Melting of confined DNA: static and dynamic properties

Dibyajyoti Mohanta

Soft Matter, 2022, 18, 2790
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Optical DNA mapping in nanofluidic devices: principles and applications

Vilhelm Müller and Fredrik Westerlund

Lab Chip, 2017, 17, 579
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DNA barcoding via counterstaining with AT/GC sensitive ligands in injection-molded all-polymer nanochannel devices

Peter Friis Østergaard, Marco Matteucci, Walter Reisner and Rafael Taboryski

Analyst, 2013, 138, 1249
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Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

Damini Gupta, Julian Sheats, Abhiram Muralidhar, Jeremy J. Miller, Derek E. Huang, Sara Mahshid, Kevin D. Dorfman and Walter Reisner

The Journal of Chemical Physics, 2014, 140
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Applications of Optical DNA Mapping in Microbiology

Diana Bogas, Lena Nyberg, Rui Pacheco, Nuno F. Azevedo, Jason P. Beech, Margarita Gomila, Jorge Lalucat, Célia M. Manaia, Olga C. Nunes, Jonas O. Tegenfeldt and Fredrik Westerlund

BioTechniques, 2017, 62, 255
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Miniaturized flow cell with pneumatically-actuated vertical nanoconfinement for single-molecule imaging and manipulation

Daniel J. Berard and Sabrina R. Leslie

Biomicrofluidics, 2018, 12
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Conformations of DNA in Triangular Nanochannels

Chiara Manneschi, Elena Angeli, Tapio Ala-Nissila, Luca Repetto, Giuseppe Firpo and Ugo Valbusa

Macromolecules, 2013, 46, 4198
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Polymer multilevel lab-on-chip systems for electrochemical sensing

Marco Matteucci, Simon Tylsgaard Larsen, Alessandro Garau, Simone Tanzi and Rafael Taboryski

Journal of Vacuum Science & Technology B, Nanotechnology and Microelectronics: Materials, Processing, Measurement, and Phenomena, 2013, 31, 06F904
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Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli

Adam N. Nilsson, Gustav Emilsson, Lena K. Nyberg, Charleston Noble, Liselott Svensson Stadler, Joachim Fritzsche, Edward R. B. Moore, Jonas O. Tegenfeldt, Tobias Ambjörnsson and Fredrik Westerlund

Nucleic Acids Research, 2014, 42, e118
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Stretching of DNA confined in nanochannels with charged walls

Chiara Manneschi, Paola Fanzio, Tapio Ala-Nissila, Elena Angeli, Luca Repetto, Giuseppe Firpo and Ugo Valbusa

Biomicrofluidics, 2014, 8
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DNA in nanochannels: theory and applications

Karolin Frykholm, Vilhelm Müller, Sriram KK, Kevin D. Dorfman and Fredrik Westerlund

Quart. Rev. Biophys., 2022, 55
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Beyond Gel Electrophoresis: Microfluidic Separations, Fluorescence Burst Analysis, and DNA Stretching

Kevin D. Dorfman, Scott B. King, Daniel W. Olson, Joel D. P. Thomas and Douglas R. Tree

Chem. Rev., 2013, 113, 2584
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Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device

Rodolphe Marie, Jonas N. Pedersen, David L. V. Bauer, Kristian H. Rasmussen, Mohammed Yusuf, Emanuela Volpi, Henrik Flyvbjerg, Anders Kristensen and Kalim U. Mir

Proc. Natl. Acad. Sci. U.S.A., 2013, 110, 4893
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Visualizing the entire DNA from a chromosome in a single frame

C. Freitag, C. Noble, J. Fritzsche, F. Persson, M. Reiter-Schad, A. N. Nilsson, A. Granéli, T. Ambjörnsson, K. U. Mir and J. O. Tegenfeldt

Biomicrofluidics, 2015, 9, 044114
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The Backfolded Odijk Regime for Wormlike Chains Confined in Rectangular Nanochannels

Abhiram Muralidhar, Michael Quevillon and Kevin Dorfman

Polymers, 2016, 8, 79
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Sequencing and Optical Genome Mapping for the Adventurous Chemist

Elizabete Ruppeka Rupeika, Laurens D’Huys, Volker Leen and Johan Hofkens

Chemical & Biomedical Imaging, 2024, 2, 784
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Topology in soft and biological matter

Luca Tubiana, Gareth P. Alexander, Agnese Barbensi, Dorothy Buck, Julyan H.E. Cartwright, Mateusz Chwastyk, Marek Cieplak, Ivan Coluzza, Simon Čopar, David J. Craik, Marco Di Stefano, Ralf Everaers, Patrícia F.N. Faísca, Franco Ferrari, Achille Giacometti, Dimos Goundaroulis, Ellinor Haglund, Ya-Ming Hou, Nevena Ilieva, Sophie E. Jackson, Aleksandre Japaridze, Noam Kaplan, Alexander R. Klotz, Hongbin Li, Christos N. Likos, Emanuele Locatelli, Teresa López-León, Thomas Machon, Cristian Micheletti, Davide Michieletto, Antti Niemi, Wanda Niemyska, Szymon Niewieczerzal, Francesco Nitti, Enzo Orlandini, Samuela Pasquali, Agata P. Perlinska, Rudolf Podgornik, Raffaello Potestio, Nicola M. Pugno, Miha Ravnik, Renzo Ricca, Christian M. Rohwer, Angelo Rosa, Jan Smrek, Anton Souslov, Andrzej Stasiak, Danièle Steer, Joanna Sułkowska, Piotr Sułkowski, De Witt L. Sumners, Carsten Svaneborg, Piotr Szymczak, Thomas Tarenzi, Rui Travasso, Peter Virnau, Dimitris Vlassopoulos, Primož Ziherl and Slobodan Žumer

Physics Reports, 2024, 1075, 1
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Nanoplumbing with 2D Metamaterials

Saroj Dangi and Robert Riehn

Small, 2019, 15
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Optical mapping of single-molecule human DNA in disposable, mass-produced all-polymer devices

Peter Friis Østergaard, Joanna Lopacinska-Jørgensen, Jonas Nyvold Pedersen, Niels Tommerup, Anders Kristensen, Henrik Flyvbjerg, Asli Silahtaroglu, Rodolphe Marie and Rafael Taboryski

J. Micromech. Microeng., 2015, 25, 105002
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Experimental Evidence of Weak Excluded Volume Effects for Nanochannel Confined DNA

Damini Gupta, Jeremy J. Miller, Abhiram Muralidhar, Sara Mahshid, Walter Reisner and Kevin D. Dorfman

ACS Macro Lett., 2015, 4, 759
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Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy

Michal Levy-Sakin and Yuval Ebenstein

Current Opinion in Biotechnology, 2013, 24, 690
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Hydrodynamics of DNA confined in nanoslits and nanochannels

K. D. Dorfman, D. Gupta, A. Jain, A. Muralidhar and D. R. Tree

Eur. Phys. J. Spec. Top., 2014, 223, 3179
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Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Wesley F. Reinhart, Jeff G. Reifenberger, Damini Gupta, Abhiram Muralidhar, Julian Sheats, Han Cao and Kevin D. Dorfman

The Journal of Chemical Physics, 2015, 142
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