Seikowski, Jan

[["dc.bibliographiccitation.artnumber","5859"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","5"],["dc.contributor.author","Lin, Chao-Chen"],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Perez-Lara, Angel"],["dc.contributor.author","Jahn, Reinhard"],["dc.contributor.author","Höbartner, Claudia"],["dc.contributor.author","Walla, Peter Jomo"],["dc.date.accessioned","2018-11-07T09:31:47Z"],["dc.date.available","2018-11-07T09:31:47Z"],["dc.date.issued","2014"],["dc.description.abstract","Fast synchronous neurotransmitter release is triggered by calcium that activates synaptotagmin-1 (syt-1), resulting in fusion of synaptic vesicles with the presynaptic membrane. Syt-1 possesses two Ca2+-binding C2 domains that tether membranes via interactions with anionic phospholipids. It is capable of crosslinking membranes and has recently been speculated to trigger fusion by decreasing the gap between them. As quantitative information on membrane gaps is key to understanding general cellular mechanisms, including the role of syt-1, we developed a fluorescence-lifetime based inter-membrane distance ruler using membrane-anchored DNAs of various lengths as calibration standards. Wild-type and mutant data provide evidence that full-length syt-1 indeed regulates membrane gaps: without Ca2+, syt-1 maintains membranes at distances of similar to 7-8 nm. Activation with 100 mu M Ca2+ decreases the distance to similar to 5 nm by binding the C2 domains to opposing membranes, respectively. These values reveal that activated syt-1 adjusts membrane distances to the level that promotes SNARE complex assembly."],["dc.identifier.doi","10.1038/ncomms6859"],["dc.identifier.isi","000347683100001"],["dc.identifier.pmid","25500905"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/31610"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","2041-1723"],["dc.title","Control of membrane gaps by synaptotagmin-Ca2+ measured with a novel membrane distance ruler"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","5505"],["dc.bibliographiccitation.issue","14"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","5509"],["dc.bibliographiccitation.volume","59"],["dc.contributor.author","Savicheva, Elizaveta A."],["dc.contributor.author","Mitronova, Guyzel Yu."],["dc.contributor.author","Thomas, Laura"],["dc.contributor.author","Böhm, Marvin J."],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Belov, Vladimir N."],["dc.contributor.author","Hell, Stefan W."],["dc.date.accessioned","2021-04-14T08:27:44Z"],["dc.date.available","2021-04-14T08:27:44Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1002/anie.201908063"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/82385"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","1521-3773"],["dc.relation.issn","1433-7851"],["dc.title","Negatively Charged Yellow‐Emitting 1‐Aminopyrene Dyes for Reductive Amination and Fluorescence Detection of Glycans"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","5329"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Analytical Chemistry"],["dc.bibliographiccitation.lastpage","5336"],["dc.bibliographiccitation.volume","92"],["dc.contributor.author","Fomin, Maksim A."],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Belov, Vladimir N."],["dc.contributor.author","Hell, Stefan W."],["dc.date.accessioned","2022-03-01T11:45:38Z"],["dc.date.available","2022-03-01T11:45:38Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1021/acs.analchem.9b05863"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103400"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1520-6882"],["dc.relation.issn","0003-2700"],["dc.title","Negatively Charged Red-Emitting Acridine Dyes for Facile Reductive Amination, Separation, and Fluorescent Detection of Glycans"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3172"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Chemical Science"],["dc.bibliographiccitation.lastpage","3180"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Halbmair, Karin"],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Tkach, Igor"],["dc.contributor.author","Höbartner, Claudia"],["dc.contributor.author","Sezer, Deniz"],["dc.contributor.author","Bennati, Marina"],["dc.date.accessioned","2016-07-05T10:41:32Z"],["dc.date.accessioned","2021-10-27T13:12:28Z"],["dc.date.available","2016-07-05T10:41:32Z"],["dc.date.available","2021-10-27T13:12:28Z"],["dc.date.issued","2016"],["dc.description.abstract","Structural information at atomic resolution of biomolecular assemblies, such as RNA and RNA protein complexes, is fundamental to comprehend biological function. Modern spectroscopic methods offer exceptional opportunities in this direction. Here we present the capability of pulse EPR to report highresolution long-range distances in RNAs by means of a recently developed spin labeled nucleotide, which carries the TEMPO group directly attached to the nucleobase and preserves Watson–Crick base-pairing. In a representative RNA duplex with spin-label separations up to 28 base pairs (z8 nm) we demonstrate that the label allows for a model-free conversion of inter-spin distances into base-pair separation (Dbp) if broadband pulse excitation at Q band frequencies (34 GHz) is applied. The observed distance distribution increases from 0.2 nm for Dbp ¼ 10 to only 0.5 nm for Dbp ¼ 28, consistent with only small deviations from the “ideal” A-form RNA structure. Molecular dynamics (MD) simulations conducted at 20 C show restricted conformational freedom of the label. MD-generated structural deviations from an “ideal” A-RNA geometry help disentangle the contributions of local flexibility of the label and its neighboring nucleobases and global deformations of the RNA double helix to the experimental distance distributions. The study demonstrates that our simple but strategic spin labeling procedure can access detailed structural information on RNAs at atomic resolution over distances that match the size of macromolecular RNA complexes."],["dc.description.sponsorship","DFG Collaborative Research Centre (CRC) [803]; Max Planck Society"],["dc.identifier.doi","10.1039/C5SC04631A"],["dc.identifier.isi","000374859300027"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13415"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/91693"],["dc.language.iso","en"],["dc.notes.intern","Migrated from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Royal Soc Chemistry"],["dc.relation.issn","2041-6539"],["dc.relation.issn","2041-6520"],["dc.relation.orgunit","Fakultät für Chemie"],["dc.rights","CC BY-NC 3.0"],["dc.rights.access","openAccess"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc/3.0"],["dc.subject","long-range distances; RNA; EPR spectroscopy"],["dc.title","High-resolution measurement of long-range distances in RNA: pulse EPR spectroscopy with TEMPO-labeled nucleotides"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1912"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","1916"],["dc.bibliographiccitation.volume","55"],["dc.contributor.author","Samanta, Biswajit"],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Hoebartner, Claudia"],["dc.date.accessioned","2018-11-07T10:19:10Z"],["dc.date.available","2018-11-07T10:19:10Z"],["dc.date.issued","2016"],["dc.description.abstract","5-Formylcytosine (5fC) and 5-formyluracil (5fU) are natural nucleobase modifications that are generated by oxidative modification of 5-methylcytosine and thymine (or 5-methyluracil). Herein, we describe chemoselective labeling of 5-formylpyrimidine nucleotides in DNA and RNA by fluorogenic aldol-type condensation reactions with 2,3,3-trimethylindole derivatives. Mild and specific reaction conditions were developed for 5fU and 5fC to produce hemicyanine-like chromophores with distinct photophysical properties. Residue-specific detection was established by fluorescence readout as well as primer-extension assays. The reactions were optimized on DNA oligonucleotides and were equally suitable for the modification of 5fU- and 5fC-modified RNA. This direct labeling approach of 5-formylpyrimidines is expected to help in elucidating the occurrence, enzymatic transformations, and functional roles of these epigenetic/epitranscriptomic nucleobase modifications in DNA and RNA."],["dc.identifier.doi","10.1002/anie.201508893"],["dc.identifier.isi","000369854000061"],["dc.identifier.pmid","26679556"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/41610"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-v C H Verlag Gmbh"],["dc.relation.issn","1521-3773"],["dc.relation.issn","1433-7851"],["dc.title","Fluorogenic Labeling of 5-Formylpyrimidine Nucleotides in DNA and RNA"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3720"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","3726"],["dc.bibliographiccitation.volume","60"],["dc.contributor.author","Savicheva, Elizaveta A."],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Kast, Jeannette I."],["dc.contributor.author","Grünig, Christoph R."],["dc.contributor.author","Belov, Vladimir N."],["dc.contributor.author","Hell, Stefan W."],["dc.date.accessioned","2022-03-01T11:45:02Z"],["dc.date.available","2022-03-01T11:45:02Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1002/anie.202013187"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103193"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","1521-3773"],["dc.relation.issn","1433-7851"],["dc.rights.uri","http://creativecommons.org/licenses/by-nc-nd/4.0/"],["dc.title","Fluorescence Assisted Capillary Electrophoresis of Glycans Enabled by the Negatively Charged Auxochromes in 1‐Aminopyrenes"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","15128"],["dc.bibliographiccitation.issue","50"],["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.bibliographiccitation.lastpage","15133"],["dc.bibliographiccitation.volume","54"],["dc.contributor.author","Kosutic, Marija"],["dc.contributor.author","Neuner, Sandra"],["dc.contributor.author","Ren, Aiming"],["dc.contributor.author","Fluer, Sara"],["dc.contributor.author","Wunderlich, Christaph"],["dc.contributor.author","Mairhofer, Elisabeth"],["dc.contributor.author","Vusurovic, Nikola"],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Breuket, Kathrin"],["dc.contributor.author","Hoebartner, Claudia"],["dc.contributor.author","Patel, Dinshaw J."],["dc.contributor.author","Kreutz, Christoph"],["dc.contributor.author","Micura, Ronald"],["dc.date.accessioned","2018-11-07T09:47:37Z"],["dc.date.available","2018-11-07T09:47:37Z"],["dc.date.issued","2015"],["dc.description.abstract","Nucleolytic ribozymes catalyze site-specific cleavage of their phosphodiester backbones. A minimal version of the twister ribozyme is reported that lacks the phylogenetically conserved stem P1 while retaining wild-type activity. Atomic mutagenesis revealed that nitrogen atoms N1 and N3 of the adenine-6 at the cleavage site are indispensable for cleavage. By NMR spectroscopy, a pK(a) value of 5.1 was determined for a (13)C2-labeled adenine at this position in the twister ribozyme, which is significantly shifted compared to the pKa of the same adenine in the substrate alone. This finding pinpoints at a potential role for adenine-6 in the catalytic mechanism besides the previously identified invariant guanine-48 and a Mg2+ ion, both of which are directly coordinated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence stems from the observation that Mn2+ or Cd2+ accelerated cleavage of phosphorothioate substrates. The relevance of this metal ion binding site is further emphasized by a new 2.6 angstrom X-ray structure of a 2'-OCH3- U5 modified twister ribozyme."],["dc.identifier.doi","10.1002/anie.201506601"],["dc.identifier.isi","000368057400023"],["dc.identifier.pmid","26473980"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/35151"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-v C H Verlag Gmbh"],["dc.relation.issn","1521-3773"],["dc.relation.issn","1433-7851"],["dc.title","A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2104"],["dc.bibliographiccitation.issue","19"],["dc.bibliographiccitation.journal","EMBO Journal"],["dc.bibliographiccitation.lastpage","2119"],["dc.bibliographiccitation.volume","35"],["dc.contributor.author","Haag, Sara"],["dc.contributor.author","Sloan, Katherine E."],["dc.contributor.author","Ranjan, Namit"],["dc.contributor.author","Warda, Ahmed S."],["dc.contributor.author","Kretschmer, Jens"],["dc.contributor.author","Blessing, Charlotte"],["dc.contributor.author","Hübner, Benedikt"],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Dennerlein, Sven"],["dc.contributor.author","Rehling, Peter"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Höbartner, Claudia"],["dc.contributor.author","Bohnsack, Markus T."],["dc.date.accessioned","2017-09-07T11:44:33Z"],["dc.date.available","2017-09-07T11:44:33Z"],["dc.date.issued","2016"],["dc.description.abstract","Mitochondrial gene expression uses a non-universal genetic code in mammals. Besides reading the conventional AUG codon, mitochondrial (mt-)tRNA(Met) mediates incorporation of methionine on AUA and AUU codons during translation initiation and on AUA codons during elongation. We show that the RNA methyltransferase NSUN3 localises to mitochondria and interacts with mt-tRNA(Met) to methylate cytosine 34 (C34) at the wobble position. NSUN3 specifically recognises the anticodon stem loop (ASL) of the tRNA, explaining why a mutation that compromises ASL basepairing leads to disease. We further identify ALKBH1/ABH1 as the dioxygenase responsible for oxidising m(5)C34 of mt-tRNA(Met) to generate an f(5)C34 modification. In vitro codon recognition studies with mitochondrial translation factors reveal preferential utilisation of m(5)C34 mt-tRNA(Met) in initiation. Depletion of either NSUN3 or ABH1 strongly affects mitochondrial translation in human cells, implying that modifications generated by both enzymes are necessary for mt-tRNA(Met) function. Together, our data reveal how modifications in mt-tRNA(Met) are generated by the sequential action of NSUN3 and ABH1, allowing the single mitochondrial tRNA(Met) to recognise the different codons encoding methionine."],["dc.identifier.doi","10.15252/embj.201694885"],["dc.identifier.gro","3141604"],["dc.identifier.isi","000385707500006"],["dc.identifier.pmid","27497299"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13845"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/235"],["dc.identifier.url","https://sfb1190.med.uni-goettingen.de/production/literature/publications/5"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation","SFB 1190: Transportmaschinen und Kontaktstellen zellulärer Kompartimente"],["dc.relation","SFB 1190 | P13: Protein Transport über den mitochondrialen Carrier Transportweg"],["dc.relation","SFB 1190 | P14: Die Rolle humaner Nucleoporine in Biogenese und Export makromolekularer Komplexe"],["dc.relation","SFB 1190 | P16: Co-translationaler Einbau von Proteinen in die bakterielle Plasmamembran"],["dc.relation.eissn","1460-2075"],["dc.relation.issn","0261-4189"],["dc.relation.workinggroup","RG M. Bohnsack (Molecular Biology)"],["dc.relation.workinggroup","RG Rehling (Mitochondrial Protein Biogenesis)"],["dc.relation.workinggroup","RG Rodnina"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","NSUN3 and ABH1 modify the wobble position of mt-tRNA(Met) to expand codon recognition in mitochondrial translation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","7267"],["dc.bibliographiccitation.issue","11"],["dc.bibliographiccitation.journal","The Journal of Organic Chemistry"],["dc.bibliographiccitation.lastpage","7275"],["dc.bibliographiccitation.volume","85"],["dc.contributor.author","Belov, Vladimir N."],["dc.contributor.author","Stoldt, Stefan"],["dc.contributor.author","Rüttger, Franziska"],["dc.contributor.author","John, Michael"],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Schimpfhauser, Jens"],["dc.contributor.author","Hell, Stefan W."],["dc.date.accessioned","2021-04-14T08:25:52Z"],["dc.date.available","2021-04-14T08:25:52Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1021/acs.joc.0c00653"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/81752"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","1520-6904"],["dc.relation.issn","0022-3263"],["dc.title","Synthesis of Fluorescent Jasplakinolide Analogues for Live-Cell STED Microscopy of Actin"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]