List of Publications

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Minero GAS , Møllebjerg A , Thiesen C , Johansen MI , Jørgensen NP , Birkedal V et al. Extracellular G-quadruplexes and Z-DNA protect biofilms from DNase I, and G-quadruplexes form a DNAzyme with peroxidase activity. Nucleic Acids Research. 2024 Feb;52(4):1575-1590. Epub 2024 Jan 31. doi: 10.1093/nar/gkae034

Aznauryan M , Birkedal V. Dynamics of G-Quadruplex Formation under Molecular Crowding. The Journal of Physical Chemistry Letters. 2023 Nov 23;14(46):10354-10360. doi: 10.1021/acs.jpclett.3c02453

Kristoffersen EL , Coletta A , Lund LM , Schiøtt B , Birkedal V. Inhibited complete folding of consecutive human telomeric G-quadruplexes. Nucleic Acids Research. 2023 Feb;51(4):1571-1582. doi: 10.1093/nar/gkad004

Bednarz AM , Sønderskov SM , Dong M , Birkedal V. Ion-mediated control of structural integrity and reconfigurability of DNA nanostructures. Nanoscale. 2023 Jan;15(3):1317-1326. doi: 10.1039/D2NR05780H

Valero J , Civit L , Dupont DM , Selnihhin D , Reinert LS , Idorn M et al. A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry. Proceedings of the National Academy of Sciences (PNAS). 2021 Dec;118(50):e2112942118. doi: 10.1073/pnas.2112942118

Madsen M , Bakke MR , Gudnason DA , Sandahl AF , Hansen RA , Knudsen JB et al. A Single Molecule Polyphenylene-Vinylene Photonic Wire. ACS Nano. 2021 Jun;15(6):9404-9411. doi: 10.1021/acsnano.0c10922

Thomas SP , Thomas R , Grønbech TBE , Bondesgaard M , Mamakhel AH , Birkedal V et al. Bandgap Tuning in Molecular Alloy Crystals Formed by Weak Chalcogen Interactions. Journal of Physical Chemistry Letters. 2021 Apr;12(12):3059-3065. doi: 10.1021/acs.jpclett.1c00614

Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC et al. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife. 2021 Mar;10:60416. doi: 10.7554/eLife.60416

Aznauryan M , Noer SL , Pedersen CW, Mergny JL, Teulade-Fichou MP, Birkedal V. Ligand Binding to Dynamically Populated G-Quadruplex DNA. ChemBioChem. 2021 May;22(10):1811-1817. doi: 10.1002/cbic.202000792

Thomas R , Thomas SP , Lakhotiya H , Mamakhel AH , Bondesgaard M , Birkedal V et al. Tuning of bandgaps and emission properties of light-emitting diode materials through homogeneous alloying in molecular crystals. Chemical Science. 2021 Oct 7;12(37):12391-12399. doi: 10.1039/d1sc03714e

Uhd J, Miotke L, Ji HP, Dunaeva M, Pruijn GJM, Jørgensen CD et al. Ultra-fast detection and quantification of nucleic acids by amplification-free fluorescence assay. Analyst. 2020 Sept;145(17):5836-5844. doi: 10.1039/d0an00676a

Jepsen MDE , Sørensen RS, Maffeo C, Aksimentiev A, Kjems J , Birkedal V. Single molecule analysis of structural fluctuations in DNA nanostructures. Nanoscale. 2019;11(39):18475-18482. doi: 10.1039/c9nr03826d

Gudnason DA , Madsen M , Krissanaprasit A , Gothelf KV , Birkedal V. Controlled aggregation of DNA functionalized poly(phenylene-vinylene). Chemical Communications. 2018;54(44):5534-5537. doi: 10.1039/c8cc00943k

Selnihhin D , Sparvath SM , Preus S , Birkedal V , Andersen ES. Multifluorophore DNA Origami Beacon as a Biosensing Platform. ACS Nano. 2018 May 15;12(6):5699–5708. doi: 10.1021/acsnano.8b01510

Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kuehnemuth R, Adariani SR et al. Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nature Methods. 2018 Sept 30;15(9):669-676. doi: 10.1038/s41592-018-0085-0

Aznauryan M , Birkedal V. Single - Molecule Fluorescence Microscopy of Folding Dynamics of G-Quadruplex DNA. Biophysical Journal. 2017 Feb 3;112(3):214A-215A.

Sprengel A, Lill P, Stegemann P, Bravo-Rodriguez K, Schöneweiß EC, Merdanovic M et al. Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions. Nature Communications. 2017;8:14472 (2017). doi: 10.1038/ncomms14472

Aznauryan M , Søndergaard S , Noer SL , Schiøtt B , Birkedal V. A direct view of the complex multi-pathway folding of telomeric G-quadruplexes. Nucleic Acids Research. 2016;44(22):11024-11032. doi: 10.1093/nar/gkw1010

Dyla M , Andersen J , Kjaergaard M , Birkedal V, Terry DS, Altman RB et al. Engineering a prototypic P-type ATPase Listeria Monocytogenes Ca(2+)-ATPase 1 for single-molecule FRET studies. Bioconjugate Chemistry. 2016;27(9):2176-2187. doi: 10.1021/acs.bioconjchem.6b00387

Zhang Z , Birkedal V , Gothelf KV. Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction. New Journal of Physics. 2016 May 6;18(5):055002. doi: 10.1088/1367-2630/18/5/055002

Kragh SL , Preus S , Gudnason DA , Aznauryan M, Mergny JL, Birkedal V. Folding dynamics and conformational heterogeneity of human telomeric G-quadruplex structures in Na+ solutions by single molecule FRET microscopy. Nucleic Acids Research. 2016 Jan 8;44(1):464-471. doi: 10.1093/nar/gkv1320

Preus S , Hildebrandt LL , Birkedal V. Optimal Background Estimators in Single-Molecule FRET Microscopy. Biophysical Journal. 2016 Sept 20;111(6):1278-1286. doi: 10.1016/j.bpj.2016.07.047

Krissanaprasit A , Madsen M , Knudsen JB , Gudnason DA, Surareungchai W, Birkedal V et al. Programmed Switching of Single Polymer Conformation on DNA Origami. ACS Nano. 2016 Jan 14;10(2):2243–2250. doi: 10.1021/acsnano.5b06894

M. Zadegan R , Jepsen MDE , Hildebrandt L , Birkedal V , Kjems J. Construction of a fuzzy and all Boolean logic gates based on DNA. Small. 2015 Apr 17;11(15):1811-1817. doi: 10.1002/smll.201402755

Søndergaard S , Aznauryan M, Haustrup EK, Schiøtt B , Birkedal V, Corry B. Dynamics of Fluorescent Dyes Attached to G-Quadruplex DNA and their Effect on FRET Experiments. ChemPhysChem. 2015 Aug 24;16(12):2562-2570. doi: 10.1002/cphc.201500271

Preus S , Noer SL , Hildebrandt LL , Gudnason D , Birkedal V. iSMS: single-molecule FRET microscopy software. Nature Methods. 2015 Jul;12(7):593-594. doi: 10.1038/nmeth.3435

Hildebrandt L , Preus S , Birkedal V. Quantitative single molecule FRET efficiency using TIRF microscopy. Faraday Discussions. 2015 Dec 1;184:131-142. doi: 10.1039/c5fd00100e

Knudsen JB , Liu L , Kodal ALB , Madsen M , Li Q , Song J et al. Routing of individual polymers in designed patterns. Nature Nanotechnology. 2015 Aug 31;10:892-898. doi: 10.1038/nnano.2015.190

Zhang Z , Hejesen C , Kjelstrup MB , Birkedal V , Gothelf KV. A DNA-Mediated Homogeneous Binding Assay for Proteins and Small Molecules. Journal of American Chemical Society. 2014 Aug 6;136(31):11115-11120. doi: 10.1021/ja505519b

Liu W, Kavaliauskas D, Schrader J, Poruri K, Birkedal V, Goldman E et al. Labeled EF-Tus for rapid kinetic studies of pretranslocation complex formation. A C S Chemical Biology. 2014;9(10):2421-2431.

Hildebrandt L , Preus S , Zhang Z , Voigt NV , Gothelf KV , Birkedal V. Single Molecule FRET Analysis of the 11 Discrete Steps of a DNA Actuator. Journal of the American Chemical Society. 2014 Jun 25;136(25):8957-8962. doi: 10.1021/ja502580t

Kragh SL , Preus S , Gudnason DA, Mergny JL, Birkedal V. Structural Dynamics and Polymorphism of Telomeric G-Quadruplex DNA Structures. Biophysical Journal. 2014;106(2, supplement 1):65a. doi: 10.1016/j.bpj.2013.11.438

Beerens N, Jepsen MDE, Nechyporuk-Zloy V, Krüger AC, Darlix JL, Kjems J et al. Role of the primer activation signal in tRNA annealing onto the HIV-1 genome studied by single-molecule FRET microscopy. RNA. 2013 Apr;19(4):517-26. doi: 10.1261/rna.035733.112

Krüger AC , Birkedal V. Single molecule FRET data analysis procedures for FRET efficiency determination: Probing the conformations of nucleic acid structures. Methods. 2013;64:36–42 . doi: 10.1016/j.ymeth.2013.04.001

Krüger AC , Hildebrandt L , Kragh SL , Birkedal V. Structural Dynamics of Nucleic Acids by Single-Molecule FRET. In Methods in Cell Biology. Vol. 113. Academic Press. 2013. p. 1-37. (Methods in Cell Biology). doi: 10.1016/B978-0-12-407239-8.00001-X

Juul S, Iacovelli F, Falconi M, Kragh SL , Christensen BS , Hougaard RF et al. Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage. ACS Nano. 2013 Oct 29;7(11):9724-9734. doi: 10.1021/nn4030543

Zadegan RM , Jepsen MDE , Thomsen KE , Okholm AH , Schaffert DH , Andersen ES et al. Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami. A C S Nano. 2012 Nov 27;6(11):10050-10053. doi: 10.1021/nn303767b

Kristiansen M , Kryger M , Zhang Z , Voigt NV , Birkedal V , Gothelf KV. Extended DNA Tile Actuators. ChemPlusChem. 2012;77(8):636-642. doi: 10.1002/cplu.201200149

Jepsen M, Beerens N, Krüger AC , Kjems J , Birkedal V. tRNA Annealing onto the HIV-1 Genome Studied by FRET Spectroscopy and Microscopy. Biophysical Journal. 2012 Jan 31;102(3, Supplement 1):278a . doi: 10.1016/j.bpj.2011.11.1533

Zhang Z , Olsen EM , Kryger M , Voigt NV , Tørring T, Gültekin E et al. A DNA tile actuator with eleven discrete states. Angewandte Chemie International Edition. 2011;50(17):3983-7. doi: 10.1002/anie.201007642

Birkedal V , Dong M , Golas MM , Sander B , Andersen ES , Gothelf KV et al. Single molecule microscopy methods for the study of DNA origami structures. Microscopy Research and Technique. 2011 Jul;74(7):688-698. doi: 10.1002/jemt.20962

Krüger AC , Raarup MK , Nielsen MM , Kristensen M , Besenbacher F , Kjems J et al. Interaction of hnRNP A1 with telomere DNA G-quadruplex structures studied at the single molecule level. European Biophysics Journal. 2010;39(9):1343-1350. doi: 10.1007/s00249-010-0587-x

Pillai S , Arpanaei A , Meyer RL , Birkedal V, Gram LK, Besenbacher F et al. Preventing protein adsorption by coating surfaces with an aqueous protein extract from fish. Biomacromolecules. 2009;10:2759-2766.

Andersen ES , Dong M , Nielsen MM , Jahn K , Subramani R , Mamdouh W et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature. 2009;459(7243):73-6. doi: 10.1038/nature07971

Andresen ER , Paulsen HN , Birkedal V , Thøgersen J , Keiding SR. Broadband multiplex coherent anti-Stokes Raman scattering microscopy employing photonic-crystal fibers. Optical Society of America. Journal B: Optical Physics. 2006;22(9):1934-1938.

Birkedal V , Keiding SR , Petersen C, Madsen ESY, Jensen SK, Seegert A et al. Observation of a persistent infrared absorption following two photon ionization of liquid water. Chemical Physics. 2006;328(1-3):119-124.

Andresen ER , Birkedal V , Thøgersen J , Keiding SR. Tunable light source for coherent anti-Stokes Raman scattering microspectroscopy based on the soliton self-frequency shift. Optics Letters. 2006;13(9):1328-1330.

Andresen ER, Paulsen HN, Birkedal V , Thøgersen J , Keiding SR. Broadband multiplex coherent anti-Stokes Raman scattering microscopy employing photonic-crystal fibers. J. Opt. Soc. Am. B. 2005;22(9):1934-1938.

Carter SG, Birkedal V, Wang CS, Coldren LA, Maslov AV, Citrin DS et al. Quantum Coherence in an Optical Modulator. Kexue (Shanghai). 2005;310:651-653.

Carter SG, Birkedal V, Hanson M, Huntington AS, Wang CS, Gossard AC et al. Terahertz-optical mixing in undoped and doped GaAs quantum wells: From excitonic to electronic intersubband transitions. Physical Review B. 2005;72(15):155309 1-5. 155309. doi: 10.1103/PhysRevB.72.155309

Displaying results 1 to 50 out of 60

2005 and before

S. G. Carter, V. Birkedal, C. S. Wang, L. A. Coldren, A. V. Maslov, D. S. Citrin, M. S. Sherwin, 2005, "Quantum coherence in an optical modulator", Science 310 pp. 651-653.

S. G. Carter, V. Ciulin, M. S. Sherwin, M. Hanson, A. Huntington, C. S. Wang, A. C. Gossard, L. A. Coldren, 2005, "Terahertz-optical mixing in undoped and doped GaAs quantum wells: from excitonic to electronic intersubband transitions", Phys. Rev. B 72, 155309, 5 pages.

E. R. Andresen, H. N. Paulsen, V. Birkedal, J. Thøgersen. S. R. Keiding, 2005, "Broad multiplex coherent anti-Stokes Raman scattering microscopy employing photonic crystal fibers", J. Opt. Soc. Am. B 22, pp. 1934-1938.

P. Kossacki, H. Boukari, M. Bertolini, D. Ferrand, J. Cibert, S. Tatarenko, J. A. Gaj, B. Deveaud, V. Ciulin, M. Potemski, 2004, "Photoluminescence of p-doped quantum wells with strong spin splitting", Phys. Rev. B 70 195337.

H. Boukari, P. Kossacki, M. Bertolini, D. Ferrand, J. Cibert, S. Tatarenko, J. A. Gaj, B. Deveaud, V. Ciulin, 2004, "Photoluminescence of p-doped quantum wells with strong spin splitting", Acta Phys. Pol. A 106, pp. 299-310.

M. T. Portella-Oberli, J. H. Berney, B. Deveaud, V. Ciulin, M. Kutrowski, T. Wojtowicz, 2004, "Many-body interaction evidenced through exciton-trion-electron correlated dynamics", Acta Phys. Pol. A 106, pp. 423-434.

V. Ciulin, S. G. Carter, M. S. Sherwin, A. Huntington, L. A. Coldren, 2004, "Non linear terahertz optical mixing in single GaAs quantum wells: dc electric field and THz frequency dependence" Phys. Rev. B 70, 115312, 6 pages.

L. Vina, R. Andre, V. Ciulin, J.D. Ganiere, B. Deveaud, 2004, "Oscillatory behaviour in the nonlinear emission of semiconductor microcavities", Semicond. Sci. Technol. 19, pp. S333-S335.

M. T. Portella-Oberli, V. Ciulin, J.-H. Berney, M. Kutrowski, T. Wojtowicz, B. Deveaud, 2004, "Interacting many-body systems in quantum wells: Evidence for exciton-trion-electrons correlations" Phys. Rev. B 69, 235311, 5 pages.

M. T. Portella-Oberli, V. Ciulin, J.-H. Berney, M. Kutrowski, T. Wojtowicz, B. Deveaud, 2004, "Correlated dynamics of trions and excitons in modulation doped CdTe quantum wells" Phys. Stat. Sol. C 1, pp. 484-488.

S. G. Carter, V. Ciulin, M. S. Sherwin, M. Hanson, A. Huntington, L. A. Coldren, A. C. Gossard, 2004, "THz electro-optic wavelength conversion in GaAs quantum wells: Improved efficiency and room temperature operation" Appl. Phys. Lett. 84, pp. 840-842.

M. T. Portella-Oberli, V. Ciulin, M. Kutrowski, T. Wojtowicz, B. Deveaud, 2003, "Non linear optical dynamics of excitons and trions", Phys. Stat. Sol. B 238, pp. 513-516.

M. T. Portella-Oberli, V. Ciulin, S. Haacke, J.-D. Ganiere, P. Kossacki, M. Kutrowski, T. Wojtowicz, B. Deveaud, 2002, "Trions and excitons in CdTe quantum wells: lifetimes, coherence, diffusion and localization", Phys. Stat. Sol. B 234, pp. 294-303.

M. T. Portella-Oberli, V. Ciulin, P. Kossaki, S. Haacke, M. Kutrowski, T. Wojtowicz, J.-D. Ganière, B. Deveaud, 2002, "Diffusion, localization, and dephasing of trions and excitons in CdTe quantum wells" Phys. Rev. B 66, pp. 155305-155309.

M. T. Portella-Oberli, V. Ciulin, P. Kossaki, S. Haacke, M. Kutrowski, T. Wojtowicz, J.-D. Ganière, B. Deveaud, 2002, "Dynamics of excitons and trions in CdTe quantum wells: Direct observation of diffusion and localization" Phys. Stat. Sol. A 190, pp. 787-791.

V. Ciulin, P. Kossacki, M. Kutrowski, J.-D. Ganière, T. Wojtowicz, B. Deveaud, 2002, "Spin relaxation of negatively charged excitons in CdTe quantum wells" Phys. Stat. Sol. B 229, pp. 627-631.

P. Kossacki, V. Ciulin, M. Kutrowski, J.-D. Ganière, T. Wojtowicz, B. Deveaud, 2002, "Formation time of negatively charged excitons in CdTe-based quantum wells" Phys. Stat. Sol. B 229, pp. 659-663.

M. Kutrowski, T. Wojtowicz, P. Kossacki, V. Ciulin, J. Kossut, 2002, "Neutral and charged exciton photoluminescence in a magnetic field studied for different electron concentrations and g-factors" Phys. Stat. Sol. B 229, pp. 791-795.

V Ciulin, P. Kossacki, M. Kutrowski, A. Esser, S. Haacke, J.-D. Ganière, T. Wojtowitcz, B. Deveaud, 2001, "Negatively charged excitons in CdTe based quantum wells: a time resolved study" Phys. Stat. Sol. B 227, pp. 307-311.

V. Ciulin, P. Kossacki, M. Kutrowski, A. Esser, S. Haacke, J.-D. Ganière, T. Wojtowitcz, B. Deveaud, 2000, "Radiative behavior of negatively charged excitons in CdTe quantum wells: A spectral and temporal analysis" Phys. Rev. B. 62, R16310-R16313.

V. Ciulin, P. Kossacki, J.-D. Ganière, S. Haacke, B. Deveaud, A. Moradi, B. Stébé, 2000, "Radiative lifetime of negative trions in GaAs and CdTe quantum wells" Phys. Stat. Sol. A 178, pp. 495-499.

P. Kossacki, V. Ciulin, J. Cibert, Y. M. d'Aubigné, A. Arnoult, C. Bourgognon, A. Wasiela, S. Tatarenko, J. L. Staehli, J.-D. Granière, B. Deveaud, J. A. Gaj, 2000, "Oscillator strengths of charged excitons: combining magnetoabsorption and photoluminescence dynamics in semimagnetic quantum wells" J. Cryst. Growth 214, pp. 837-841.

A. Sassara, G. Zerza, V. Ciulin, M. T. Portella Oberli, J.-D. Ganière, B. Deveaud, M. Chergui, 1999, "Picosecond and femtosecond studies of the energy redistribution in matrix-isolated C60 molecules" J. Lumin. 83-4, pp. 29-32.

A. Sassara, G. Zerza, M. Chergui, V. Ciulin, J.-D. Ganière, B. Deveaud, 1999, "Picosecond studies of the intramolecular relaxation processes in isolated C60 and C70 molecules" J. Chem. Phys. 111, pp. 689-697.

V. Ciulin, G. Finkelstein, S. Haacke, J.-D. Ganière, V. Umansky, I. Bar-Joseph, B. Deveaud, 1998, "Dynamics of charged excitons in GaAs quantum wells under high magnetic field" Physica B 258, pp. 466-469.

G. Finkelstein, V. Umansky, I. Bar-Joseph, V. Ciulin, S. Haacke, J.-D. Ganière, B. Deveaud, 1998, "Charged exciton dynamics in GaAs quantum wells" Phys. Rev. B 58, pp. 12637-12640.

*In earlier publications, V. Birkedal appears as V. Ciulin, her maiden name.

Figures gallery

2014, J. Am. Chem. Soc., 136 (25), pp 8957–8962

2013, Methods in Cell Biology 113, Laboratory Methods in Cell Biology, p. 1-37, Ed. P. Michael Conn

2011, Angew. Chem. Int. Ed. 50, p. 3983-3987

2011, Microscopy Research and Technique 74, pp.688-98

2010, Euro. Biophys. J. 39, p. 1343-1350

2009, Biomacromolecules 10 pp. 2759-2766

Revised 17.04.2023

Ditte Høyer Engholm