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A nanofluidic device for parallel single nanoparticle catalysis in solution.

Levin S, Fritzsche J, Nilsson S, Runemark A, Dhokale B, Ström H, Sundén H, Langhammer C, Westerlund F.

Nat Commun. 2019 Sep 27;10(1):4426. doi: 10.1038/s41467-019-12458-1.


Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects.

Feng B, Sosa RP, Mårtensson AKF, Jiang K, Tong A, Dorfman KD, Takahashi M, Lincoln P, Bustamante CJ, Westerlund F, Nordén B.

Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17169-17174. doi: 10.1073/pnas.1909122116. Epub 2019 Aug 14.


Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak.

Bikkarolla SK, Nordberg V, Rajer F, Müller V, Kabir MH, Kk S, Dvirnas A, Ambjörnsson T, Giske CG, Navér L, Sandegren L, Westerlund F.

MBio. 2019 Jul 9;10(4). pii: e00347-19. doi: 10.1128/mBio.00347-19.


Enzyme-free optical DNA mapping of the human genome using competitive binding.

Müller V, Dvirnas A, Andersson J, Singh V, Kk S, Johansson P, Ebenstein Y, Ambjörnsson T, Westerlund F.

Nucleic Acids Res. 2019 Sep 5;47(15):e89. doi: 10.1093/nar/gkz489.


Annealing of ssDNA and compaction of dsDNA by the HIV-1 nucleocapsid and Gag proteins visualized using nanofluidic channels.

Jiang K, Humbert N, Kk S, Lequeu T, Lin YL, Mely Y, Westerlund F.

Q Rev Biophys. 2019 Jan;52:e2. doi: 10.1017/S0033583518000124.


A nanofluidic device for real-time visualization of DNA-protein interactions on the single DNA molecule level.

Öz R, Kk S, Westerlund F.

Nanoscale. 2019 Jan 23;11(4):2071-2078. doi: 10.1039/c8nr09023h.


Genetic variation in the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain.

Ferreira C, Bogas D, Bikarolla SK, Varela AR, Frykholm K, Linheiro R, Nunes OC, Westerlund F, Manaia CM.

Chemosphere. 2019 Apr;220:748-759. doi: 10.1016/j.chemosphere.2018.12.130. Epub 2018 Dec 23.


Bacterial response to graphene oxide and reduced graphene oxide integrated in agar plates.

Mokkapati VRSS, Pandit S, Kim J, Martensson A, Lovmar M, Westerlund F, Mijakovic I.

R Soc Open Sci. 2018 Nov 14;5(11):181083. doi: 10.1098/rsos.181083. eCollection 2018 Nov.


Interspecies plasmid transfer appears rare in sequential infections with extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae.

Lindblom A, Kk S, Müller V, Öz R, Sandström H, Åhrén C, Westerlund F, Karami N.

Diagn Microbiol Infect Dis. 2019 Apr;93(4):380-385. doi: 10.1016/j.diagmicrobio.2018.10.014. Epub 2018 Nov 1.


Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis.

Krog J, Alizadehheidari M, Werner E, Bikkarolla SK, Tegenfeldt JO, Mehlig B, Lomholt MA, Westerlund F, Ambjörnsson T.

J Chem Phys. 2018 Dec 7;149(21):215101. doi: 10.1063/1.5051319.


The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis.

Johnning A, Karami N, Tång Hallbäck E, Müller V, Nyberg L, Buongermino Pereira M, Stewart C, Ambjörnsson T, Westerlund F, Adlerberth I, Kristiansson E.

Microb Genom. 2018 Nov;4(11). doi: 10.1099/mgen.0.000233. Epub 2018 Nov 21.


Alpha-Synuclein Modulates the Physical Properties of DNA.

Jiang K, Rocha S, Westling A, Kesarimangalam S, Dorfman KD, Wittung-Stafshede P, Westerlund F.

Chemistry. 2018 Oct 17;24(58):15685-15690. doi: 10.1002/chem.201803933. Epub 2018 Sep 19.


PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction.

Schmitt A, Jiang K, Camacho MI, Jonna VR, Hofer A, Westerlund F, Christie PJ, Berntsson RP.

Mol Microbiol. 2018 Aug;109(3):291-305. doi: 10.1111/mmi.13980. Epub 2018 Jul 31.


Identification and DNA annotation of a plasmid isolated from Chromobacterium violaceum.

Lima DC, Nyberg LK, Westerlund F, Batistuzzo de Medeiros SR.

Sci Rep. 2018 Mar 28;8(1):5327. doi: 10.1038/s41598-018-23708-5.


Hairpins in the conformations of a confined polymer.

Werner E, Jain A, Muralidhar A, Frykholm K, St Clere Smithe T, Fritzsche J, Westerlund F, Dorfman KD, Mehlig B.

Biomicrofluidics. 2018 Mar 9;12(2):024105. doi: 10.1063/1.5018787. eCollection 2018 Mar.


Facilitated sequence assembly using densely labeled optical DNA barcodes: A combinatorial auction approach.

Dvirnas A, Pichler C, Stewart CL, Quaderi S, Nyberg LK, Müller V, Kumar Bikkarolla S, Kristiansson E, Sandegren L, Westerlund F, Ambjörnsson T.

PLoS One. 2018 Mar 9;13(3):e0193900. doi: 10.1371/journal.pone.0193900. eCollection 2018.


Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms.

Pandit S, Ravikumar V, Abdel-Haleem AM, Derouiche A, Mokkapati VRSS, Sihlbom C, Mineta K, Gojobori T, Gao X, Westerlund F, Mijakovic I.

Front Microbiol. 2017 Dec 22;8:2599. doi: 10.3389/fmicb.2017.02599. eCollection 2017.


Corrigendum: Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules.

Nyberg LK, Quaderi S, Emilsson G, Karami N, Lagerstedt E, Müller V, Noble C, Hammarberg S, Nilsson AN, Sjöberg F, Fritzsche J, Kristiansson E, Sandegren L, Ambjörnsson T, Westerlund F.

Sci Rep. 2017 Dec 22;7:46911. doi: 10.1038/srep46911.


Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation.

Clark AG, Naufer MN, Westerlund F, Lincoln P, Rouzina I, Paramanathan T, Williams MC.

Biochemistry. 2018 Feb 6;57(5):614-619. doi: 10.1021/acs.biochem.7b01036. Epub 2018 Jan 5.


Fluorescence Microscopy of Nanochannel-Confined DNA.

Westerlund F, Persson F, Fritzsche J, Beech JP, Tegenfeldt JO.

Methods Mol Biol. 2018;1665:173-198. doi: 10.1007/978-1-4939-7271-5_10.


Exploring DNA-protein interactions on the single DNA molecule level using nanofluidic tools.

Frykholm K, Nyberg LK, Westerlund F.

Integr Biol (Camb). 2017 Aug 14;9(8):650-661. doi: 10.1039/c7ib00085e. Review.


Noise reduction in single time frame optical DNA maps.

Torche PC, Müller V, Westerlund F, Ambjörnsson T.

PLoS One. 2017 Jun 22;12(6):e0179041. doi: 10.1371/journal.pone.0179041. eCollection 2017.


Applications of optical DNA mapping in microbiology.

Bogas D, Nyberg L, Pacheco R, Azevedo NF, Beech JP, Gomila M, Lalucat J, Manaia CM, Nunes OC, Tegenfeldt JO, Westerlund F.

Biotechniques. 2017 Jun 1;62(6):255-267. doi: 10.2144/000114555.


Binding of Thioflavin-T to Amyloid Fibrils Leads to Fluorescence Self-Quenching and Fibril Compaction.

Lindberg DJ, Wenger A, Sundin E, Wesén E, Westerlund F, Esbjörner EK.

Biochemistry. 2017 Apr 25;56(16):2170-2174. doi: 10.1021/acs.biochem.7b00035. Epub 2017 Apr 17.


Vitamin C Pretreatment Enhances the Antibacterial Effect of Cold Atmospheric Plasma.

Helgadóttir S, Pandit S, Mokkapati VR, Westerlund F, Apell P, Mijakovic I.

Front Cell Infect Microbiol. 2017 Feb 22;7:43. doi: 10.3389/fcimb.2017.00043. eCollection 2017.


A nano flow cytometer for single lipid vesicle analysis.

Friedrich R, Block S, Alizadehheidari M, Heider S, Fritzsche J, Esbjörner EK, Westerlund F, Bally M.

Lab Chip. 2017 Feb 28;17(5):830-841. doi: 10.1039/c6lc01302c.


Optical DNA mapping in nanofluidic devices: principles and applications.

Müller V, Westerlund F.

Lab Chip. 2017 Feb 14;17(4):579-590. doi: 10.1039/c6lc01439a. Review.


Single Particle Nanoplasmonic Sensing in Individual Nanofluidic Channels.

Fritzsche J, Albinsson D, Fritzsche M, Antosiewicz TJ, Westerlund F, Langhammer C.

Nano Lett. 2016 Dec 14;16(12):7857-7864. Epub 2016 Nov 21.


DNA intercalation optimized by two-step molecular lock mechanism.

Almaqwashi AA, Andersson J, Lincoln P, Rouzina I, Westerlund F, Williams MC.

Sci Rep. 2016 Dec 5;6:37993. doi: 10.1038/srep37993.


Direct identification of antibiotic resistance genes on single plasmid molecules using CRISPR/Cas9 in combination with optical DNA mapping.

Müller V, Rajer F, Frykholm K, Nyberg LK, Quaderi S, Fritzsche J, Kristiansson E, Ambjörnsson T, Sandegren L, Westerlund F.

Sci Rep. 2016 Dec 1;6:37938. doi: 10.1038/srep37938.


Super-Resolution Genome Mapping in Silicon Nanochannels.

Jeffet J, Kobo A, Su T, Grunwald A, Green O, Nilsson AN, Eisenberg E, Ambjörnsson T, Westerlund F, Weinhold E, Shabat D, Purohit PK, Ebenstein Y.

ACS Nano. 2016 Nov 22;10(11):9823-9830. Epub 2016 Sep 23.


Rapid Tracing of Resistance Plasmids in a Nosocomial Outbreak Using Optical DNA Mapping.

Müller V, Karami N, Nyberg LK, Pichler C, Torche Pedreschi PC, Quaderi S, Fritzsche J, Ambjörnsson T, Åhrén C, Westerlund F.

ACS Infect Dis. 2016 May 13;2(5):322-8. doi: 10.1021/acsinfecdis.6b00017. Epub 2016 Mar 29.


Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels.

Fornander LH, Frykholm K, Fritzsche J, Araya J, Nevin P, Werner E, Çakır A, Persson F, Garcin EB, Beuning PJ, Mehlig B, Modesti M, Westerlund F.

Langmuir. 2016 Aug 23;32(33):8403-12. doi: 10.1021/acs.langmuir.6b01877. Epub 2016 Aug 12.


Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules.

Nyberg LK, Quaderi S, Emilsson G, Karami N, Lagerstedt E, Müller V, Noble C, Hammarberg S, Nilsson AN, Sjöberg F, Fritzsche J, Kristiansson E, Sandegren L, Ambjörnsson T, Westerlund F.

Sci Rep. 2016 Jul 27;6:30410. doi: 10.1038/srep30410. Erratum in: Sci Rep. 2017 Dec 22;7:46911.


DNA compaction by the bacteriophage protein Cox studied on the single DNA molecule level using nanofluidic channels.

Frykholm K, Berntsson RP, Claesson M, de Battice L, Odegrip R, Stenmark P, Westerlund F.

Nucleic Acids Res. 2016 Sep 6;44(15):7219-27. doi: 10.1093/nar/gkw352. Epub 2016 Apr 29.


Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation.

Almaqwashi AA, Andersson J, Lincoln P, Rouzina I, Westerlund F, Williams MC.

Biophys J. 2016 Mar 29;110(6):1255-63. doi: 10.1016/j.bpj.2016.02.016.


Extension of nanoconfined DNA: Quantitative comparison between experiment and theory.

Iarko V, Werner E, Nyberg LK, Müller V, Fritzsche J, Ambjörnsson T, Beech JP, Tegenfeldt JO, Mehlig K, Westerlund F, Mehlig B.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Dec;92(6):062701. doi: 10.1103/PhysRevE.92.062701. Epub 2015 Dec 2.


A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps.

Bahira M, McCauley MJ, Almaqwashi AA, Lincoln P, Westerlund F, Rouzina I, Williams MC.

Nucleic Acids Res. 2015 Oct 15;43(18):8856-67. doi: 10.1093/nar/gkv864. Epub 2015 Sep 13.


Hydride formation thermodynamics and hysteresis in individual Pd nanocrystals with different size and shape.

Syrenova S, Wadell C, Nugroho FA, Gschneidtner TA, Diaz Fernandez YA, Nalin G, Świtlik D, Westerlund F, Antosiewicz TJ, Zhdanov VP, Moth-Poulsen K, Langhammer C.

Nat Mater. 2015 Dec;14(12):1236-44. doi: 10.1038/nmat4409. Epub 2015 Sep 7.


MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures.

Mondal T, Subhash S, Vaid R, Enroth S, Uday S, Reinius B, Mitra S, Mohammed A, James AR, Hoberg E, Moustakas A, Gyllensten U, Jones SJ, Gustafsson CM, Sims AH, Westerlund F, Gorab E, Kanduri C.

Nat Commun. 2015 Jul 24;6:7743. doi: 10.1038/ncomms8743.


Bacteriophage strain typing by rapid single molecule analysis.

Grunwald A, Dahan M, Giesbertz A, Nilsson A, Nyberg LK, Weinhold E, Ambjörnsson T, Westerlund F, Ebenstein Y.

Nucleic Acids Res. 2015 Oct 15;43(18):e117. doi: 10.1093/nar/gkv563. Epub 2015 May 27.


Fast size-determination of intact bacterial plasmids using nanofluidic channels.

Frykholm K, Nyberg LK, Lagerstedt E, Noble C, Fritzsche J, Karami N, Ambjörnsson T, Sandegren L, Westerlund F.

Lab Chip. 2015 Jul 7;15(13):2739-43. doi: 10.1039/c5lc00378d. Epub 2015 May 21.


Evidence for hydrophobic catalysis of DNA strand exchange.

Feng B, Westerlund F, Nordén B.

Chem Commun (Camb). 2015 Apr 30;51(34):7390-2. doi: 10.1039/c5cc01515d.


Steady-state and time-resolved Thioflavin-T fluorescence can report on morphological differences in amyloid fibrils formed by Aβ(1-40) and Aβ(1-42).

Lindberg DJ, Wranne MS, Gilbert Gatty M, Westerlund F, Esbjörner EK.

Biochem Biophys Res Commun. 2015 Mar 6;458(2):418-23. doi: 10.1016/j.bbrc.2015.01.132. Epub 2015 Feb 7.


Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex.

Almaqwashi AA, Paramanathan T, Lincoln P, Rouzina I, Westerlund F, Williams MC.

Nucleic Acids Res. 2014 Oct;42(18):11634-41. doi: 10.1093/nar/gku859. Epub 2014 Sep 22.


The conquest of middle-earth: combining top-down and bottom-up nanofabrication for constructing nanoparticle based devices.

Diaz Fernandez YA, Gschneidtner TA, Wadell C, Fornander LH, Lara Avila S, Langhammer C, Westerlund F, Moth-Poulsen K.

Nanoscale. 2014 Dec 21;6(24):14605-16. doi: 10.1039/c4nr03717k. Epub 2014 Sep 11.


Sensing conformational changes in DNA upon ligand binding using QCM-D. Polyamine condensation and Rad51 extension of DNA layers.

Sun L, Frykholm K, Fornander LH, Svedhem S, Westerlund F, Akerman B.

J Phys Chem B. 2014 Oct 16;118(41):11895-904. doi: 10.1021/jp506733w. Epub 2014 Oct 8.


Single-molecule electronics: from chemical design to functional devices.

Sun L, Diaz-Fernandez YA, Gschneidtner TA, Westerlund F, Lara-Avila S, Moth-Poulsen K.

Chem Soc Rev. 2014 Nov 7;43(21):7378-411. doi: 10.1039/c4cs00143e. Epub 2014 Aug 7.


Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.

Nilsson AN, Emilsson G, Nyberg LK, Noble C, Stadler LS, Fritzsche J, Moore ER, Tegenfeldt JO, Ambjörnsson T, Westerlund F.

Nucleic Acids Res. 2014 Sep;42(15):e118. doi: 10.1093/nar/gku556. Epub 2014 Jul 10.


A versatile self-assembly strategy for the synthesis of shape-selected colloidal noble metal nanoparticle heterodimers.

Gschneidtner TA, Diaz Fernandez YA, Syrenova S, Westerlund F, Langhammer C, Moth-Poulsen K.

Langmuir. 2014 Mar 25;30(11):3041-50. doi: 10.1021/la5002754. Epub 2014 Mar 14.

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