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DNA and mRNA as molecular speed bumps in Escherichia coli's cytoplasm [New & Notable]

AJ Boersma

Biophysical Journal

Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions

B Monterroso, W Margolin, AJ Boersma, G Rivas, B Poolman, S Zorrilla
Chemical Reviews

Two-Photon Excited-State Dynamics of mEGFP–Linker–mScarlet–I Crowding Biosensor in Controlled Environments

SA Mersch, S Bergman, ED Sheets, AJ Boersma, AA Heikal

Physical Chemistry Chemical Physics doi: 10.1039/D3CP04733D.


A physicochemical perspective on cellular ageing

SN Mouton, AJ Boersma, LM Veenhoff
Trends in Biochemical Sciences doi: 10.1016/j.tibs.2023.08.007. Online ahead of print.

Genetically-encoded probes to determine nonspecific hydrophobic and electrostatic binding in cells

W Zuo, MR Huang, F Schmitz, AJ Boersma

bioRxiv doi:

Microgels As Platforms for Antibody-mediated Cytokine Scavenging
S Boesveld, Y Kittel, Y Luo, A Jans, B Oezcifci, M Bartneck, C Preisinger, D Rommel, T Haraszti, SP Centeno, AJ Boersma, L De Laporte, C Trautwein, AJC Kuehne, P Strnad
Advanced Healthcare Materials 2023: e2300695. Online ahead of print.

Self-association of a nucleoid-binding protein increases with macromolecular crowding in Escherichia coli

T Pittas, AJ Boersma

bioRxiv doi:

Cell wall damage increases macromolecular crowding effects in the Escherichia coli cytoplasm

T Pittas, W Zuo, AJ Boersma

iScience 2023 DOI:


High macromolecular crowding in liposomes from microfluidics

LPB Guerzoni, AVC de Goes, M Kalacheva, J Hadula, M Mork, L De Laporte, AJ Boersma

Advanced Science 9 (27), 2201169

A FRET-based method for monitoring structural transitions in protein self-organization

Q Wan, SN Mouton, LM Veenhoff, AJ Boersma

Cell Reports Methods 2 (3), 100184


Molecular Brightness Approach for FRET Analysis of Donor-Linker-Acceptor Constructs at the Single Molecule Level: A Concept

Kay TM, Aplin CP, Simonet R,  Beenken J, Miller RC, Libal C, Boersma AJ, Sheets ED, Heikal AA.

Front Mol Biosci. 2021 p. 878

Activation of the Catalytic Activity of Thrombin for Fibrin Formation by Ultrasound.

Zhao P, Huo S, Fan J, Chen J, Kiessling F, Boersma AJ, Göstl R, Herrmann A.

Angew Chem Int Ed Engl. 2021 May 3. doi: 10.1002/anie.202105404. Online ahead of print.

Fluorescence Depolarization Dynamics of Ionic Strength Sensors using Time-Resolved Anisotropy.

Aplin CP, Miller RC, Kay TM, Heikal AA, Boersma AJ, Sheets ED.

Biophys J. 2021 Feb 11:S0006-3495(21)00138-7. doi: 10.1016/j.bpj.2021.01.035. Online ahead of print.

Engineering Crowding Sensitivity into Protein Linkers.

Pittas T, Zuo W, Boersma AJ.

Methods Enzymol. 2021 doi: 10.1016/bs.mie.2020.09.007

Controlling Optical and Catalytic Activity of Genetically Engineered Proteins by Ultrasound.

Zhou Y, Huo S, Loznik M, Göstl R, Boersma AJ, Herrmann A.

Angew Chem Int Ed Engl. 2021 Oct 26. doi: 10.1002/anie.202010324. Online ahead of print.


A physicochemical perspective of aging from single-cell analysis of pH, macromolecular and organellar crowding in yeast.

Mouton SN, Thaller DJ, Crane MM, Rempel IL, Terpstra OT, Steen A, Kaeberlein M, Lusk CP, Boersma AJ, Veenhoff LM.

Elife. 2020 Sep 29;9:e54707. doi: 10.7554/eLife.54707.

Macromolecular Crowding Measurements with Genetically Encoded Probes Based on Förster Resonance Energy Transfer in Living Cells.

Mouton SN, Veenhoff LM, Boersma AJ.

Methods Mol Biol. 2020; 2175:169-180. doi: 10.1007/978-1-0716-0763-3_12.

The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes.

Löwe M, Kalacheva M, Boersma AJ, Kedrov A.

FEBS J. 2020 May 28. doi: 10.1111/febs.15429. Online ahead of print.

Modular and Versatile trans-Encoded Genetic Switches.

Paul A, Warszawik EM, Loznik M, Boersma AJ, Herrmann A

Angew Chem Int Ed Engl. 2020 Apr 30. doi: 10.1002/anie.202001372. Online ahead of print.

FRET Analysis of Ionic Strength Sensors in the Hofmeister Series of Salt Solutions Using Fluorescence Lifetime Measurements

Miller RC, Aplin CP, Kay TM, Leighton R, Libal C, Simonet R, Cembran A, Heikal AA, Boersma AJ, Sheets ED

J Phys Chem B. 2020 Apr 30;124(17):3447-3458. doi: 10.1021/acs.jpcb.9b10498. Epub 2020 Apr 16.

Supercharged Proteins and Polypeptides.

Ma C, Malessa A, Boersma AJ, Liu K, Herrmann A.

Adv Mater. 2020 Jan 15:e1905309. doi: 10.1002/adma.201905309


A Trifunctional Linker for Palmitoylation and Peptide and Protein Localization in Biological Membranes.

Syga Ł, de Vries RH, van Oosterhout H, Bartelds R, Boersma AJ, Roelfes G, Poolman B.

Chembiochem. 2019 Dec 9. doi: 10.1002/cbic.201900655.

DNA Nanotechnology Enters Cell Membranes.

Huo S, Li H, Boersma AJ, Herrmann A.

Adv Sci (Weinh). 2019 Mar 20;6(10):1900043. doi: 10.1002/advs.201900043

  • Highlighted in Advanced Science News, April 2019.

  • This article is part of the Advanced Science 5th anniversary interdisciplinary article series.

Decreased Effective Macromolecular Crowding in Escherichia coli Adapted to Hyperosmotic Stress.

Liu B, Hasrat Z, Poolman B, Boersma AJ.

J Bacteriol. 2019 Apr 24;201(10). pii: e00708-18. doi: 10.1128/JB.00708-18

  • Selected as Article of Significant Interest (spotlight) in J. Bacteriol.

Macromolecular crowding effects on energy transfer efficiency and donor-acceptor distance of hetero-FRET sensors using time-resolved fluorescence.

Schwarz J, J Leopold H, Leighton R, Miller RC, Aplin CP, Boersma AJ, Heikal AA, Sheets ED.

Methods Appl Fluoresc. 2019 Feb 19;7(2):025002. doi: 10.1088/2050-6120/ab0242

Crowding Effects on Energy-Transfer Efficiencies of Hetero-FRET Probes As Measured Using Time-Resolved Fluorescence Anisotropy.

Leopold HJ, Leighton R, Schwarz J, Boersma AJ, Sheets ED, Heikal AA.

J Phys Chem B. 2019 Jan 17;123(2):379-393. doi: 10.1021/acs.jpcb.8b09829


How Important Is Protein Diffusion in Prokaryotes?

Schavemaker PE, Boersma AJ, Poolman B.

Front Mol Biosci. 2018 Nov 13;5:93. doi: 10.3389/fmolb.2018.00093.

  • Special issue on biochemical reactions in cytomimetic media edited by A.P. Minton and G. Rivas

Rotational and translational diffusion of size-dependent fluorescent probes in homogeneous and heterogeneous environments.

Lee HB, Cong A, Leopold H, Currie M, Boersma AJ, Sheets ED, Heikal AA.

Phys Chem Chem Phys. 2018 Oct 7;20(37):24045-24057. doi: 10.1039/c8cp03873b

Influence of Fluorescent Protein Maturation on FRET Measurements in Living Cells.

Liu B, Mavrova SN, van den Berg J, Kristensen SK, Mantovanelli L, Veenhoff LM, Poolman B, Boersma AJ.

ACS Sens. 2018 Sep 28;3(9):1735-1742. doi: 10.1021/acssensors.8b00473

  • Selected in "Rising Stars in Sensing" virtual issue of ACS Sensors 2020

Genetically Encoded Förster Resonance Energy Transfer-Based Biosensors Studied on the Single-Molecule Level.

Höfig H, Otten J, Steffen V, Pohl M, Boersma AJ, Fitter J.

ACS Sens. 2018 Aug 24;3(8):1462-1470. doi: 10.1021/acssensors.8b00143


Ionic Strength Sensing in Living Cells.

Liu B, Poolman B, Boersma AJ.

ACS Chem Biol. 2017 Oct 20;12(10):2510-2514. doi: 10.1021/acschembio.7b00348

Fluorescence Dynamics of a FRET Probe Designed for Crowding Studies.

Currie M, Leopold H, Schwarz J, Boersma AJ, Sheets ED, Heikal AA.

J Phys Chem B. 2017 Jun 15;121(23):5688-5698. doi: 10.1021/acs.jpcb.7b01306.

Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding.

Liu B, Åberg C, van Eerden FJ, Marrink SJ, Poolman B, Boersma AJ.

Biophys J. 2017 May 9;112(9):1929-1939. doi: 10.1016/j.bpj.2017.04.004.

Microorganisms maintain crowding homeostasis.

van den Berg J, Boersma AJ, Poolman B.

Nat Rev Microbiol. 2017 May;15(5):309-318. doi: 10.1038/nrmicro.2017.17


Semisynthetic Nanoreactor for Reversible Single-Molecule Covalent Chemistry.

Lee J, Boersma AJ, Boudreau MA, Cheley S, Daltrop O, Li J, Tamagaki H, Bayley H.

ACS Nano. 2016 Sep 27;10(9):8843-50. doi: 10.1021/acsnano.6b04663

  • Highlighted in, 2016.


Associative Interactions in Crowded Solutions of Biopolymers Counteract Depletion Effects.

Groen J, Foschepoth D, te Brinke E, Boersma AJ, Imamura H, Rivas G, Heus HA, Huck WT.

J Am Chem Soc. 2015 Oct 14;137(40):13041-8. doi: 10.1021/jacs.5b07898

  • Highlighted in Derek Lowe’s “in the pipeline” blog

Protein engineering: The power of four.

Boersma AJ, Roelfes G.

Nat Chem. 2015 Apr;7(4):277-9. doi: 10.1038/nchem.2220

A sensor for quantification of macromolecular crowding in living cells.

Boersma AJ, Zuhorn IS, Poolman B.

Nat Methods. 2015 Mar;12(3):227-9, 1 p following 229. doi: 10.1038/nmeth.3257

  • Highlighted in NWO newsletter, 2015

  • Highlighted in Biophysical Society newsletter (with interview), 2015

  • News articles in, University of Groningen website,, Science Newsline,, Technobahn, EurekAlert!, Science Daily, Bioportfolio, Nanowerk Nanotechnology News, and others.

Characterisation of the interactions between substrate, copper(II) complex and DNA and their role in rate acceleration in DNA-based asymmetric catalysis.

Draksharapu A, Boersma AJ, Browne WR, Roelfes G.

Dalton Trans. 2015 Feb 28;44(8):3656-63. doi: 10.1039/c4dt02734e.

Binding of copper(II) polypyridyl complexes to DNA and consequences for DNA-based asymmetric catalysis.

Draksharapu A, Boersma AJ, Leising M, Meetsma A, Browne WR, Roelfes G.

Dalton Trans. 2015 Feb 28;44(8):3647-55. doi: 10.1039/c4dt02733g.


Continuous stochastic detection of amino acid enantiomers with a protein nanopore.

Boersma, A.J.; Bayley, H. Angew. Chem. Int. Ed. 2012, 51, 9606.

Real-time detection of multiple neurotransmitters with a protein nanopore.

Boersma, A.J.; Brain, K.L.; Bayley, H. ACS Nano 2012, 6, 5304.

  • Highlighted in Nanomedicine, 2012.

Ligand denticity controls enantiomeric preference in DNA-based asymmetric catalysis.

Boersma, A.J.; de Bruin, B.; Feringa, B.L.; Roelfes, G. Chem. Commun. 2012, 2394.

  • Highlighted in Chemistry & Industry, 2012.

Catalytic enantioselective syn hydration of enones in water using a DNA-based catalyst.

Boersma, A.J.; Coquière, D.; Geerdink, D.; Rosati, F.; Feringa, B.L.; Roelfes, G. Nature Chem. 2010, 2, 991.

  • Highlighted on the NWO website, Chemisch2Weekblad

  • Synfacts highlight of the month February

  • Selected in Faculty of 1000

On the role of DNA in DNA-based catalytic enantioselective conjugate addition reactions.

Dijk, E.W.; Boersma, A.J.; Feringa, B.L.; Roelfes, G. Org. Biomol. Chem. 2010, 8, 3868.

DNA-based asymmetric catalysis.

Boersma, A.J.; Megens, R.P.; Feringa, B.L.; Roelfes, G. Chem. Soc. Rev. 2010, 39, 2083.

A kinetic and structural investigation of DNA-based asymmetric catalysis using the first generation ligands.

Rosati, F.; Boersma, A.J.; Klijn, J.E.; Meetsma, A.; Feringa, B.L.; Roelfes, G. Chem. Eur. J. 2009, 15, 9596.

Enantioselective Friedel-Crafts reactions in water using a DNA-based catalyst.

Boersma, A.J.; Feringa, B.L.; Roelfes, G. Angew. Chem. Int. Ed. 2009, 48, 3346.

  • Highlighted in Synfacts 2009(7)

DNA-based asymmetric catalysis: Sequence-dependent rate acceleration and enantioselectivity.

Boersma, A.J.; Klijn, J.E.; Feringa, B.L.; Roelfes, G. J. Am. Chem. Soc. 2008, 130, 11783.

  • Highlighted in JACS Select #4

α,β-Unsaturated 2-acyl imidazoles as a practical class of dienophiles for the DNA-based catalytic asymmetric Diels-Alder reaction in water.

Boersma, A.J.; Feringa, B.L.; Roelfes, G. Org. Lett. 2007, 9, 3647.

  • Highlighted on, august 2008

Highly enantioselective DNA-based catalysis.

Roelfes, G.; Boersma, A.J.; Feringa, B.L. Chem. Commun. 2006, 635.

  • Hot paper in Chemical Communications.

  • Highlighted in Chemistry World, march 2006

  • Highlighted in Nature news & views, 7 dec 2006

Metal-catalyzed cotrimerization of arynes and alkenes.

Quintana, I.; Boersma, A.J.; Peña, D.; Pérez, D.; Guitián, E. Org. Lett. 2006, 8, 3347.

Catalytic enantioselective conjugate addition of dialkylzinc reagents to N-substituted-2,3-dehydro-4-piperidones.

Sebesta, R.; Pizzuti, M.G.; Boersma, A.J.; Minnaard, A.J.; Feringa, B.L. Chem. Commun. 2005, 1711.

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