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CDNA Publications 2017


Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials. Kékedy-Nagy, L., Ferapontova, E. E., Brand, I., J. Phys. Chem. B, 2017, doi: 10.1021/acs.jpcb.6b12363 (PR)


Revealing the structural detail of individual polymers using a combination of electrospray deposition and UHV-STM. Jethwa, S. J., Madsen, M., Knudsen, J. B., Lammich, L., Gothelf, K.V., Linderoth, T.R., Chem. Commun., 2017, doi: 10.1039/C6CC09167A (PR)

176)Computer-Aided Design of RNA Origami Structures. Sparvath, S. L., Geary, C. W., Andersen, E. S.,Methods Mol. Biol., 2017, doi: 10.1007/978-1-4939-6454-3_5 (PR)


CDNA Publications 2016

175)The utility of DNA nanostructures for drug delivery in vivo. Okholm, A. H., Kjems, J., Expert Opin. Drug Deliv., 2016, doi: 0.1080/17425247.2017.1266335 (PR)
174)DNA nanovechicles and the biological barriers. Okholm, A. H., Kjems, J., Adv. Drug Deliv. Rev., 2016, doi: 10.1016/j.addr.2016.05.024. (PR)
173)Optimal Background Estimators in Single-Molecule FRET microscopy. Preus, S., Hildebrandt, L. L., Birkedal, V., Biophys. J., 2016, doi: 10.1016/j.bpj.2016.07.047 (PR)
172)Chip-Free Microscale-Incubator-Based Synthesis of Chitosan-Based Gene Silencing Nanoparticles. Galianone, N., Hvam, M. L., Aslan, H., Dong, M., Howard, K. A., Ho, Y.-P. Part. Part. Syst. Charact., 2016, doi: 10.1002/ppsc.201500225 (PR)



Super flexibility and stability of grapheme nanoribbons under severe twist. Xia, D., Li, Q., Xue, Q., Liang, C., Dong, M. , Phys. Chem. Chem. Phys., 2016, doi: 10.1039/C6CP02580C (PR)


Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes. Kekedy-Nagy, L., Shipovskov, S., Ferapontova, E. E.  Anal. Chem., 2016, doi: 10.1021/acs.analchem.6b01020 (PR)



Intracellular Delivery of a Planar DNA Origami Structure by the Transferrin-Receptor Internalization Pathway. Schaffert, D. H., Okholm, A. H., Sørensen, R. S., Nielsen, J. S., Tørring, T., Rosen, C. B., Kodal, A. L. B., Mortensen, M. R., Gothelf, K. V., Kjems, J., Small, 2016, doi: 10.1002/smll.201503934 (PR)



Protein patterning by DNA origami framework. Aslan, H., Krissanaprasit, A., Besenbacher, F., Gothelf, K. V., Dong, M. Nanoscale, 2016, doi: 10.1039/C6NR03199D (PR)


Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction, Zhang, Z., Birkedal, V., Gothelf, K. V., 2016, New J. Phys., doi: 10.1088/1367-2630/18/5/055002 (PR) (OA) 


DNA-Templated Introduction of an Aldehyde Handle in Proteins, Kodal, A. L. B., Rosen, C. B., Mortensen, M. R., Tørring, T., Gothelf, K. V., 2016,  ChemBioChem, doi: 10.1002/cbic.201600254 (PR)


Dynamic chemistry of disulfide terminated oligonucleotides in duplexes and double-crossover tiles., De Stefano, M., Gothelf, K. V., ChemBioChem, 2016, doi: 10.1002/cbic.201600076 (PR)


Correction to "Effect of the DNA End of Tethering to Electrodes on Electron Transfer in Methylene Blue-Labeled DNA Duplexes". Farjami, E., Campos, R., Ferapontova, E. E. Langmuir, 2016, doi: 10.1021/acs.langmuir.5b03487 (PR)


Programmed Switching of Single Polymer Conformation on DNA Origami. Krissanaprasit, A., Madsen, M., Knudsen, J. B., Gudnason, D., Surareungchai, W., Birkedal, V., Gothelf, K. V., ACS Nano, 2016, doi: 10.1021/acsnano.5b06894 (PR) (CO)


Synthesis and biophysical properties of (l)-aTNA based G-quadruplexes. Kumar, V., Gothelf, K. V. Org. Biomol. Chem. 2016, doi: 10.1039/C5OB02525G (PR)

CDNA Publications 2015


Alignment of gold nanoparticle-decorated DNA origami nanoutubes substrate prepatterning vs. molecular combing., Teschome, B., Facsko, S., Gothelf, K., Keller, A., Langmuir, 2015, 31, 12823-12829, doi:10.1021/acs.langmuir.5b02569 (PR)


Suspending DNA origami between four gold nanodots., Morales, P., Wang, L., Krissanaprasit, A., Dalmastri, C., Caruso, M., Stefano, MD., Mosiello, L., Rapone, B., Rinaldi, A., Vespucci, S., Vinther, J., Retterer, S., Gothelf, KV., Small, 2015, doi: 10.1002/smll.201501782 (PR)


iSMS: singlemolecule FRET microscopy software., Preus S., Noer SL., Hildebrandt LL., Gudnason D., Birkedal V., Nat. Methods, 2015, 12, 593-594, doi: 10.1038/nmeth.3435 (PR)


Folding dynamics and conformational heterogeneity of human telomeric G-quadruplex structures in Na+ solutions by single molecule FRET microscopy, Noer, S. L., Preus, S., Gudnason, D., Aznauryan, M., Mergny, J.-L., Birkedal, V.,  2016, Nucleic Acids Res. 44, 464-471. doi: 10.1093/nar/gkv1320 (PR)


Biomolecular self-assembly: DNA origami rewired. Andersen ES.,  Nat. Nanotechnol., 2015, 10, 733-734, doi: 10.1038/nnano.2015.204 (PR)


Electronically addressable nanmechanical switching of i-motif DNA origami assembled on basal plane HOPG. Campos R., Zhang S., Majikes JM., Ferraz LC., LaBean TH., Dong M., Ferapontova EE., Chem. Commun. (Camb), 2015, 51, 74, 14111-14114, doi: 10.1039/c5cc04678e (PR) (CO)


Routing of individual polymers in designed patterns. Knudsen JB., Liu L., Bank Kodal AL., Madsen M., Li Q., Song J., Woehrstein JB., Wickham SF., Strauss MT., Schueder F., Vinther J., Krissanaprasit A., Gudnason D., Smith AA., Ogaki R., Zelikin AN., Besenbacher F., Birkedal V., Yin P., Shih WM., Jungmann R., Dong M., Gothelf KV. Nat. Nanotechnol., 2015, doi: 10.1038/nnano.2015.190 (PR) (CO)


Serum-induced degradation of 3D DNA box origami observed with high-speed atomic force microscopy. Jiang ZX., Zhang S., Yang CX., Kjems J., Huang YD., Besenbacher F., Dong MD. Nano Res., 2015, 8, 7, 2170-2178, doi: 10.1007/s12274-015-0724-z (PR) (CO)


Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools. Dupont DM., Larsen N., Jensen JK., Andreasen PA., Kjems J., Nanoscale, 2015, 7, 25, 10970-10973, doi: 10.1039/c5nr01945a (PR)


Dynamics of Fluorescent Dyes Attached to G-Quadruplex DNA and their Effect on FRET Experiments, Søndergaard, S., Aznauryan, M., Haustrup, E.K., Schiøtt, B., Birkedal, V., Corry, B., 2016,  ChemPhysChem 16, 2562-2570. doi:10.1002/cphc.201500271 (PR)


A DNA-based system for selecting and displaying the combined result of two input variables, Liu, H., Wang, J., Song, S., Fan, C., Gothelf, K.V., 2016, Nat. Commun. 6. doi:10.1038/ncomms10089 (PR) (OA)


Monitoring patterned enzymatic polymerization on DNA origami at single-molecule level. Okholm AH., Aslan H., Besenbacher F., Dong M., Kjems J., Nanoscale, 2015, 7, 25, 10970-10973, doi: 10.1039/c5nr01945a (PR)


Surface state of the dopamine RNA aptamer affects specific recognition and binding of dopamine by the aptamer-modified electrodes. Álvarez-Martos I., Campos R., Ferapontova EE. Analyst, 2015, 140, 12, 4089-4096,  doi: 10.1039/c5an00480b (PR)


Selection of conformational states in self-assembled surface structures formed from an oligo(naphthylene-ethynylene) 3-bit binary switch. Ning Y., Cramer JR., Nuermaimaiti A., Svane K., Yu M., Lægsgaard E., Besenbacher F., Xue QK., Ma X., Hammer B., Gothelf KV., Linderoth T.R, J. Chem. Phys., 2015, 142 (10), 101922, doi: 10.1063/1.4908062. (PR) (CO)


Computer-aided design of DNA origami structures. Selnihhin D., Andersen E.S Methods Mol. Biol., 2015, 1244, 23-44, doi: 10.1007/978-1-4939-1878-2_2 (PR)


Highly stable triple helix formation by homopyrimidine (l)-acyclic threoninol nucleic acids with single stranded DNA and RNA. Kumar V., Kesavan V., Gothelf KV. Org. Biomol. Chem. 2015, 13 (8), 2366-74, doi: 10.1039/c4ob02328e (PR) (CO)


Electroanalysis of pM-levels of urokinase plasminogen activator in serum by phosphorothioated RNA aptamer. Jarczewska M., Kékedy-Nagy L., Nielsen JS., Campos R., Kjems J., Malinowska E., Ferapontova EE. Analyst, 2015 (PR)


Construction of a Fuzzy and Boolean Logic Gates Based on DNA. Zadegan RM., Jepsen MD., Hildebrandt LL., Birkedal V., Kjems J., Small, 2015doi: 10.1002/smll.201402755  (PR) (CO)


Oxidative activation of dihydropyridine amides to reactive acyl donors. Funder, Erik Daa, Trads, Julie B., Gothelf, Kurt V. Org. Biomol. Chem. 2015, 13, 185-198, doi: 10.1039/c4ob01931h (PR)

CDNA Publications 2014


Synthesis, Dynamic Combinatorial Chemistry, and PCR Amplification of 3 '-5 ' and 3 '-6 ' Disulfide-linked Oligonucleotides. Hansen, DJ., Manuguerra, I., Kjelstrup, MB., Gothelf, KV. Angew. Chem. Int. Ed. 2014, 53, 14415-14418, doi: 10.1002/anie.201405761 (PR)


Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays. Keller, A., Rackwitz, J., Cauet, E., Lievin, J., Korzdorfer, T., Rotaru, A., Gothelf, KV., Besenbacher, F., Bald, I. Sci. Rep. 2014, 4, doi: 10.1038/srep07391 (PR) (CO) (OA)


DNA brick crystals with prescribed depths. Ke, YG., Ong, LL., Sun, W., Song, J., Dong, MD., Shih, WM., Yin, P. Nat. Chem. 2014,6, 994-1002, doi: 10.1038/NCHEM.2083 (PR) (CO)



DNA-mediated electron transfer in DNA duplexes tethered to gold electrodes via phosphorothioated dA tags. Campos, R.; Kotlyar, A.; Ferapontova, E. E. Langmuir. 2014, 30 (40), 11853-11857, DOI: 10.1021/la502766g (PR) (CO)


A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Geary, C.; Rothemund, P. W. K.; Andersen, E. S. Science. 2014, 345 (6198), pp799-804, DOI: 10.1126/science.1253920 (PR) (CO)


A DNA-mediated homogenous binding assay for proteins and small molecules. Zhang, Z.; Hejesen, C.; Kjelstrup, M.; Birkedal, V.; Gothelf, K. J. Am. Chem. Soc. 2014, 136 (31), 11115-11120, DOI: 10.1021/ja505519b (PR)


Template-directed covalent conjugation of DNA to native antibodies, transferrin and other metal-binding proteins. Rosen, C. B.; Kodal, A. L.; Nielsen, J. S.; Schaffert, D. H.; Scavenius, C.; Okholm, A. H.; Voigt, N. V.; Enghild, J. J.; Kjems, J.; Tørring, T.; Gothelf, K. V. Nat. Chem. 2014, 6, pp804-809, doi:10.1038/nchem.2003 (PR)


Single molecule FRET analysis of the 11 Discrete steps of a DNA actuator.Hildebrandt, L. L.; Preus, S.; Zhang, Z.; Voigt, N. V.; Gothelf, K. V., Birkedal, V. J. Am. Chem. Soc. 2014DOI: 10.1021/ja502580t (PR)


Electrochemical switching with 3D DNA tetrahedral nanostructures self-assembled at gold electrodes. Abi, A.; Lin, M.; Pei, H.; Fan, C.; Ferapontova, E. E. ACS Appl. Mater. Interfaces. 2014, 6 (11) pp8929-8931, DOI: 10.1021/am501823q (PR) (CO)


Quantification of cellular uptake of DNA nanostructures by qPCR. Okholm, A. H.; Nielsen, J. S.; Vinther, M.; Sørensen, R. S.; Schaffert, D.; Kjems, J. Methods. 2014, 67 (2), 193-197 (PR) DOI: 10.1016/j.ymeth.2014.01.013 (PR)


Electrochemistry of weakly adsorbed species: Voltammetric analysis of electron transfer between gold electrodes and Ru hexaamine electrostatically interacting with DNA duplexes. Campos, R.; Ferapontova, E. E. Electrochim. Acta. 2014, 126, pp151-157, DOI: 10.1016/j.electacta.2013.07.083 (PR)


Singlet oxygen in DNA nanotechnology Tørring, T.; Helmig, S. D.; Ogilby, P. R.; Gothelf. K. V. Acc. Chem. Res. 2014DOI10.1021/ar500034y (PR)


Synthesis of homochiral tris-indanyl molecular rods Kjeldsen, N. D.; Funder, E. D.; Gothelf, K. V. Org. Biomol. Chem. 2014, 12, 3679-3685, DOI: 10.1039/C4OB00011K (PR)


Structural Dynamics and Polymorphism of Telomeric G-Quadruplex DNA Structures. Kragh, S. L.; Preus, S.; Gudnason, D.; Mergny, J. L.; Birkedal, V. Biophys. J. 2014, 106 (2), pp65A-65A, Supplement 1 (PR) (CO)


Function and Movement of a DNA Actuator Investigated by Single Molecule Fret Microscopy Hildebrandt, L. L.; Zhang, Z.; Preus, S.; Gothelf K. V.; Birkedal, V. Biohys. J. 2014, 106 (2), pp266A-226A, Supplement 1 (PR)

CDNA Publications 2013

127)Efficient colorimetric and fluorescent detection of fluoride in DMSO-water mixtures with arylaldoximes, Rosen, C.B., Hansen, D.J., Gothelf, K.V. Rosen, C.B., Hansen, D.J., Gothelf, K.V., 2016,  Org. Biomol. Chem. 11, 7916-7922. (PR) 


Self-assembly of DNA origami and single-stranded tile structures at room temperature.  Zhang, Z.; Song, J.; Besenbacher, F.; Dong, M.; Gothelf, K.V. Angew. Chem. Int. Ed. Engl. 2013, 52 (35), 9219-9223, doi:10.1002/anie.201303611 (PR) (CO)


Tailoring on-surface supramolecular architectures based on adenine directed self-assembly. Tan, Q.; Zhang, C.; Wang, N.; Zhu, X.; Sun, Q.; Jacobsen, M.F.; Gothelf, K.V.; Besenbacher, F.; Hu, A.; Xu, W. Chem. Commun. (Camb). 2013, DOI: 10.1039/C3CC46149A, pubs.rsc.org/en/content/articlepdf/2014/cc/c3cc46149a  (PR) (CO)


Isothermal hybridization kinetics of DNA assembly of two-dimensional DNA origami. Song, J., Zhang, Z., Zhang, S., Liu, L., Li, Q., Xie, E., Gothelf, K.V., Besenbacher, F., Dong, M. Small. 2013, 9 (17), 2954-2959, doi: 10.1002/smll.201202861, (PR) (CO)


Steering supramolecular patterns by nucleobase-terminated molecules. Shen, C., Cramer, J.R., Jacobsen, M.F., Liu, L., Zhang, S., Dong, M., Gothelf, K.V., Besenbacher, F. Chem. Commun. (Camb). 2013, 49 (5), 508-510, doi: 10.1039/c2cc37522b (PR)


Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage. Juul, S.; Iacovelli, F.; Falconi, M.; Kragh, S.L.; Christensen, B.; Frøhlich, R.; Franch, O.; Kristoffersen, E.L.; Stougaard, M.; Leong, K.W.; Ho, Y.P.; Sørensen, E.S.; Birkedal, V.; Desideri, A.; Knudsen, B.R. ACS Nano. 2013, 7 (11), 9724-9734, DOI: 10.1021/nn4030543, pubs.acs.org/doi/pdf/10.1021/nn4030543 (PR) (CO) 


A quencher-free molecular beacon design based on pyrene excimer fluorescence using pyrene-labeled UNA (unlocked nucleic acid). Karlsen, K.K.; Okholm, A.; Kjems, J. and Wengel, J. Bioorganic & medicinal chemistry. 2013, 21 (20), 6186-6190, dx.doi.org/10.1016/j.bmc.2013.04.062


Electron-induced damage of biotin studied in the gas phase and in the condensed phase at a single-molecule level. Keller, A.; Kopyra, J.; Gothelf, K.V.; Bald, I. New J. Phys. 2013; 15 083045, 14pp, DOI: 10.1088/1367-2630/15/8/083045, iopscience.iop.org.ez.statsbiblioteket.dk/1367-2630/15/8/083045/pdf/1367-2630_15_8_083045.pdf (PR) (CO)


Enzymatic Ligation of Large Biomolecules to DNA. Sørensen, R.S.; Okholm, A.H.; Schaffert, D.; Kodal, A.L.; Gothelf, K.V.; Kjems, J. ACS Nano. 2013, 1 (9), 8098-8104, DOI: 10.1021/nn403386f, pubs.acs.org/doi/pdf/10.1021/nn403386f  (PR)


A DNA tweezer-actuated enzyme nanoreactor. Liu, M.; Fu, J.; Hejesen, C.; Yang, Y.; Woodbury, N.W.; Gothelf, K.; Liu, Y.; Yan, H. Nat. Commun. 2013, 4 2127, 5pp, doi: 10.1038/ncomms3127 (PR) (CO) (OA)


DNA nanotechnology: a curiosity or a promising technology? Tørring, T.; Gothelf, K.V. F1000Prime Rep. 2013, 5 (14), pp4, doi: 10.12703/P5-14, (PR) (OA)


On electrogenerated acid-facilitated electrografting of aryltriazenes to create well-defined aryl-tethered films. Vinther, J.; Iruthayaraj, J.; Gothelf, K.; Pedersen, S.U.; Daasbjerg, K. Langmuir. 2013, 29 (17), 5181-5189, doi: 10.1021/la305081c, pubs.acs.org/doi/pdf/10.1021/la305081c (PR) (CO)


A traceless aryl-triazene linker for DNA-directed chemistry. Hejesen, C.; Petersen, L.K.; Hansen, N.J.; Gothelf, K.V. Org Biomol Chem. 2013, 11 (15), 2493-2497, doi: 10.1039/c3ob27504c, pubs.rsc.org/en/content/articlepdf/2013/ob/c3ob27504c  (PR) (CO)


Electroanalysis of single-nucleotide polymorphism by hairpin DNA architectures.Abi, A.; Ferapontova, E.E. Anal. Bioanal. Chem. 2013; 405 (11), 3693-3703; doi: 10.1007/s00216-012-6633-z, download.springer.com/static/pdf/114/art%253A10.1007%252Fs00216-012-6633-z.pdf  (PR) Open Access


Transfer of a protein pattern from self-assembled DNA origami to a functionalized substrate. Busuttil, K.; Rotaru, A.; Dong, M.; Besenbacher, F.; Gothelf, K.V. Chem Commun (Camb). 2013, 49 (19), 1927-1929, doi: 10.1039/c3cc37408d, pubs.rsc.org/en/content/articlepdf/2013/cc/c3cc37408d (PR)


Single-Step Rapid Assembly of DNA Origami Nanostructures for Addressable Nanoscale Bioreactors. Fu, Y.; Zeng, D.; Chao, J.; Jin, Y.; Liu, H.; Li, D.; Ma, H.; Huang, Q.; Gothelf, K.V.; Fan, C. J. Am. Chem. Soc. 2013, 135 (2), 696-702, DOI: 10.1021/ja3076692, pubs.acs.org/doi/pdf/10.1021/ja3076692 (PR) (CO)


RNA aptamer-based electrochemical biosensor for selective and label-free analysis of dopamine. Farjami, E.; Campos, R.; Nielsen, J.S.; Gothelf, K.V.; Kjems, J.; Ferapontova, E.E. Anal Chem. 2013, 85 (1), 121-128, doi: 10.1021/ac302134s, pubs.acs.org/doi/pdf/10.1021/ac302134s (PR) (OA)

CDNA Publications 2012


Practical and innate carbon-hydrogen functionalization of heterocycles. Fujiwara, Y.; Dixon, J. A. O'Hara, F.; Funder, E. D.; Dixon, D. D.; Rodriguez, R. A.; Baxter, R. D.; Herle, B.; Sach, N.; Collins, M. R.; Ishihara, Y.; Baran, P. S. Nature. 2012, 492, 95-99. (PR) (CO)


Materials science. LEGO-like DNA Structures. Gothelf, K. V. Science. 2012, 338, 1159-1160


Construction of a 4 Zeptoliters Switchable 3D DNA Box Origami. Zadegan, R. M.; Jepsen, M. D.; Thomsen, K. E.; Okholm, A. H.; Schaffert, D. H.; Andersen, E. S.; Birkedal, V.; Kjems, J. ACS. 2012, 6, 10050-10053. (PR)


Effect of the DNA end of tethering to electrodes on electron transfer in methylene blue-labeled DNA duplexes. Farjami, E.; Campos, R.; Ferapontova, E. E. Langmuir. 2012, 28, 16218-16226. (PR)


Carbon/Silicon Heterojunction Formed by Inserting Carbon Nanotubes into Silicon Nanotubes: Molecular Dynamics Simulations. Xia, D.; Xue, Q.; Zhang, T.; Chu, L.; Dong, M. J. Phys. Chem. C. 2012, 116 (44), 23181-23187. (PR) (CO)


Unmediated by DNA electron transfer in redox-labeled DNA duplexes end-tethered to gold electrodes. Abi, A.; Ferapontova, E. E. J. Am. Chem. Soc. 2012, 134, 14499–14507. (PR) Paid OA


Electrochemical sandwich assay for attomole analysis of DNA and RNA from beer spoilage bacteria Lactobacillus brevis. Shipovskov, S.; Saunders A.M.; Nielsen J.S., Hansen M.N.; Gothelf K.V., and Ferapontova E. E. Biosens. Bioelectron. 2012, 37, 99-106. (PR)


Extended DNA-tile actuators. Kristiansen, M.; Kryger, M. B. L.; Zhang, Z.; Voigt, N. V.; Birkedal, V.; Gothelf, K. V. ChemPlusChem 2012, 77, 636-642. (PR)


Increased anticoagulant activity of thrombin-binding DNA aptamers by nanoscale organization on DNA nanostructures. Rangnekar, A.; Zhang, A. M.; Li, S. S.; Bompiani, K. M.; Hansen, M. N.; Gothelf, K. V.; Sullenger, B. A.; LaBean, T. H. Nanomed.-Nanotechnol. 2012; 8, 673-681. (PR) (CO)


Chitosan/siRNA Nanoparticles Encapsulated in PLGA Nanofibers for siRNA Delivery. Chen; M. L.; Gao, S.; Dong; MD; Song, J.; Yang; C. X.; Howard, K. A.; Kjems; J.; Besenbacher, F. ACS Nano. 2012, 6, 4835-4844. (PR)


Direct Visualization of Transient Thermal Response of a DNA Origami. Song, J.; Arbona, J.; Zhang, Z.; Liu, L.; Xie, E.; Elezgaray, J.; Aime, J.; Gothelf, K.V.; Besenbacher, F.; Dong, M. J. Am. Chem. Soc. 2012, 134, 9844-9847. (PR) (CO)


Two design strategies for enhancement of multilayer-DNA-origami folding: underwinding for specific intercalator rescue and staple-break positioning. Ke, Y.; Bellot, G.; Voigt, N. V.; Fradkov, E.; Shih, W. M. Chem. Sci. 2012, 3, 2587-2597. (PR) (CO)


Probing Electron-Induced Bond Cleavage at the Single-Molecule Level Using DNA Origami Templates. Keller, A.; Bald, I.; Rotaru, A.; Cauët, E.; Gothelf, K. V.; Besenbacher, F. ACS nano, 2012, 6 (5), 4392-4399. (PR) (CO)


Synthesis of Dopamine and Serotonin Derivatives for Immobilization on a Solid Support. Funder, E. D.; Jensen, A. B.; Torring, T.; Kodal, A. L. B.; Azcargorta, A. R.; Gothelf, K. V. J Org. Chem. 2012, 77, 3134-3142. (PR)


Self-assembled nanoparticles of glycol chitosan - Ergocalciferol succinate conjugate, for controlled release. Perez Quinones, J.; Gothelf, K. V.; Kjems, J.; Caballero, A. M. H.; Schmidt, C.; Covas, C. P. Anal. Chem. 2012, 84, 1854-1861. (PR) (CO)


Direct detection of DNA conformation in hybridization processes. Papadakis, G.; Tsortos, A.; Bender, F.; Ferapontova, E.; Gizeli, E. Anal. Chem. 84, 1854-1861. (PR) (CO)


Multilayer DNA Origami Packed on Hexagonal and Hybrid Lattices. Ke, Y.; Voigt, N. V.; Gothelf, K. V.; Shih, W. M. J. Am. Chem. Soc. 2012, 134 (3), 1770. (PR) (CO)


RNA secondary structure prediction on an ad-hoc peer-to-peer network infrastructure: The Collaborative Mini-Grid Project. Sükösd, Z.; Venkataraman, N. N.; Bardram, J. E.; Mørch Abell, T.; Værum, M.; Andersen, E. S.; Knudsen, B.; Kjems, J. ITU Technical Report Series : IT University of Copenhagen. 2012, 25 p.

CDNA Publications 2011


MicroRNA cloning and sequencing in osteosarcoma cell lines: differential role of miR-93. Montanini, L.; Lasagna, L.; Barili, V.; Jonstrup, S. P.; Murgia, A.; Pazzaglia, L.; Conti, A.; Novello, C.; Kjems, J.; Perris, R.; Benassi, M. S.  Cellular oncology. 2011, 35, 29-41. (PR) (CO)


A Revertible, Autonomous, Self-Assembled DNA-Origami Nanoactuator. Marini, M.; Piantanida, L.; Musetti, R.; Bek, A.; Dong, M.; Besenbacher, F.; Lazzarino, M.; Firrao, G. Nano Lett. 2011, 11, 5449-5454. (PR) (CO)


DNA origami: a quantum leap for self-assembly of complex structures. Tørring, T.; Voigt, N. V.; Nangreave, J.; Yan, H.; Gothelf, K. V. Chem. Soc. Rev. 2011, 40, 5636-5646. (PR) (CO)


DNA-Programmed Glaser-Eglinton reactions for the synthesis of conjugated molecular wires. Ravnsbæk, J. B.; Jacobsen, M. F.; Rosen, C. B.; Voigt, N. V.; Gothelf, K. V. Angew. Chem. Int. Ed. 2011, 50, 10851–10854. (PR)


Development of a lipase-based optical assay for detection of DNA. Pinijsuwan, S.; Shipovskov, S.; Surareungchai, W.; Ferapontova, E. E.; Gothelf, K. V. Org. Biomol. Chem. 2011, 9, 6352–6356. (PR) (CO)


Building layer-by-layer supramolecular nanostructures at the terephthalic acid/stearic acid interface. Li, Y.; Liu, L.; Subramani, R.; Pan, Y.; Liu, B.; Yang, Y.; Wang, C.; Mamdouh, W.; Besenbacher F., Dong; M. Chem. Commun. 2011, 47, 9155-9157 (PR) (CO)


Homochiral Xanthine Quintet Networks Self-Assembled on Au(111) Surfaces. Yu, M.; Wang, J.; Mura, M.; Meng, Q.-Q.; Xu, W.; Gersen, H.; Lægsgaard, E.; Stensgaard, I.; Kelly, R. E. A.; Kjems, J.; Linderoth, T. R.; Kantorovich, L. N.; Besenbacher, F. ACS Nano. 2011, 5, 6651-6660. (PR) (CO)


Single molecule microscopy methods for the study of DNA origami structures. Birkedal, V.; Dong, M.; Golas, M. M.; Sander, B.; Andersen, E. S.; Gothelf, K. V.; Besenbacher, F.; Kjems, J. Microscopy Res. Tech. 2011, 74, 688–698. (PR)


beta-olefination of 2-alkynoates leading to trisubstituted 1,3-dienes. Jacobsen, M. J.; Funder, E. D.; Cramer, J. R.; Gothelf, K. V. Org. Lett. 2011, 13, 3418–3421. (PR)


Design and synthesis of DNA four-helix bundles
Rangnekar, A.; Gothelf, K. V.; LaBean, T. H. Nanotechnology 2011, 22, 235601. (PR)


Functional patterning of DNA origami by parallel enzymatic modification of staple strands 
Jahn, K.; Tørring, T.; Voigt, N. V.; Sørensen, R. S.; Kodal, A. L. B: Andersen, E. S.; Gothelf, K. V.; Kjems, J. Bioconjug. Chem. 2011, 22, 819–823. (PR)


A DNA Tile Actuator with 11 Discrete States
Zhang, Z.; Olsen, E. M.; Kryger, M.; Voigt, N. V.; Tørring, T.; Gültekin, E.; Nielsen, M.; Zadegan, R. M.; Andersen, E.; Nielsen, M. M.; Kjems, J.; Birkedal, V.; Gothelf, K. V Angew. Chem. Int. Ed. 2011, 50, 3983–3987. (PR)


Control of self-assembled 2D nanostructures by methylation of guanine. Bald, I.; Wang, Y.-g.; Dong, M.; Rosen, C. B.; Ravnsbæk, J. B.; Zhuang, G.- l.; Gothelf, K. V.; Wang, J.-g.; Besenbacher, F. Small. 2011, 7, 939–949. (PR)


Design and Construction of Double-Decker Tile as a Route to 2 Three-Dimensional Periodic Assembly of DNA
Majumder, U.; Rangnekar,A.; Gothelf K. V.; Reif, J. H.; LaBean, T. H. J. Am. Chem. Soc. 2011, 133, 3843–3845. (PR)


Combining aryltriazenes and electrogenerated acids to create well-defined aryl-tethered films and patterns on surfaces. Kongsfelt, M.; Vinther, J.; Malmos, K.; Ceccato, M.; Torbensen, K.; Knudsen, C. S.; Gothelf, K. V.; Pedersen, S. U.; Daasbjerg, K. J. Am. Chem. Soc. 2011, 133, 3788–3791. (PR) (CO)


Tuning the hydrophobicity of mica surfaces by hypethermal Ar ion irradiation. Keller, A.; Fritzsche, M.; Ogaki, R.; Bald, I.; Facsko, S.; Dong, M.; Kingshott, P.; Besenbacher, F. J. Chem. Phys. 2011, 134, 104705 (PR) (CO)


"Off–On" electrochemical hairpin-DNA-based genosensor for cancer diagnostics. Farjami, E.; Clima, L.; Gothelf, K. V.; Ferapontova, E. E. Anal. Chem. 2011, 83; 1594–1602. (PR).


Recent advances in electrochemical aptamer-based sensors. Ferapontova, E. E.; Gothelf, K. V. Curr. Org. Chem. 2011, 15, 498–505. (PR)


Electrochemical indicators for DNA electroanalysis. Ferapontova, E. E. Curr. Anal. Chem. 2011, 7, 51–62. (PR)


Site-specific chemical labeling of long RNA molecules 
Jahn, K.; Olsen, E. M.; Nielsen, M. M.; Zadegan, R. M.; Andersen, E. S.; Gothelf, K. V.; Kjems, J. Bioconjug. Chem. 2011, 22, 95-100. (PR)


A nanomechanical interface to rapid single-molecule interactions. Dong, M;, Sahin, O. Nature Commun. 2011, 2, 247. (PR)

CDNA Publications 2010 


Small molecule induced control in duplex and triplex DNA-directed chemical reactions 
Jacobsen, M. F.; Ravnsbæk, J. B.; Gothelf, K. V. Org. Biomol. Chem. 2010, 8, 50–52. (PR)

70)A Nucleic Acid Dependent Chemical Photocatalysis in Live Human Cell
Arian, D., Cló, E., Gothelf, K. V., Mokhir, A. Chem. Eur. J. 2010, 16, 288–295. (PR) (CO)
69)Single molecule chemical reactions on DNA origami
Voigt, N. V., Tørring, T., Rotaru, A., Jacobsen, M. F., Ravnsbæk, J. B., Subramani, R., Mamdouh, W., Kjems, J., Mokhir, A., Besenbacher, F., Gothelf, K. V. Nature Nanotech. 2010, 5, 200–203. (PR) (CO)
68)Interaction of hnRNP A1 with telomere DNA G-quadruplex structures studied at the single molecule level
Krüger, A. C., Raarup, M. K., Nielsen, M. M., Kristensen, M., Besenbacher, F., Kjems, J., Birkedal, V. Eur. Biophys. J. 2010, 39, 1343–1350. (PR)
67)Utilization of unlocked nucleic acid (UNA) to enhance siRNAs performance in vitro and in vivo
Laursen, M. B., Pakula, M. M., Gao, S., Fluiter, K., Mook, O. R., Baas, F., Langklær, N., Wengel, S., Wengel, J., Kjems, J., Bramsen, J. B. Mol. Biosys. 2010, 6, 862–870. (PR) (CO)
66)RNA aptamers as conformational probes and regulatory agent for plasminogen activator inhibitor-1
Madsen, J., Dupont, D., Andersen, T., Nielsen, A., Sang, L., Brix, D., Jensen, J., Broos, T., Hendrickx, M., Christensen, A., Kjems, J., Andreasen, P. Biochemistry 2010, 49, 4103–4115. (PR)
65)Two-dimensional network stability of nucleobases and amino acids on graphite under ambient conditions: Adenine, L-serine and L-tyrosine
Bald, I., Weigelt, S., Ma, X., Xie, P., Subramani, R., Dong, M., Wang, C., Mamdouh, W., Wang, J., Besenbacher, F. Phys. Chem. Chem. Phys. 2010, 12, 3616–3621. (PR) (CO)
64)DNA Interactions with a Methylene Blue Redox Indicator Depend on the DNA Length and are Sequence Specific
Farjami, E.; Clima, L.; Gothelf, K. V.; Ferapontova, E. E. Analyst 2010, 1135, 1443–1448. (PR) (CO)
63)Synthesis and Application of a Triazene-Ferrocene-Modifier for Immobilization and Characterization of Oligonucleotides at Electrodes 
Hansen, M. N.; Farjami, E.; Kristiansen, M.; Clima, L.; Pedersen, S. U.; Daasbjerg, K.; Ferapontova, E. E.; Gothelf, K. V. J. Org. Chem. 2010, 75, 2474–2481. (PR) (CO)
62)Electrochemical DNA Sandwich Assay with a Lipase Label for Attomole Detection of Bacterial DNA 
Ferapontova, E. E.; Hansen, M. N.; Saunders, A. M.; Shipovskov, S.; Sutherland, D. S.; Gothelf, K. V. Chem. Commun. 2010, 46, 1836–1838. (PR) (CO)
61)Peroxidase biocathodes for a biofuel cell development
Gomez, C., Shipovskov, S., Ferapontova, E. E. J. Renewable Sustainable Energy 2010, 2, 013103-1–013103-12. (PR) (CO) (OA)
60)Selective dsDNA-templated formation of copper nanoparticles in solution
Rotaru, A.; Jentzsch, E.; Dutta, S.; Gothelf, K. V.; Mokhir, A. Angew. Chem. Int. Ed. 2010, 49, 5665–5667. (PR) (CO)
59)Prediction and design of DNA and RNA structures
Andersen, E. S. New Biotechnology 2010, 27, 184–191. (PR)
58)Weave Tile Architecture: A Novel Construction Strategy for DNA Nanotechnology 
Hansen, M.; Zhang, A.; Rangnekar, A.; Bompiani, K.; Carter, J.; Gothelf, K. V.; Labean, T. J. Am. Chem. Soc. 2010, 132, 14481–14486. (PR) (CO)
57)A Novel Secondary DNA Binding Site in Human Topoisomerase I Unravelled by using a 2D DNA Origami Platform
Subramani, R.; Juul, S.; Rotaru, A.; Andersen, F.; Gothelf, K. V.; Mamdouh, W.; Besenbacher, F.; Dong, M.; Knudsen. B. A. ACS Nano 2010, 4, 5969–5977. (PR)
56)Reversible pH-regulated control of photosensitized singlet oxygen production using a DNA i-motif
Tørring, T., Toftegaard, R., Arnbjerg, J., Ogilby, P. R., Gothelf, K. V. Angew. Chem. Int. Ed. 2010, 49, 7923–7925. (PR)
55)David versus Goliath
Mollenhauer, J., Stamou, D., Flyvbjerg, A., Wengel, J., Gether, U., Kjems, J., Bjørnholm, T., Besenbacher, F Nanomedicine 2010, 6, 504–509. (PR) (CO)
54)siRNA nanoparticle functionalization of nanostructured scaffolds enables controlled multilineage differentiation of stem cells
Andersen, M. Ø., Nygaard, J. V., Burns, J. S., Raarup, M. K., Nyengaard, J. R., Bünger, C., Besenbacher, F., Howard, K. A., Kassem, M., Kjems, J. Molecular Therapy 2010, 18, 2018–2027. (PR) (CO)
53)Serum-stable 2'-fluoro-pyrimidine-modified RNA aptamers to urokinase-type plasminogen activator blocking the association to its receptor
Dupont, D. M., Madsen, J. B., Hartmann, R. K., Tavitian, B., Ducongé, F., Kjems, J., Andreasen, P. A. RNA 2010, 16, 2360–2369. (PR) (CO)
52)Supramolecular porous network formed by molecular recognition between chemically modified nucleobases G and C
Xu, W., Wang, J.-G., Jacobsen, M. F., Mura, M., Yu, M., Kelly, R. E. A., Meng, Q.-Q., Lægsgaard, E., Stensgaard, I., Linderoth, T. R., Kjems, J., Kantorovich, L. N., Gothelf, K. V., Besenbacher, F. Angew. Chem. Int. Ed. 2010, 49, 9373–9377. (PR) (CO)
51)DNA Origami
Tørring, T., Voigt, N. V., Gothelf, K. V. Dansk Kemi 2010, 91(8), 14–17.
50)DNA-Templated Covalent Coupling of G4 PAMAM Dendrimers 
Liu, H.; Tørring, T.; Dong, M.; Besenbacher, F.; Gothelf, K. V. J. Am. Chem. Soc. 2010, 132, 18054–18056. (PR) (CO)
49)Single Molecule Atomic Force Microscopy Studies of Photosensitized Singlet Oxygen Behavior on a DNA Origami Template 
Helmig, S.; Rotaru, A.; Arian, D.; Arnbjerg, J.; Ogilby, P. R.; Kjems, J.; Mokhir, A.; Besenbacher, F.; Gothelf, K. V. ACS Nano 2010, 4, 7475–7480. (PR) (CO)
48)Guanine and potassium based two-dimensional coordination network self-assembled on Au(111)
Xu, W., Wang, J., Yu, M., Lægsgaard, E., Stensgaard, I., Linderoth, T. R. Hammer, B., Wang, C., Besenbacher, F. ). J. Am. Chem. Soc. 2010, 132, 15927–15929. (PR) (CO)
47)Long-range electron transfer in recombinant peroxidases anisotropically orientated on gold electrodes
Kartashov, A.V., Serafini, G., Dong, M., Shipovskov, S., Gazaryan, I., Besenbacher, F., Ferapontova, E. E. Phys. Chem. Chem. Phys. 2010, 12, 10098–10107. (PR) (CO)
46)News and Views: Steps towards automated synthesis
Rotaru, A., Gothelf, K. V. Nature Nanotech. 2010, 5, 760–761.

CDNA Publications 2009

45)A Yoctoliter-Scale DNA Reactor for Small Molecule Evolution 
Hansen, M. H.; Blakskjær,P.; Petersen, L. K.; Hansen, T. H.; Højfeldt, J. W.; Gothelf, K. V.; Hansen, N. J. V J. Am. Chem. Soc. 2009, 131, 1322–1327. (PR) (CO)
44)Distance Dependent Interhelical Couplings of Organic Rods Incorporated in DNA 4-Helix Bundles 
Andersen, C. S.; Knudsen, M. M.; Chhabra, R.; Liu, Y.; Yan, H.; Gothelf, K. V. Bioconjugate Chem. 2009, 20, 1538–1546. (PR) (CO)
43)Effect of Polymer Crosslinks on Oxygen Diffusion in Glassy PMMA Films 
Klinger, M.; Tolbod, L. P.; Gothelf, K. V.; Ogilby, P. R. ACS Appl. Mater. Interfaces 2009, 1, 661–667. (PR)
42)Effect of Serum on an RNA Aptamer-Based Electrochemical Sensor for Theophylline 
Ferapontova, E.; Gothelf, K. Langmuir 2009, 25, 4279–4283. (PR)
41)Optimization of the electrochemical RNA-aptamer based biosensor for theophylline by using a Methylene Blue redox label 
Ferapontova, E.; Gothelf, K. Electroanalysis 2009, 21, 1261–1266. (PR)
40)Self-assembly of a nano-scale DNA box with a controllable lid 
Andersen, E. S.; Dong, M.; Nielsen, M. M.; Jahn, K.; Subramani, R.; Mamdouh, W.; Golas, M. M.; Sander, B.; Stark, H.; Oliveira, C. L. P.; Pedersen, J. S. P.; Birkedal, V.; Besenbacher, F.; Gothelf,* K. V.; Kjems,* J. Nature 2009, 459, 73–76. (PR) (CO)
39)Self-assembly of artificial nucleobase 1H-benzoimidazole-4,7-dione at the liquid/solid interface
Mamdouh, W.; Kelly, R. E. A.; Dong, M.; Jacobsen, M. F.; Ferapontova, E.; Kantorovich, L.; Gothelf, K. V.; Besenbacher,F. J. Phys. Chem. B 2009, 113, 8675–8681. (PR) (CO)
38)Synthesis and electrochemical studies of an anthraquinone-conjugated nucleoside and derived oligonucleotides 
Jacobsen, M. F.; Ferapontova, E. F.; Gothelf, K. V. Org. Biomol. Chem. 2009, 7, 905–908. (PR)
37)Synthesis of functional molecular rod oligomers
Andersen, C. S.; Gothelf, K. V. Org. Biomol. Chem. 2009, 7, 58–60. (PR)
36)Adenine monolayers on the Au(111) surface: Structure identification by scanning tunneling microscopy experiment and ab initio calculations
Lukas, M., Kelly, R. E. A., Kantorovich, L. N., Otero Martin, R., Xu, W., Lægsgaard, E., Stensgaard, I., Besenbacher, F. J. Chem. Phys. 2009, 130, 024705. (PR) (CO)
35)Influence of tunable external stimuli on the self-assembly of guanosine supramolecular nanostructures studied by atomic force microscope
Li, Y., Dong, M., Otzen, D., Yao, Y., Liu, B., Besenbacher, F., Mamdouh, W. Langmuir, 2009, 25, 13432–13437. (PR) (CO)
34)Prochiral guanine adsorption on AU (111): An entropy-stabilized intermixed guanine-quartet chiral structure
Xu, W., Kelly, R. E. A., Gersen, H., Lægsgaard, E., Stensgaard, I., Kantorovich, L.N., Besenbacher, F. Small, 2009, 5, 1952–1956. (PR) (CO)
33)The effect of chemical modification and nanoparticle formulation on stability and biodistribution of siRNA in mice
Gao, S., Dagnæs-Hansen, F., Nielsen, E. J. B., Wengel, J., Besenbacher, F., Howard, K. A., Kjems, J. Molecular Therapy, 2009, 17, 1225–1233. (PR) (CO)
32)Structure of the HIV-1 Rev response element alone and in complex with Rev studied by AFM
Pallesen, J., Dong, M., Besenbacher, F., Kjems, J. FEBS J., 2009, 276, 4223–4232. (PR)
31)A DNA nanoswitch incorporating the fluorescent base analogue 2-aminopurine detects single nucleotide mismatches in unlabelled targets
Campbell, C. J., Mountford, C. P., Stoquert, H. C., Buck, A. H., Dickinson, P., Ferapontova, E. E., Terry, J. G., Beattie, J. S., Walton, A. J., Crain, J., Ghazal, P., Mount, A. R. Analyst, 2009, 134, 1873–1879. (PR) (CO)
30)A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity
Bramsen, J.B., Laursen, M. B., Bus, C., Hansen, T.B., Langklær, N., Babu, B. R., Højland, T., Abramov, M., Bobkov, G. V., Mikhailov, S. N., Van Aerschot, A., Herdewijn, P., Odadzic, D., Smicius, R., Haas, J. Andree, C., Fava, E., Hess, S., Müller, E., Meyer, T. F., Zerial, M., Engels, J. W., Herdewijn. P., Wengel, J., Kjems, J. Nucleic. Acids Res., 2009, 37, 2867–2881. (PR) (CO)
29)Scaffolded DNA origami of a tetrahedron molecular container
Ke, Y., Sharma, J., Liu, M., Jahn, K., Liu, Y., Yan, H. Nano Lett., 2009, 9, 2445–2447. (PR) (CO)


CDNA Publications 2008

28)DNA Origami Design of Dolphin-Shaped Structures with Flexible Tails
Andersen, E. S.; Dong, M.; Nielsen, M.; Jahn, K.; Thomsen, A. L.; Mamdouh, W.; Gothelf, K. V.; Besenbacher, F.; Kjems, J. ACS Nano 2008, 2, 1213–1218. (PR)
27)Molecular recognition with DNA nanoswitches: Effects of single base mutations on structure
Mountford C.P., Buck A. H., Campbell C. J., Dickinson P., Ferapontova E. E., Terry J. G., Beattie J. S., Walton A. J., Ghazal P., Mount A.J., Crain J. J. Phys. Chem. B 2008, 112, 2439–2444. (PR) (CO)
26)An RNA Aptamer-Based Electrochemical Biosensor for Detection of Theophylline in Serum 
Ferapontova, E. E.; Olsen, E. M.; Gothelf, K. V. J. Am. Chem. Soc. 2008, 130, 4256–4258. (PR)
25)Electrochemical control of a DNA Holliday Junction nanoswitch by Mg2+ ions
Ferapontova E. E., Mountford C. P., Crain J., Buck A. H., Dickinson P., Beattie J. S., Ghazal P., Terry J. G., Walton A. J., Mount A. R. Biosens. Bioelectron. 2008, 24, 422–428. (PR) (CO)
24)Biocatalysis of theophylline oxidation by microbial theophylline oxidase in the presence of non-physiological electron acceptors
Shipovskov S., Ferapontova E.E. Biocat. Biotrans. 2008, 26, 508–518. (PR) (CO)
23)Coexistence of homochiral and heterochiral adenine domains at the liquid-solid interface
Mamdouh, W., Dong, M., Kelly, R., Kantorovich, L., Besenbacher, F. J. Phys. Chem. B. 2008, 111, 12048–12052. (PR) (CO)
22)Supramolecular nanopatterns self-assembled by adenine and thymine quartets at the liquid-solid interface
Mamdouh, W., Dong, M., Xu, S., Rauls, E., Besenbacher, F. J. Am. Chem. Soc. 2008, 128, 13305–13311. (PR) (CO)
21)Intracellular siRNA and precursor miRNA trafficking using bioresponsive copolypeptides
Rahbek, U. L., Howard. K. A., Oupicky, D., Dong, M., Nielsen, A. F., Raarup, M-R., Besenbacher, F., Kjems, J. J. Gene Med. 2008, 10, 81–93. (PR)
20)Labeling of DNA via rearrangement of S-2-aminoethyl phosphorothioates to N-(2-mercaptoethyl)phosphoramidates 
Chen, M.; Gothelf, K. V. Org. Biomol. Chem. 2008, 6, 908–911. (PR)
19)Toward Reliable Gold Nanoparticle Patterning On Self-Assembled DNA Nanoscaffold 
Sharma, J.; Chhabra, R.; Andersen, C. S.; Gothelf, K. V.; Yan, H.; Liu, Y. J. Am. Chem. Soc. 2008, 130, 7820–7821. (PR) (CO)
18)Perylene attached to 2'-amino-LNA: synthesis, incorporation into oligonucleotides, and remarkable fluorescence properties in vitro and in cell culture
Astakhova, I. V., Korshun, V.A., Jahn, K., Kjems, J., Wengel, J. Bioconjug. Chem. 2008, 19, 1995–2007. (PR) (CO)
17)Bridging One Helical Turn in dsDNA by Templated Dimerization of Molecular Rods 
Andersen, C. S.; Yan, H.; Gothelf, K. V. Angew. Chem. Int. Ed. 2008, 47, 5569–5572. (PR) (CO)
16)Elementary structural motifs in a random network of cytosine adsorbed on a gold (111) surface
Otero, R., Lukas, M., Kelly, R. E. A., Xu, W., Lægsgaard, E., Stensgaard, I., Kantorovich, L. N., Besenbacher, F. Science 2008, 319, 312–315. (PR) (CO)
15)An investigation into the interactions between self-assembled adenine molecules and the Au(111) surface
Kelly, R. E. A., Xu, W., Lukas, M., Otero, R., Mura, M., Lee, Y-J., Lægsgaard, E:, Stensgaard, I., Kantorovich, L. N., Besenbacher, F. Small 2008, 4, 1494–1500. (PR) (CO)
14)Understanding the disorder of the DNA base cytosine on the Au(111) surface
Kelly, R. E. A., Lukas, M., Kantorovich, L. N., Otero, R., Xu, W., Mura, M., Lægsgaard, E., Stensgaard, I, Besenbacher, F. J. Chem. Phys. 2008, 129, 184707. (PR) (CO)
13)Two-dimensional supramolecular nanopatterns formed by the co-adsorption of guanine and uracil at the liquid/solid interface
Mamdouh, W., Kelly, R. E. A., Dong, M., Kantorovich, L. N., Besenbacher, F. Small 2008, 130, 695–702. (PR) (CO)
12)Specificity of Watson-Crick base pairing on a solid surface studied at the atomic scale
Xu, W., Kelly, R. E. A., Kantorovitch, L. N., Otero, R., Kjems, J., Lukas, M., Lægsgaard, E., Stensgaard, I., Besenbacher, F. Angew. Chem. Int. Ed. 2008, 47, 9673–9676. (PR) (CO)


CDNA Publications 2007

11)Model Systems for Activation of Nucleic Acid Encoded Prodrugs 
Jacobsen, M. F.; Cló, E., Mokhir, A.; Gothelf, K. V. ChemMedChem 2007, 2, 793–799. (PR) (CO)
10)Rearrangement of S-2-Aminoethyl Phosphorothioates to N-2-Mercaptoethyl-phosphoramidates 
Chen, M.; Maetzke, A.; Jensen, S. J. K.; Gothelf, K. V. Eur. J. Org. Chem. 2007, 5826–5833. (PR)
9)Synthesis of Rigid Dimers and Trimers of Adenine and Thymine 
Jacobsen, M. F.; Andersen, C. S.; Knudsen, M. M.; Gothelf, K. V. Org. Lett. 2007, 9, 2851–2854. (PR)
8)Scanning probe microscopies beyond imaging: manipulation of molecules and nanostructures
Mamdouh, W., Besenbacher, F. Small 2007, 3, 512–513. (PR)
7)Coexistence of homochiral and heterochiral adenine domains at the liquid/solid interface
Mamdouh, W., Dong, M., Kelly, R. A., Kantorovich, L., Besenbacher, F. J. Phys. Chem. B 2007, 111, 12048–12052. (PR) (CO)
6)Direct force measurements between siRNA and chitosan molecules
Xu, S. L., Dong, M., Liu, X., Howard, K. A., Kjems, J., Besenbacher, F. Biophys J. 2007, 93, 952–959. (PR)
5)Efficient inhibition of HIV-1 expression by LNA modified antisense oligonucleotides and DNAzymes targeted to functionally selected binding sites
Jakobsen, M.R., Haasnoot, J., Wengel, J., Berkhout, B., Kjems, J. Retrovirology 2007, 4, 29. (PR) (CO)
4)Improved silencing properties of small interfering RNAs with segmented sense strand
Bramsen, J.B., Lauersen, M.B., Damgaard, C.K., Willsen, S.L., Wengel, J., Kjems, J. Nucleic Acids Res. 2007, 35, 5886–5897. (PR) (CO) (OA)
3)An Electrochemical Sensor Based On The Human Estrogen Receptor Ligand Binding Domain 
Hansen, J. A.; Sumbayev, V. V.; Gothelf, K. V. Nano Lett. 2007, 7, 2831–2834. (PR)
2)Control and Selectivity of Photosensitized Singlet Oxygen Production: Challenges in Complex Biologiscal System 
Cló, E.; Snyder, J. W.; Ogilby, P. R.; Gothelf, K. V. ChemBioChem 2007, 8, 475–481. (PR)
1)Probing the hierarchy of thymine-thymine interactions in self-assembled structures by STM manipulation
Xu, W., Kelly, R.E.A., Otero, R., Schöck, M., Lægsgaard, E., Stensgaard, I., Kantorovich, L.N., Besenbacher, F. Small 2007, 3, 2011–2014. (PR) (CO)


Book Chapters

2014, “The power of single molecule FRET microscopy applied to DNA nanotechnology”, in Kjems/Ferapontova/Gothelf (Eds.): Nucleic Acids Nanotechnology. Series “Nucleic Acids and Molecular Biology” (Series Editor: J. Bujnicki), Springer, Volume 29, pp 53-68.

2014, Selnihhin, D., Andersen, E.S., Computer-aided design of DNA origami structures, Methods in Molecular Biology.

2014, Andersen, E.S. The art of editing RNA structural alignments. Methods in molecular biology 1097, 379-394.

2014, Sukosd, Z., Andersen, E.S., and Lyngso, R. SCFGs in RNA secondary structure prediction RNA secondary structure prediction: a hands-on approach. Methods in molecular biology 1097, 143-162.

2013, Kjems, J, Ferapontova, E., Gothelf, K.V. Nucleic Acid Nanotechnology, Nucleic Acids and Molecular Biology. Vol 29, Springer. (PR)

2013, Bramsen, J.B. and Kjems, J. Engineering small interfering RNAs by strategic chemical modification. Methods in molecular biology (Clifton, N.J.), 942, 87-109. (PR)

2013, Krüger, A.C., Hildebrandt, L., Kragh, S.L.; Birkedal, V. Nucleic acids structural dynamics by single molecule fluorescence resonanence energy transfer. Methods in Cell Biology: Laboratory Methods in Cell Biology . Vol. 113 2013. (PR)

2013. Kragh, S. L. and Birkedal ,V. The power of single molecule FRET microscopy applied to DNA nanotechnology, in Kjems/Ferapontova/Gothelf (Eds.): Nucleic Acids Nanotechnology. Series “Nucleic Acids and Molecular Biology” (Series Editor: J. Bujnicki), Springer, in press

2011, Andersen, Ebbe Sloth. Fremtidens bio-nanoteknologi – design dine egne molekyler. I ”Bioteknologi – en temabog”, ed. Gasbjerg, P. K., Jensen, G. S., Sørensen, A. B. Systime.

2011, Bramsen, J.B., Kjems, J. Using chemical modification to enhance siRNA performance. Handbook of RNA Biochemistry, 2nd edition. Wiley-VCH. (PR)

2008, Howard, K.A., Andersen, M.O., Kjems, J., RNAi using a chitosan/siRNA nanoparticle system. In "Methods in Molecular Medicine," publisher: Humana Press. (PR)

2007, LaBean, T., Gothelf, K.V., Reif, J.H. Self-assembling DNA Nanostructures for Patterned Molecular Assembly", in Niemeyer, C., Mirkin, C. (red.) Nanobiotechnology II: More concepts and applications, Wiley-VCH, Weinheim.