng; Christensen, Niels Johan; Kulakova, Alina Vitaliyivna; Song, Shixi; Brown, Tom; Jensen, Knud J.; Wengel, Jesper; Lou, Chenguang; Mao, Hanbin. Chirality transmission in macromolecular domains. Nature Communications (2022), 13, 76. []
[BioNEC-79] Araújo, Daniela; Mil-Homens, Dalila; Rodrigues, Maria Elisa; Henriques, Mariana; Jørgensen, Per Trolle; Wengel, Jesper; Silva, Sónia. Antisense locked nucleic acid gapmers to control Candida albicans filamentation. Nanomedicine: Nanotechnology, Biology and Medicine (2022), 39, 102469. []
[BioNEC-78] Mishra, Narendra Kumar; Øestergaard, Mads; Midtgaard, Søren Roi; Strindberg, Sophie S.; Winkler, Stefan; Wu, Shunliang; Sørensen, Thomas Just; Hassenkam, Tue; Poulsen, Jens-Christian N.; Lo Leggio, Leila; Nielsen, Hanne Mørck; Arleth, Lise; Christensen, Niels Johan; Thulstrup, Peter Waaben; Jensen, Knud Jørgen. Controlling the fractal dimension in self-assembly of terpyridine modified insulin by Fe2+ and Eu3+ to direct in vivo effects. Nanoscale (2021), 18, 8467–8473. []
[BioNEC-77] Paprocki, Maciej P.; Rasmussen, Jakob E.; Sørensen, Kasper K.; Jensen, Knud J. Safety-catch linkers for Fmoc solid-phase synthesis of peptide thioesters and hydrazides by amide-to-imide activation. Journal of Peptide Science (2021), e3364. []
[BioNEC-76] Moses, Matias E.; Lund, Philip M.; Bohr, Soeren S.-R.; Iversen, Josephine F.; Kaestel-Hansen, Jacob; Kallenbach, Amalie S.; Iversen, Lars; Christensen, Sune M.; Hatzakis, Nikos S. Single-molecule study of thermomyces lanuginosus lipase in a detergency application system reveals diffusion pattern remodeling by surfactants and calcium. ACS Appl. Mater. Interfaces (2021), 13, 33704-33712. []
[BioNEC-75] Danielsen, Mathias B; Wengel, Jesper. Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides. Beilstein J. Org. Chem. (2021), 17, 1828-1848. []
[BioNEC-74] Jensen, Simon Bo; Thodberg, Sara; Parween, Shaheena; Moses, Matias E.; Hansen, Cecilie C.; Thomsen, Johannes; Sletfjerding, Magnus B.; Knudsen, Camilla; Del Giudice, Rita; Lund, Philip M.; Castaño, Patricia R.; Bustamante, Yanet G.; Velazquez, Maria Natalia Rojas; Jørgensen, Flemming Steen; Pandey, Amit V.; Laursen, Tomas; Møller, Birger Lindberg; Hatzakis, Nikos S. Biased cytochrome P450-mediated metabolism via small-molecule ligands binding P450 oxidoreductase. Nature Communications (2021), 12, 2260. []
[BioNEC-73] Streck, Sarah; Bohr, Søren S.-R.; Birch, Ditlev; Rades, Thomas; Hatzakis, Nikos S.; McDowell, Arlene; Mørck Nielsen, Hanne. Interactions of cell-penetrating peptide-modified nanoparticles with cells evaluated using single particle tracking. ACS Applied Bio Materials (2021) 4, 3155-3165. []
[BioNEC-72] Holmstrøm, Thomas; Galsgaard Malle, Mette; Wu, Shunliang; Jensen, Knud Jørgen; Hatzakis, Nikos S.; Pedersen, Christian Marcus. Carbohydrate-derived metal-chelator-triggered lipids for liposomal drug delivery. Chemistry - A European Journal (2021) 27, 6917-6922. []
[BioNEC-71] Lerner, Eitan; Razvag, Yair; Barth, Anders; Hanke, Christian A; Seidel, Claus Am; Hendrix, Jelle; Ambrose, Benjamin; Craggs, Timothy D; Birkedal, Victoria; Blanchard, Scott, C; Hatzakis, Nikos S; et al. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife (2021), 10:e60416. []
[BioNEC-70] Pereira, Sara; Yao, Ruwei; Gomes, Mariana; Jørgensen, Per T.; Wengel, Jesper; Azevedo, Nuno F.;Santos, Rita S. Can vitamin B12 assist the internalization of antisense LNA oligonucleotides into bacteria? Antibiotics (2021), 10, 379. []
[BioNEC-69] Maas, Marijn N.; Hintzen, Jordi C. J.; Löffler, Philipp M. G.; Mecinovi膰, Jasmin. Targeting SARS-CoV-2 spike protein by stapled hACE2 peptides. Chem. Commun., (2021), 57, 3283-3286. []
[BioNEC-68] Danielsen, Mathias B; Christensen, Niels Johan; Jørgensen, Per T; Jensen, Knud J; Wengel, Jesper; Lou, Chenguang. Polyamine-Functionalized 2'-Amino-LNA in oligonucleotides: Facile synthesis of new monomers and high-affinity binding towards ssDNA and dsDNA. Chemistry - A European Journal (2021), 27(4), 1416-1422. []
[BioNEC-67] Omer, Marjan; Andersen, Veronica Liv; Nielsen, Jesper Sejrup; Wengel, Jesper; Kjems, Jørgen. Improved cancer targeting by multimerizing aptamers on nanoscaffolds. Molecular Therapy - Nucleic Acids (2020), 22, 994-1003. []
[BioNEC-66] Thomsen Johannes; Sletfjerding Magnus Berg; Jensen Simon Bo; Malle Mette Galsgaard; Hatzakis Nikos S; Stella Stefano; Paul Bijoya; Montoya Guillermo; Petersen Troels Christian; Hatzakis Nikos S. DeepFRET, a software for rapid and automated single-molecule FRET data classification using deep learning. (2020), 9, e60404. []
[BioNEC-65] Singh, Pradeep Kumar; Bohr, Søren S-R; Hatzakis, Nikos S. Direct observation of sophorolipid micelle docking in model membranes and cells by single particle studies reveals optimal fusion conditions. Biomolecules (2020), 10, 1291. []
[BioNEC-64] Bohr, Søren S-R; Thorlaksen, Camilla; Kühnel, Ronja M., Günther-Pomorski, Thomas; Hatzakis, Nikos S. Label-free fluorescence quantification of hydrolytic enzyme activity on native substrates reveals how lipase function depends on membrane curvature. Langmuir (2020), 36, 6473−6481. []
[BioNEC-63] Gouda, Alaa S.; Przypis, Lukasz; Walczak, Krzysztof; Jørgensen Per T.; Wengel, Jesper. Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties. Organic & Biomolecular Chemistry(2020), 18, 6935-6948. []
[BioNEC-62] Arias-Alpizar, Gabriela; Kong, Li; Vlieg, Redmar C; Rabe, Alexander; Papadopoulou, Panagiota; Meijer, Michael S; Bonnet, Sylvestre; Vogel, Stefan; van Noort, John; Kros, Alexander; Campbell, Frederick. Light-triggered switching of liposome surface charge directs delivery of membrane impermeable payloads in vivo. Nature Communications (2020), 11, 3638. []
[BioNEC-61] Østergaard, Mads; Mishra, Narendra Kumar; Jensen, Knud J. The ABC of insulin: The organic chemistry of a small protein. Chemistry - A European Journal (2020), 26(25), 8341-8357. []
[BioNEC-60] Lou Chenguang; Boesen Josephine Tuborg; Christensen Niels Johan; Sørensen Kasper K; Jensen Knud Jørgen; Thulstrup Peter Waaben; Pedersen Martin Nors; Giralt Ernest; Wengel Jesper. Self-assembly of DNA-peptide supermolecules: Coiled-coil peptide structures templated by D-DNA and L-DNA triplexes exhibit chirality-independent but orientation-dependent stabilizing cooperativity. Chemistry - A European Journal (2020), 26(25), 5676-5684. []
[BioNEC-59] Abdelrahman, Asmaa; Gouda, Alaa S.; Jørgensen, Per T.; Wengel, Jesper. Novel assemblies based on oligonucleotides containing intercalating nucleic acid monomers. Nucleosides, Nucleotides and Nucleic Acids(2020), 39(1-3), 82-96. []
[BioNEC-58] Löffler, Philipp M. G.; Rabe, Alexander; Vogel, Stefan. Lipid-modified peptide nucleic acids: Synthesis and application to programmable liposome fusion. Book chapter in: Peter E. Nielsen (ed.), Peptide Nucleic Acids: Methods and Protocols. Methods in Molecular Biology (Clifton, N.J.) (2020), 2105, 75-96. []
[BioNEC-57] Aloisi, Adriano; Christensen, Niels Johan; Sørensen, Kasper K.; Guilbaud-Chereau, Chloe; Jensen, Knud J.; Bianco, Alberto. Synthesis and characterization of adamantane-containing heteropeptides with a chirality switch. European Journal of Organic Chemistry (2020), 2020(7), 815-820. []
[BioNEC-56] Danielsen, Mathias B.; Lou, Chenguang; Lisowiec-Wachnicka, Jolanta; Pasternak, Anna; Jørgensen, Per T.; Wengel, Jesper. Gapmer antisense oligonucleotides containing 2',3'-dideoxy-2'-fluoro-3'-C-hydroxymethyl-β-D-lyxofuranosyl nucleotides display site-specific RNase H cleavage and induce gene silencing. Chemistry - A European Journal (2020), 26(6), 1368-1379. []
[BioNEC-55] Löffler, Philipp M. G.; Ries, Oliver; Vogel, Stefan. DNA-Mediated liposome fusion observed by fluorescence spectrometry. Book chapter in: Astakhova K., Bukhari S. (eds) Nucleic Acid Detection and Structural Investigations. Methods in Molecular Biology (Clifton, N.J.) (2020), 2063, 101-118. []
[BioNEC-54] Jepsen, Mette D. E.; Sørensen, Rasmus S.; Maffeo, Christopher, Aksimentiev, Aleksei; Kjems, Jørgen; Birkedal, Victoria. Single molecule analysis of structural fluctuations in DNA nanostructures. Nanoscale (2019), 11, 18475–18482. []
[BioNEC-53] Klein, William P., Thomsen Rasmus P.; Turner Kendrick B.; Walper Scott A.; Vranish James; Kjems Jørgen; Ancona Mario G., Medintz Igor L. Enhanced catalysis from multienzyme cascades assembled on a DNA origami triangle. ACS Nano (2019), 13, 13677-13689. []
[BioNEC-52] Thomsen, Rasmus P.; Malle, Mette Galsgaard; Okholm, Anders Hauge; Krishnan, Swati; Bohr, Søren S.-R.; Sørensen, Rasmus Schøler; Ries, Oliver; Vogel, Stefan; Simmel, Friedrich C.; Hatzakis, Nikos S; Kjems, Jørgen. A large size-selective DNA nanopore with sensing applications. Nature Communications (2019), 10, 5655. [].
[BioNEC-51] Löffler, Philipp M. G.; Hansen, Anders Højgaard; Ries, Oliver; Jakobsen, Ulla; Rabe, Alexander; Sørensen, Kristian T.; Glud, Kasper; Vogel, Stefan.Lipidated polyaza crown ethers as membrane anchors for DNA controlled content mixing between liposomes. Scientific Reports (2019), 9(1), 1-11. []
[BioNEC-50] Raniolo, Sofia; Croce, Stefano; Thomsen, Rasmus P.; Okholm, Anders H.; Unida, Valeria; Iacovelli, Federico; Manetto, Antonio; Kjems, Jørgen; Desideri, Alessandro; Biocca, Silvia. Cellular uptake of covalent and non-covalent DNA nanostructures with different sizes and geometries. Nanoscale, (2019),11, 10808-10818. []
[BioNEC-49] Andersen, Veronica Liv; Vinther, Mathias; Kumar, Rajesh; Ries, Annika; Wengel, Jesper; Nielsen, Jesper Sejrup; Kjems, Jørgen.A self-assembled, modular nucleic acid-based nanoscaffold for multivalent theranostic medicine. Theranostics (2019), 9, 2662-2677. []
[BioNEC-48] Stella, Stefano; Mesa, Pablo; Thomsen, Johannes; Paul, Bijoya; Alcon, Pablo; Jensen, Simon B.; Saligram, Bhargav; Moses, Matias E.; Hatzakis, Nikos S.; Montoya, Guillermo. Conformational activation promotes CRISPRCas12a catalysis and resetting of the endonuclease activity. Cell (2018) 175, 1856–1871. []
[BioNEC-47] Ferino, Annalisa; Miglietta, Giulia; Picco, Raffaella; Vogel, Stefan; Wengel, Jesper; Xodo, Luigi E. MicroRNA therapeutics: Design of single-stranded miR-216b mimics to target KRAS in pancreatic cancer cells. RNA Biology (2018), 15, 1273-1285. []
[BioNEC-46] Martos-Maldonado, Manuel C.; Hjuler, Christian T.; Sørensen, Kasper K.; Thygesen, Mikkel B.; Rasmussen, Jakob E.; Villadsen, Klaus; Midtgaard, Søren R.; Kol, Stefan; Schoffelen, Sanne; Jensen, Knud J. Selective N-terminal acylation of peptides and proteins with a Gly-His tag sequence. Nature Communications. (2018), 9, 3307. []
[BioNEC-45] Ejlersen, Maria; Lou, Chenguang; Sanghvi, Yogesh S.; Tor, Yitzhak; Wengel, Jesper. Modification of oligodeoxynucleotides by on-column Suzuki cross-coupling reactions. Chem. Commun. (2018), 54, 8003–8006. []
BioNEC-44] Østergaard, Mads; Christensen, Niels Johan; Hjuler, Christian T.; Jensen, Knud J.; Thygesen, Mikkel B. Glycoconjugate oxime formation catalyzed at neutral pH: Mechanistic insights and applications of 1,4-diaminobenzene as a superior catalyst for complex carbohydrates. Bioconjug. Chem. (2018), 29, 1219-1230. []
[BioNEC-43] Ejlersen, Maria; Christensen, Niels Johan; Sørensen, Kasper K.; Jensen, Knud J.; Wengel, Jesper; Lou, Chenguang. Synergy of two highly specific biomolecular recognition events: Aligning an AT-hook peptide in DNA minor grooves via covalent conjugation to 2'-amino-LNA. Bioconjug. Chem. (2018), 29, 1025-1029. []
[BioNEC-42] Vejlegaard, Kim; Wegeberg, Christina; McKee Vickie; Wengel, Jesper. Novel conformationally constrained 2′-C-methylribonucleosides: Synthesis and incorporation into oligonucleotides. Org. Biomol. Chem. (2018),16, 1312-1321 []
[BioNEC-41] Mulberg, Mads Westergaard; Taskova, Maria; Thomsen, Rasmus P.; Okholm, Anders H.; Kjems, Jørgen; Astakhova, Kira. New fluorescent nanoparticles forultrasensitive detection of nucleic acids by optical methods. ChemBioChem (2017), 18, 1599-1603. []
[BioNEC-40] Hjuler, Christian T., Maolanon, Nicolai M., Sauer, Jørgen., Stougaard, Jens, Thygesen, Mikkel B.; Jensen, Knud J. Preparation of glycoconjugates from unprotected carbohydrates for protein binding-studies. Nature Protoc. (2017), 12, 2411-2422. []
[BioNEC-39] Ries, Oliver; Löffler, Philipp M. G.; Rabe, Alexander; Malavan, J. J.; Vogel, Stefan. Efficient liposome fusion mediated by lipid–nucleic acid conjugates. Org. Biomol. Chem. (2017), 15, 8936–8945. []
[BioNEC-38] Rabe, Alexander; Löffler, Philipp M. G.; Ries, Oliver; Vogel, Stefan. Programmable fusion of liposomes mediated by lipidated PNA. Chem. Commun. (2017), 53, 11921–11924. []
[BioNEC-37] Löffler, P. M. G.; Ries, O.; Rabe, A.; Okholm, A. H.; Thomsen, R. P.; Kjems, J.; Vogel, S. A DNA-programmed liposome fusion cascade. Angew. Chem. Int. Ed. (2017) 56, 13228-13231. [] [.]
[BioNEC-36] Okholm, A. H.; Kjems, J. The utility of DNA nanostructures for drug delivery in vivo. The utility of DNA nanostructures for drug delivery in vivo. Expert opinion on drug delivery (2017), 14, 137-139. [].
[BioNEC-35] Lou, C.; Christensen, N. J.; Martos-Maldonado, M. C.; Midtgaard, S. R.; Ejlersen, M.; Thulstrup, P. W.; Sørensen, K. K.; Jensen, K. J.; Wengel, J. Folding topology of a short coiled coil peptide structure templated by an oligonucleotide triplex. Chem. Eur. J. (2017) 23, 9297-9305. (Hot Paper) [] [].
[BioNEC-34] Kermanizadeh, Ali; Villadsen, Klaus; Østrem, Ragnhild G.; Jensen, Knud J.; Peter Møller, Peter; Loft, Steffen. Integrin targeting and toxicological assessment of peptide-conjugated liposome delivery systems to activated endothelial cells. Basic and Clinical Pharmacology and Toxicology (2017) 120, 380–389. [].
[BioNEC-33] Vejlegaard, Kim; Paul, Sibasish; Kosbar, Tamer; Wengel, Jesper; Caruthers, Marvin H. Oligodeoxynucleotides containing 2'-amino-LNA nucleotides as constrained morpholino phosphoramidate and phosphorodiamidate monomers. Bioorganic and Medicinal Chemistry Letters (2017), 27, 3173-3176. [].
[BioNEC-32] Kumar, Rajesh; Ries, Annika; Wengel, Jesper. Synthesis and excellent duplex stability of oligonucleotides containing 2′-amino-LNA functionalized with galactose units. Molecules (2017), 22, 852. [].
[BioNEC-31] Villadsen, K.; Martos-Maldonado, M. C.; Jensen, K. J.; Thygesen, M. B.; Chemoselective reactions for the synthesis of glycoconjugates from unprotected carbohydrates. ChemBioChem (2017), 18, 574-612. [] []
[BioNEC-30] Lou, C.; Samuelsen, S. V.; Christensen, N. J.; Vester, B.; Wengel, J. Oligonucleotides containing aminated 2’-amino-LNA nucleotides: Synthesis and strong binding to complementary DNA and RNA. Bioconjug. Chem. (2017), 28(4), 1214-1220. [].
[BioNEC-29] Taskova, Maria; Madsen, Charlotte S.; Jensen, Knud J.; Hansen, Lykke Haastrup; Vester, Birte; Astakhova, Kira. Antisense oligonucleotides internally labeled with peptides show improved target recognition and stability to enzymatic degradation. Bioconjugate Chemistry (2017), 28(3), 768-774 [
[BioNEC-28] Ejlersen, Maria; Langkjaer, Niels; Wengel, Jesper. 3'-Pyrene-modified unlocked nucleic acids: synthesis, fluorescence properties and a surprising stabilization effect on duplexes and triplexes. Organic & Biomolecular Chemistry (2017), 15, 2073–2085 [].
[BioNEC-27] Vinther, M., Kjems, J. Interfacing DNA nanodevices with biology: Challenges, solutions and perspectives. New J. Phys. 2016, 18, 85005. []
[BioNEC-26] Okholm, A. H.; Kjems J. DNA nanovehicles and the biological barriers. Adv. Drug Deliv. Rev. 2016, 106, 183-191. []
[BioNEC-25] Schaffert, D. A. H.; Okholm, A.; Sørensen, R. S.; Nielsen, J. S.; Tørring, T.; Rosen, C. B.; Kodal, A. L. B.; Gothelf, K. V.; Kjems, J. Intracellular delivery of a planar DNA origami structure by the transferrin-receptor internalization pathway. Small 2016, 12, 2634-2640. []
[BioNEC-24] Cogoi, S, Jakobsen, U, Pedersen, EB, Vogel, S & Xodo, LE. Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles: delivery and bioactivity in pancreatic cancer cells. Scientific Reports, (2016), 6, 38468. []
Abstract: KRAS is mutated in >90% of pancreatic ductal adenocarcinomas. As its inactivation leads to tumour regression, mutant KRAS is considered an attractive target for anticancer drugs. In this study we report a new delivery strategy for a G4-decoy oligonucleotide that sequesters MAZ, a transcription factor essential for KRAS transcription. It is based on the use of palmitoyl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with lipid-modified G4-decoy oligonucleotides and a lipid-modified cell penetrating TAT peptide. The potency of the strategy in pancreatic cancer cells is demonstrated by cell cytometry, confocal microscopy, clonogenic and qRT-PCR assays.
[BioNEC-23] Ries, Annika; Kumar, Rajesh; Lou, Chenguang; Kosbar, Tamer; Vengut-Climent, Empar; Jørgensen, Per T.; Morales, Juan C.; Wengel, Jesper. Synthesis and biophysical investigations of oligonucleotides containing galactose-modified DNA, LNA, and 2'-amino-LNA monomers. Journal of Organic Chemistry (2016), 81(22), 10845-10856. []
Abstract: Galactose-modified thymidine, LNA-T, and 2′-amino-LNA-T nucleosides were synthesized, converted into the corresponding phosphoramidite derivatives and introduced into short oligonucleotides. Compared to the unmodified control strands, the galactose-modified oligonucleotides in general, and the N2′-functionalized 2′-amino-LNA derivatives in particular, showed improved duplex thermal stability against DNA and RNA complements and increased ability to discriminate mismatches. In addition, the 2′-amino-LNA-T derivatives induced remarkable 3′-exonuclease resistance. These results were further investigated using molecular modeling studies.
[BioNEC-22] Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic. Nature Communications (2016), 7, 12294. []
Abstract: Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain formation have never been realized for de novo protein design. Here, we show the applicability of peptide–oligonucleotide conjugates for self-assembly of higher-ordered protein-like structures. The resulting nano-assemblies were characterized by ultraviolet-melting, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering and transmission electron microscopy. These studies revealed the formation of the desired triple helix and coiled coil domains at low concentrations, while a dimer of trimers was dominating at high concentration. CD spectroscopy showed an extraordinarily high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design.
[BioNEC-21] Jakobsen, Ulla; Vogel, Stefan.: Mismatch discrimination of lipidated DNA and LNA-probes (LiNAs) in hybridization-controlled liposome assembly. Organic & Biomolecular Chemistry (2016), 14(29), 6985-6995. []
Abstract: Assays for mismatch discrimination and detection of single nucleotide variations by hybridization-controlled assembly of liposomes, which do not require tedious surface chem., are versatile for both DNA and RNA targets. We report herein a comprehensive study on different DNA and LNA (locked nucleic acids) probe designs, including membrane-anchoring requirements, studies on different probes and target lengths (including overhangs), DNA and RNA targets (including sequences assocd. with pathogens) for lipidated nucleic acids (LiNAs). Advantages and limitations of the liposome assembly based assay in the context of mismatch discrimination and SNP detection are presented. The advantages of membrane-anchored LiNA-probes compared to chem. attached probes on solid nanoparticles (e.g. gold nanoparticles) are described. Key functionalities such as non-covalent attachment of LiNA probes without the need for long spacers and the inherent mobility of membrane-anchored probes in lipid-bilayer membranes will be described for several different probe designs.
[BioNEC-20] Munch, Henrik KofoedNygård, Jesper; Christensen, Niels Johan; Engelbrekt, Christian; Østergaard, Mads; Porsgaard, Trine; Hoeg-Jensen, Thomas; Zhang, Jingdong; Arleth, Lise; Thulstrup, Peter Waaben; Jensen, Knud Jørgen.: Construction of insulin 18-mer nanoassemblies driven by coordination to Iron(II) and Zinc(II) ions at distinct sites. Angewandte Chemie (International Edition) (2016) 55(7), 2378-2381. []
[BioNEC-19] Vogel, S. Ries, O.: Aptamer-liposome conjugates: Current art and furture prospects, in Aptamers: Tools for nanotherapy and molecular imaging, Ed. R. N. Veedu, CRC Press/Taylor & Francis Group: Boca Raton, FL, 223-251, (2016).
[BioNEC-18] Vogel, S.: DNA鈥恈ontrolled assembly of soft nanoparticles, in DNA in Supramolecular Chemistry and Nanotechnology, Ed. E. Stulz & G. H. Clever, John Wiley & Sons, Ltd., Chichester, 397-411, (2015).
[BioNEC-17] Malik, L.; Nygaard, J.; Christensen, N. J.; Madsen, C. S.; Rösner, H. I.; Kragelund, B. B.; Hoiberg-Nielsen, R.; Streicher, W. W.; Arleth, L.; Thulstrup, P. W.; Jensen. K. J. A de novo designed monomeric, compact three helix bundle protein on a carbohydrate template.ChemBioChem (2015), 16(13), 1905-1918. []
[BioNEC-16] Ries, Oliver; Löffler, Philipp M. G.; Vogel, Stefan. Convenient synthesis and application of versatile nucleic acid lipid membrane anchors in the assembly and fusion of liposomes. Organic & Biomolecular Chemistry (2015), 13(37), 9673-9680 []
[BioNEC-15] Okholm A. H., Aslan H., Besenbacher F., Dong M., Kjems J. Single molecule visualization of surface-initiated enzymatic polymerization on DNA origami. Nanoscale 2015, 7, 10970-10973. []
[BioNEC-14] Nåbo, Lina J.; Madsen, Charlotte S.; Jensen, Knud J.; Kongsted, Jacob; Astakhova, Kira. Ultramild protein-mediated Click chemistry creates efficient oligonucleotide probes for targeting and detecting nucleic acids. ChemBioChem (2015), 16(8), 1163-1167. []
[BioNEC-13] Lou, Chenguang; Vester, Birte; Wengel, Jesper. Oligonucleotides containing a piperazino-modified 2’-amino-LNA monomer exhibit very high duplex stability and remarkable nuclease resistance. Chemical Communications (2015), 51(19), 4024-4027. []
[BioNEC-12] Perlikova, Pavla; Ejlersen, Maria; Langkjaer, Niels; Wengel, Jesper. Bis-pyrene-modified unlocked nucleic acids: Synthesis, hybridization studies, and fluorescent properties. ChemMedChem (2014), 9(9), 2120-2127. [
[BioNEC-11] Astakhova, I. Kira; Wengel, Jesper. Scaffolding along Nucleic Acid Duplexes Using 2'-Amino-Locked Nucleic Acids. Accounts of Chemical Research (2014), 47(6), 1768-1777. []
[BioNEC-10] Olsen; Birgitte Brinkmann; Thisgaard, Helge; Vogel, Stefan; Thomassen, Mads; Kruse, Torben A.; Needham, David; Mollenhauer, Jan; Høilund-Carlsen, Poul Flemming. Novel radioisotope-based nanomedical approaches. European Journal of Nanomedicine (2013), 5(4), 181–193. []
[BioNEC-9] Rasmussen, Thomas E.; Jauffred, Liselotte; Brewer, Jonathan; Vogel, Stefan; Torbensen, Esben R.; Lagerholm, B. Christoffer; Oddershede, Lene; Arnspang, Eva C. Single molecule applications of quantum dots. Journal of Modern Physics (2013), 4, 27-42. []
[BioNEC-8] Jørgensen, Anna S.; Gupta, Pankaj; Wengel, Jesper; Astakhova, I. Kira. “Clickable” LNA/DNA probes for fluorescence sensing of nucleic acids and autoimmune antibodies. Chemical Communications (2013), 49(91), 10751-10753. []
[BioNEC-7] Sørensen, Rasmus Schøler; Okholm, Anders Hauge; Schaffert, David; Kodal, Anne Louise Bank; Gothelf; Kurt V.; Kjems; Jørgen. Enzymatic ligation of large biomolecules to DNA. ACS Nano (2013), 7(9), 8098–8104 []
[BioNEC-6] Karlsen, Kasper K.; Okholm, Anders; Kjems, Joergen; Wengel, Jesper. A quencher-free molecular beacon design based on pyrene excimer fluorescence using pyrene-labeled UNA (unlocked nucleic acid). Bioorganic & Medicinal Chemistry (2013), 21(20), 6186–6190. []
[BioNEC-5] Jakobsen, Ulla; Vogel, Stefan. Assembly of liposomes controlled by triple helix formation. Bioconjugate Chemistry, 24(9), 1485-1495. []
[BioNEC-4] Astakhova, I. Kira; Hansen, Lykke Haastrup; Vester, Birte; Jesper Wengel. Peptide–LNA oligonucleotide conjugates. Org. Biomol. Chem. (2013), 11(25), 4240-4249. []
[BioNEC-3] Astakhova, I. Kira; Pasternak, Karol; Campbell, Meghan A.; Gupta, Pankaj; Wengel, Jesper. A locked nucleic acid-based nanocrawler: Designed and reversible movement detected by multicolor fluorescence. Journal of the American Chemical Society (2013), 135(7), 2423-2426. []
[BioNEC-2] Astakhova, I. Kira; Wengel, Jesper. Interfacing click chemistry with automated oligonucleotide synthesis for the preparation of fluorescent DNA probes containing internal xanthene and cyanine dyes. Chem. Eur. J. (2013), 19(3), 1112-1122. []
[BioNEC-1] Astakhova, I. Kira; Santhosh Kumar, T.; Campbell, Meghan A.; Ustinov, Alexey V.; Korshun, Vladimir A.; Wengel, Jesper. Branched DNA nanostructures efficiently stabilised and monitored by novel pyrene-perylene 2'-α-l-amino-LNA FRET pairs. Chemical Communications (2013), 49(5), 511-513. []