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THE BOERSMA LAB

Welcome to the website of the Arnold Boersma Lab. We are embedded within the DWI Leibniz Institute for Interactive Materials, in Aachen, Germany. 

We re-purpose and redesign the beautiful architectures provided by the molecules of Nature as for example sensors, probes, machines, or catalysts.

We use these new molecules in cells and in buffer, and everything in between.

We have a strong focus on engineering biomolecules to

- unravel the biochemical organization inside cells

- transplant cellular organization into synthetic life-like systems

- provide native-like environments to biocatalysts

- miniaturize life-like information processing

 

RESEARCH

 

DESIGNING NEW FRET SENSORS TO UNDERSTAND THE INTRACELLULAR ENVIRONMENT

The interior of the cells is obviously not like dilute buffer. Yet, traditionally most biochemistry experiments have been performed in dilute buffer. To understand how the interior of the cell influences biochemical processes, such as biocatalysis and organization of the biopolymers, we need to know what the important parameters in the cell are, and quantify their contribution to the intracellular organization. 


By creative design, we developed a series FRET sensors for macromolecular crowding and the ionic strength: Cells are crowded with macromolecules that occupy space, generating a force that influences the organization of biomolecules in cells. The crowding sensors compress akin a polymer in crowded solutions. The sensors provide a readout for the excluded volume in bacteria, yeasts, and mammalian cells. Our efforts are towards improving these sensors, as well as applying them in different species. Further, we apply the sensors in dynamic soft materials.

Further reading:

Nature Methods, 2015, 227-229

Biophys J. 2017, 1929-1939

Nature Rev. Microbiol 2017, 309-318


Collaborators:

Prof. Veenhoff (UMCG Groningen)

Prof. Sheets and Prof. Heikal (Univ Minnesota)

Prof. Fitter (RWTH Aachen)

Dr. Aberg (UMCG Groningen)

Prof. Baldus (Utrecht Univ)

Prof. Poolman (Groningen Univ)

IONIC STRENGTH SENSING

The other sensor that we developed measures the ionic strength. The ionic strength is important for anything charged, which includes pretty much every molecule in the living cell (apart from a few small molecules). Our FRET-based ionic strength sensor allows to determine the ionic strength inside living cells, with all the advantages of FRET-based genetically-encoded sensors, such as high spatiotemporal resolution, and easy targeting to different compartments.

Further reading:

ACS Chem Biol 2017, 2510-2514

BIOCATALYSIS, LIFE-LIKE SYSTEMS, INFORMATION TRANSFER, AND MORE

These exciting topics are just (re)starting in our lab, and we will provide more information soon.

NEWS

 

A PHYSICOCHEMICAL ROADMAP OF YEAST AGING

December 2, 2019

We uploaded a preprint at BioRxiv on our work that shows how some important physicochemical parameters change with the age of a yeast cell. Sara's study was supervised by Arnold and Liesbeth Veenhoff (U. Groningen), with collaborations with the groups of Lusk (Yale) and Kaeberlein (U. Washington). Have a nice read here!

MEET THE TEAM

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ARNOLD BOERSMA

Principle Investigator

SARA MAVROVA

PhD Student (with Liesbeth Veenhoff)

QI WAN

PhD student

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WEIYAN ZUO

PhD student

THEODOROS PITTAS

PhD Student

MILARA KALACHEVA

PhD Student

 

PUBLISHED WORK

DNA nanotechnology enters cell membranes.

Huo, S.; Li, H.; Boersma, A.J.; Herrmann, A. Adv. Sci. Accepted Manuscript.

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

Liu, B.; Hasrat, Z.; Poolman, B.; Boersma, A.J. J. Bacteriol. Accepted Manuscript.

  • 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; Leopold, H.J.; Leighton, R.; Miller, R.C.; Aplin, C.P.; Boersma, A.J.; Heikal, A.A.; Sheets, E.D. Methods Appl. Fluoresc. Accepted Manuscript.

Crowding Effects on Energy Transfer Efficiencies of hetero-FRET Probes as Measured using Time-Resolved Fluorescence Anisotropy

Leopold, H.; Leighton, R.; Schwarz, J.; Boersma, A.J.; Sheets, E.D.; Heikal, A.A. J. Phys. Chem. B. Accepted Manuscript.

How important is protein diffusion in prokaryotes?

Schavemaker, P.E.; Boersma, A.J.; Poolman, B. Front. Mol. Biosci. 2018, 5, 93

  • 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, H.B.; Cong, A.; Leopold, H.; Currie, M.; Boersma, A.J.; Sheets, E.D.; Heikal A.A. Phys. Chem. Chem. Phys. 2018, 20, 24045

The influence of fluorescent protein maturation on FRET measurements in living cells

Liu, B.; Mavrova, S.N.; van den Berg, J.; Kristensen, S.K.; Mantovanelli, L.; Veenhoff, L.M.; Poolman, B.; Boersma, A.J. ACS Sens. 2018, 3, 1735

Genetically encoded FRET-based biosensors studied on the single molecule level.

Höfig, H.; Otten, J.; Steffen, V.; Pohl, M.; Boersma, A. J.; Fitter, J. ACS Sens. 2018, 3, 1462

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Ionic strength sensing in living cells.

Liu, B.; Poolman, B.; Boersma, A.J.* ACS Chem. Biol. 2017, 12, 2510.

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Kinetics model for the wavelength-dependence of excited-state dynamics of hetero-FRET sensors.

Schwarz, J.; Leighton, R.; Leopold, H. J.; Currie, M.; Boersma, A. J.; Sheets, E. D.; Heikal, A. A. Proc. SPIE 2017, 10380, 103800S

Fluorescence dynamics of a FRET probe designed for crowding studies.

Currie, M.; Leopold, H.; Schwarz, J.; Boersma, A. J.; Sheets, E.; Heikal, A. J. Phys. Chem. B 2017, 121, 5688.

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Design and properties of genetically encoded probes for sensing macromolecular crowding.

Liu, B.; Aberg, C.; van Eerden, F.; Marrink, S.J.; Poolman, B.; Boersma, A.J.* Biophys. J. 2017, 112, 1929.

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Lipid phase separations in the presence of hydrocarbons in giant unilamellar vesicles

Bartelds R.; Barnaud, J.; Boersma, A.J.; Marrink, S.J.; Poolman, B. AIMS Biophys. 2017, 4, 528.

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Microorganisms maintain crowding homeostasis.

Van den Berg, J.; Boersma, A.J.; Poolman, B. Nature Rev. Microbiol. 2017, 15, 309.

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​​​​​​​​Semisynthetic nanoreactor for reversible single-molecule covalent chemistry.

Lee, J.; Boersma, A.J.; Boudreau, M.A.; Cheley, S.; Daltrop, O.; Li, J.; Tamagaki, H.; Bayley, H. ACS Nano 2016, 10, 8843.

  • Highlighted in Nanotechweb.org, 2016.

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Associative interactions in crowded solutions of biopolymers counteract depletion effects.

Groen, J.; Foschepoth, D.; te Brinke, E.; Boersma, A.J.; Imamura, H.; Rivas, G.; Heus, H.A.; Huck, W.T.S. J. Am. Chem. Soc. 2015, 40, 13041.

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

The power of four (News & Views)

Boersma, A.J.*; Roelfes, G. Nature Chemistry 2015, 7, 277.

*corresponding author

A sensor for quantification of macromolecular crowding in living cells.

Boersma, A.J.*; Zuhorn, I.S.; Poolman, B. Nature Methods 2015, 12, 227.

*corresponding author

  • Highlighted in NWO newsletter, 2015

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

  • News articles in kennislink.nl, University of Groningen website, AzoSensors.com, Science Newsline, Phys.org, Technobahn, EurekAlert!, Science Daily, Bioportfolio, Nanowerk Nanotechnology News, and others.

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

Draksharapu, A; Boersma, A.J.; Browne, W.R.; Roelfes, G. Dalton Trans. 2015, 44, 3656.

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

Draksharapu, A; Boersma, A.J.; Leising, M.; Meetsma, A.; Browne, W.R.; Roelfes, G. Dalton Trans. 2015, 44, 3647.

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 organic-chemistry.org, 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.

 

AVAILABLE POSITIONS

Student internships: Students that would like to obtain experience in one of our research topics, please contact Arnold.


PhD and Postdoc positions: Currently we do not have PhD and post-doc positions advertized, but strong candidates are encouraged to get in contact with Arnold.


 

CONTACT US

DWI Leibniz Institut für Interaktive Materialien
Forckenbeckstrasse 50
D-52056 Aachen, Germany

boersma[at]dwi.rwth-aachen.de