Finn Kirpekar

Search results

• 2021

  Spatial variability of prokaryotic and viral abundances in the Kermadec and Atacama Trench regions

  Schauberger, C., Middelboe, M., Larsen, M., Peoples, L. M., Bartlett, D. H., Kirpekar, F., Rowden, A. A., Wenzhöfer, F., Thamdrup, B. & Glud, R. N., 28. Feb 2021, (E-pub ahead of print) In: Limnology and Oceanography.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • trench
  • sediments
  • virus
  • sediment
  • total organic carbon
• 2020

  Proteomic Changes of Klebsiella pneumoniae in Response to Colistin Treatment and crrB Mutation-Mediated Colistin Resistance

  Sun, L., Rasmussen, P. K., Bai, Y., Chen, X., Cai, T., Wang, J., Guo, X., Xie, Z., Ding, X., Niu, L., Zhu, N., You, X., Kirpekar, F. & Yang, F., Jun 2020, In: Antimicrobial Agents and Chemotherapy. 64, 6, e02200-19.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Colistin
  • Polymyxins
  • Mutation
  • 4-amino-4-deoxyarabinose
  • Enterobactin

• The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA

  Pinto, R., Vågbø, C. B., Jakobsson, M. E., Kim, Y., Baltissen, M. P., O'Donohue, M-F., Guzmán, U. H., Małecki, J. M., Wu, J., Kirpekar, F., Olsen, J. V., Gleizes, P-E., Vermeulen, M., Leidel, S. A., Slupphaug, G. & Falnes, P. Ø., 24. Jan 2020, In: Nucleic acids research. 48, 2, p. 830-846

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • 28S Ribosomal RNA
  • N(6)-methyladenosine
  • Methyltransferases
  • Messenger RNA
  • Enzymes
  24 Downloads (Pure)

• The hyperthermophilic partners Nanoarchaeum and Ignicoccus stabilize their tRNA T-loops via different but structurally equivalent modifications

  Rose, S., Auxilien, S., Havelund, J. F., Kirpekar, F., Huber, H., Grosjean, H. & Douthwaite, S., 9. Jul 2020, In: Nucleic acids research. 48, 12, p. 6906-6918

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Nanoarchaeota
  • Desulfurococcaceae
  • Transfer RNA
  • Nucleotides
  • Pseudouridine
  24 Downloads (Pure)
• 2019

  Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing

  Enroth, C., Poulsen, L. D., Iversen, S., Kirpekar, F., Albrechtsen, A. & Vinther, J., 18. Nov 2019, In: Nucleic acids research. 47, 20, p. e126 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Arabidopsis
  • Transfer RNA
  • RNA
  • sodium borohydride
  • Small Nucleolar RNA
  23 Downloads (Pure)

• Excision of uracil from DNA by hSMUG1 includes strand incision and processing

  Alexeeva, M., Moen, M. N., Grøsvik, K., Tesfahun, A. N., Xu, X. M., Muruzábal-Lecumberri, I., Olsen, K. M., Rasmussen, A., Ruoff, P., Kirpekar, F., Klungland, A. & Bjelland, S., 2019, In: Nucleic Acids Research. 47, 2, p. 779-793

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Uracil
  • DNA
  • Uracil-DNA Glycosidase
  • DNA Repair
  • human APEX1 protein
  95 Downloads (Pure)
• 2018

  Mapping of ribosomal 23S ribosomal RNA modifications in Clostridium sporogenes

  Kirpekar, F., Hansen, L. H., Mundus, J., Tryggedsson, S., Teixeira Dos Santos, P., Ntokou, E. & Vester, B., Aug 2018, In: RNA Biology. 15, 8, p. 1060–1070

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • 23S Ribosomal RNA
  • Ribosomal RNA
  • Clostridium
  • Enzymes
  • Clostridium botulinum
  87 Downloads (Pure)
• 2016

  Identification of the methyltransferase targeting C2499 in Deinococcus radiodurans 23S ribosomal RNA

  Nielsen, J. M., Flyvbjerg, K. F. & Kirpekar, F., Jan 2016, In: Extremophiles. 20, 1, p. 91-99

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • 23S Ribosomal RNA
  • Deinococcus
  • Cytidine
  • Methyltransferases
  • Chloramphenicol Resistance
  114 Downloads (Pure)
• 2015

  Automated N-glycan profiling of a mutant Trypanosoma rangeli sialidase expressed in Pichia pastoris, using tandem mass spectrometry and bioinformatics

  Li, H., Rasmussen, M. I., Larsen, M. R., Guo, Y., Jers, C., Palmisano, G., Mikkelsen, J. D. & Kirpekar, F., Dec 2015, In: Glycobiology. 25, 12, p. 1350-1361

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Trypanosoma rangeli
  • Mass spectrometry
  • Pichia
  • Neuraminidase
  • Tandem Mass Spectrometry

• Modulating the regioselectivity of a Pasteurella multocida sialyltransferase for biocatalytic production of 3'- and 6'-sialyllactose

  Guo, Y., Jers, C., Meyer, A. S., Li, H., Kirpekar, F. & Mikkelsen, J. D., Oct 2015, In: Enzyme and Microbial Technology. 78, p. 54-62

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Regioselectivity
  • 6'-sialyllactose
  • 3'-sialyllactose
  • Sialyltransferases
  • Pasteurella multocida
• 2014

  A Pasteurella multocida sialyltransferase displaying dual trans-sialidase activities for production of 3'-sialyl and 6'-sialyl glycans

  Guo, Y., Jers, C., Meyer, A. S., Arnous, A., Li, H., Kirpekar, F. & Mikkelsen, J. D., 20. Jan 2014, In: Journal of Biotechnology. 170, p. 60-67 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • 6'-sialyllactose
  • 3'-sialyllactose
  • Casein
  • trans-sialidase
  • Sialyltransferases

• Biocatalytic production of 3′-sialyllactose by use of a modified sialidase with superior trans-sialidase activity

  Michalak, M., Larsen, D. M., Jers, C., Almeida, J. R. M., Willer, M., Li, H., Kirpekar, F., Kjærulff, L., Gotfredsen, C. H., Nordvang, R. T., Meyer, A. S. & Mikkelsen, J. D., 1. Feb 2014, In: Process Biochemistry. 49, 2, p. 265-270 6 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Human Milk
  • 3'-sialyllactose
  • Casein
  • trans-sialidase
  • caseinomacropeptide

• Characterization of an extensin-modifying metalloprotease: N-terminal processing and substrate cleavage pattern of Pectobacterium carotovorum Prt1

  Feng, T., Nyffenegger, C., Højrup, P., Vidal-Melgosa, S., Yan, K-P., Fangel, J. U., Meyer, A. S., Kirpekar, F., Willats, W. G. & Mikkelsen, J. D., 20. Nov 2014, In: Applied Microbiology and Biotechnology. 98, 24, p. 10077-10089

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Pectobacterium carotovorum
  • Metalloproteases
  • Cell Wall
  • Plant Cells
  • Enzymes

• Enzyme catalysed production of sialylated human milk oligosaccharides and galactooligosaccharides by Trypanosoma cruzi trans-sialidase

  Holck, J., Larsen, D. M., Michalak, M., Li, H., Kjærulff, L., Kirpekar, F., Gotfredsen, C. H., Forssten, S., Ouwehand, A. C., Mikkelsen, J. D. & Meyer, A. S., Mar 2014, In: New Biotechnology. 31, 2, p. 156-165 10 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Human Milk
  • caseinomacropeptide
  • Casein
  • trans-sialidase
  • 3'-sialyllactose

• Protozoan ALKBH8 Oxygenases Display both DNA Repair and tRNA Modification Activities

  Zdżalik, D., Vågbø, C. B., Kirpekar, F., Davydova, E., Puścian, A., Maciejewska, A. M., Krokan, H. E., Klungland, A., Tudek, B., van den Born, E. & Falnes, P. Ø., 2014, In: PLOS ONE. 9, June, e98729.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Oxygenases
  • Transfer RNA
  • oxygenases
  • DNA repair
  • Protozoa

• Rational design of a new Trypanosoma rangeli trans-sialidase for efficient sialylation of glycans

  Jers, C., Michalak, M., Larsen, D. M., Kepp, K. P., Li, H., Guo, Y., Kirpekar, F., Meyer, A. S. & Mikkelsen, J. D., 3. Jan 2014, In: PLOS ONE. 9, 1, p. e83902

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Trypanosoma rangeli
  • trans-sialidase
  • sialidase
  • Neuraminidase
  • Polysaccharides
• 2013

  Distinction between the Cfr Methyltransferase Conferring Antibiotic Resistance and the Housekeeping RlmN Methyltransferase

  Atkinson, G. C., Hansen, L. H., Tenson, T., Rasmussen, A., Kirpekar, F. & Vester, B., Aug 2013, In: Antimicrobial Agents and Chemotherapy. 57, 8, p. 4019-4026 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Housekeeping
  • Methyltransferases
  • Microbial Drug Resistance
  • Enzymes
  • Peptidyl Transferases
• 2012

  Identification and characterization of the Thermus thermophilus 5-methylcytidine (m⁵C) methyltransferase modifying 23 S ribosomal RNA (rRNA) base C1942

  larsen, L. H. G., Rasmussen, A., Giessing, A., Jogl, G. & Kirpekar, F., 2012, In: Journal of Biological Chemistry. 287, p. 27593–27600

  Research output: Contribution to journal › Journal article › Research › peer-review

• Mass spectrometry in the biology of RNA and its modifications

  Giessing, A. & Kirpekar, F., 2012, In: Journal of Proteomics. 75, p. 3434-3449

  Research output: Contribution to journal › Journal article › Research › peer-review

• Recognition of guanosine by unrelated tRNA methyltransferases

  Sakagushi, R., Giessing, A., Dai, Q., Liukeviciute, Z., Klimasaukas, S., Piccirilli, J., Kirpekar, F. & Hou, Y-M., 2012, In: R N A. 18, p. 1687-1701

  Research output: Contribution to journal › Journal article › Research › peer-review
• 2011

  3-(3-amino-3-carboxypropyl)-5,6-Dihydrouridine is one of two novel post-transcriptional modifications in tRNA^Lys(UUU) from Trypanosoma brucei

  Krog, J. S., Español, Y., Giessing, A. M. B., Dziergowska, A., Malkiewicz, A., Ribas de Pouplana, L. & Kirpekar, F., 2011, In: F E B S Journal. 278, 24, p. 4782-96

  Research output: Contribution to journal › Journal article › Research › peer-review

  • RNA, Transfer, Lys
  • Transfer RNA
  • Nucleosides
  • Nucleotides
  • Ribonucleases

• ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA

  van den Born, E., Vagbo, C. B., Songe-Moller, L., Leihne, V., Lien, G. F., Leszczynska, G., Malkiewicz, A., Krokan, H. E., Kirpekar, F., Klungland, A. & Falnes, P. O., 2011, In: Nature Communications. 2

  Research output: Contribution to journal › Journal article › Research › peer-review

• A Nano-Chip-LC/MS Based Strategy for Characterization of Modified Nucleosides Using Reduced Porous Graphitic Carbon as a Stationary Phase

  Giessing, A., Scott, L. G. & Kirpekar, F., 2011, In: Journal of the American Society for Mass Spectrometry. 22, 7, p. 1242-1251

  Research output: Contribution to journal › Journal article › Research › peer-review

• A Nano-Chip-LC/MS Based Strategy for Characterization of Modified Nucleosides Using Reduced Porous Graphitic Carbon as a Stationary Phase

  Giessing, A., Scott, L. G. & Kirpekar, F., 2011.

  Research output: Contribution to conference without publisher/journal › Poster › Research

• Biomolecular Chemistry - third edition

  Kirpekar, F. (ed.) & Pedersen, E. B. (ed.), 2011, 3. ed. Harlow, England: Pearson Longman.

  Research output: Book/report › Monograph › Education

• Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA

  Havelund, J. F., Giessing, A. M. B., Hansen, T. M., Rasmussen, A., Scott, L. G. & Kirpekar, F., 2011, In: Journal of Molecular Biology. 411, 3, p. 529-536 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • 23S Ribosomal RNA
  • Nucleosides
  • Nucleotides
  • Deinococcus
  • Escherichia coli

• Minimal Substrate Features for Erm Methyltransferases Defined by Using a Combinatorial Oligonucleotide Library

  Hansen, L. H., Lobedanz, S., Douthwaite, S., Arar, K., Wengel, J., Kirpekar, F. & Vester, B., 24. Jan 2011, In: ChemBioChem. 12, 4, p. 610-614 5 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Methylation
  • Methyltransferases
  • Oligonucleotides
  • Substrates
  • Nucleotides

• Platinum Interference with siRNA Non-seed Regions Fine-Tunes Silencing Capacity

  Hedman, H. K., Kirpekar, F. & Elmroth, S. K. C., 10. Aug 2011, In: Journal of the American Chemical Society. 133, 31, p. 11977-84 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • RNA
  • Platinum
  • Oxaliplatin
  • MicroRNAs
  • Small Interfering RNA

• Roles of Trm9- and ALKBH8-like proteins in the formation of modified wobble uridines in Arabidopsis tRNA

  Leihne, V., Kirpekar, F., Vågbø, C. B., van den Born, E., Krokan, H. E., Grini, P. E., Meza, T. J. & Falnes, P. Ø., 2011, In: Nucleic Acids Research. 39, 17, p. 7688-7701

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Arabidopsis
  • Uridine
  • Transfer RNA
  • Ribose
  • 5-carbamoylmethyluridine
• 2010

  Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding

  Songe-Møller, L., van den Born, E., Leihne, V., Vågbø, C. B., Kristoffersen, T., Krokan, H. E., Kirpekar, F., Falnes, P. Ø. & Klungland, A., 1. Apr 2010, In: Molecular and Cellular Biology. 30, 7, p. 1814-27 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

• Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus

  Demirci, H., Larsen, L. H. G., Hansen, T., Rasmussen, A., Cadambi, A., Gregory, S. T., Kirpekar, F. & Jogl, G., 1. Aug 2010, In: RNA: A publication of the RNA Society. 16, 8, p. 1584-96 12 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Methyltransferases
  • Ribosomes
  • Escherichia coli
  • 5-methylcytidine
  • Catalytic Domain

• Novel complex modifications in tRNA^Lys(UUU) from Trypanosoma brucei revealed by mass spectrometry

  Krog, J. S., Español, Y., de Pouplana, L. R. & Kirpekar, F., 2010.

  Research output: Contribution to conference without publisher/journal › Poster › Research
• 2009

  An amide-HILIC nano-LC/MS based platform for oligonucleotide profiling

  Giessing, A. & Kirpekar, F., 2009.

  Research output: Contribution to conference without publisher/journal › Poster › Research

• Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria

  Giessing, A., Jensen, S. S., Rasmussen, A., Hansen, L. H., Gondela, A., Long, K., Vester, B. & Kirpekar, F., 1. Feb 2009, In: RNA: A publication of the RNA Society. 15, 2, p. 327-336 9 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • 8-methyladenosine
  • Methyltransferases
  • Microbial Drug Resistance
  • Nucleosides
  • Bacteria

• Identification of RNA molecules by specific enzyme digestion and mass spectrometry: software for and implementation of RNA mass mapping

  Matthiesen, R. & Kirpekar, F., 1. Apr 2009, In: Nucleic Acids Research. 37, 6, p. e48

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Digestion
  • Mass Spectrometry
  • Software
  • RNA
  • Enzymes

• PARTICLES AND THEIR USE IN A METHOD FOR ISOLATING NUCLEIC ACID OR A METHOD FOR ISOLATING PHOSPHOPROTEINS

  Engholm-Keller, K., Kirpekar, F., Larsen, M. R., Jensen, O. N., Fonnum, G., Stene, T., Kjus, N. H., Pope, R. M. & Liang, X., 2009, Patent No. EP2066709, 9. Jun 2009

  Research output: Patent
• 2008

  Biomolecular Chemistry: Second Edition with Index

  Kirpekar, F. (ed.) & Pedersen, E. B. (ed.), 2008, 2. ed. England: AAAI Press. 290 p.

  Research output: Book/report › Monograph › Education

• The activity of rRNA resistance methyltransferases assessed by MALDI mass spectrometry

  Douthwaite, S., Jensen, R. L. & Kirpekar, F., 2008, Methods in Molecular Medicine: New Antibiotic Targets. Champney, W. S. (ed.). Totowa, New Jersey, USA: Humana Press, Vol. 142. p. 223-237

  Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Communication
• 2007

  Collision-induced dissociation of cytidine and its derivatives

  Jensen, S. S., Ariza, X., Nielsen, P., Vilarrasa, J. & Kirpekar, F., 1. Jan 2007, In: Journal of Mass Spectrometry. 42, 1, p. 49-57 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

• Identifying modifications in RNA by MALDI mass spectrometry

  Douthwaite, S. & Kirpekar, F., 2007, In: Methods in Enzymology. 425, p. 1-20 19 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Mass spectrometry
  • Ionization
  • Desorption
  • Mass Spectrometry
  • RNA
• 2006

  Biomolecular Chemistry

  Kirpekar, F. (ed.) & Pedersen, E. B. (ed.), 2006, Pearson Longman.

  Research output: Book/report › Monograph › Education

• Identifying RNA by enzyme digestion and mass spectrometry: RNA mass mapping

  Matthiesen, R., Rasmussen, A., Schoenhals, G. J. & Kirpekar, F., 2006.

  Research output: Contribution to conference without publisher/journal › Poster › Research

• Methylation of tRNA^Asp by the DNA methyltransferase homolog Dnmt2

  Goll, M. G., Kirpekar, F., Maggert, K. A., Yoder, J. A., Hsieh, C-L., Zhang, X., Golic, K. G., Jakobsen, S. E. & Bestor, T. H., 2006, In: Science. 311, 5759, p. 395-398

  Research output: Contribution to journal › Journal article › Research › peer-review

• Modifications in Thermus thermophilus 23 S ribosomal RNA are centered in regions of RNA-RNA contact

  Mengel-From, J., Jensen, S. S., Rasmussen, A., Pøhlsgaard, J., Iversen, J. J. L. & Kirpekar, F., 2006, In: Journal of Biological Chemistry. 281, p. 22108-22117

  Research output: Contribution to journal › Journal article › Research › peer-review

• RNA Mapping

  Kirpekar, F., 2006, The Encyclopedia of Mass Spectrometry: Biological Applications Part B. Pergamon Press, Vol. 3. p. 10-15

  Research output: Chapter in Book/Report/Conference proceeding › Encyclopedia chapter › Research
• 2005

  The archaeon Haloarcula marismortui has few modifications in the central parts of its 23S ribosomal RNA

  Kirpekar, F., Hansen, L. H., Rasmussen, A., Pøhlsgaard, J. & Vester, B., 2005, In: Journal of Molecular Biology. 348, p. 563-573

  Research output: Contribution to journal › Journal article › Research › peer-review

• Typing of multiple SNPs using ribonuclease cleavage of DNA/RNA chimeric single base extension primers and detection by MALDI-TOF mass spectrometry

  Mengel-From, J., Sanchez, J. J., Børsting, C., Kirpekar, F. & Morling, N., 2005, In: Analytical Chemistry. 77, p. 5229-5235

  Research output: Contribution to journal › Journal article › Research › peer-review
• 2004

  A novel partial modification at C2501 in Escherichia coli 23S ribosomal RNA

  Andersen, T. E., Porse, B. T. & Kirpekar, F., 1. Jun 2004, In: RNA: A publication of the RNA Society. 10, 6, p. 907-13 6 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • RNA-Directed DNA Polymerase
  • 23S Ribosomal RNA
  • Electrospray Ionization Mass Spectrometry
  • Tandem Mass Spectrometry
  • Escherichia coli

• MALDI-TOF mass spectrometric detection of multiplex single base extended primers - a study of 17 Ychromosome SNPs.

  Mengel-From, J., Sanchez, J. J., Børsting, C., Kirpekar, F. & Morling, N., 2004, In: Analytical Chemistry. 76, p. 6039-6045

  Research output: Contribution to journal › Journal article › Research › peer-review

• Synthesis of Linear and Tripoidal Oligo(phenyleneethynylene)-Based Building Blocks for Application in Modular DNA-Programmed Assembly.

  Nielsen, M., Thomsen, A. H., Cló, E., Kirpekar, F. & Gothelf, K. V., 2004, In: Journal of Organic Chemistry. 69, p. 2240-2250

  Research output: Contribution to journal › Journal article › Research › peer-review