Optimising broadband pulses for DEER depends on concentration and distance range of interest

Abstract. EPR distance determination in the nanometre region has become an important tool for studying the structure and interaction of macromolecules. Arbitrary waveform generators (AWGs), which have recently become commercially available for EPR spectrometers, have the potential to increase the sensitivity of the most common technique, double electron–electron resonance (DEER, also called PELDOR), as they allow the generation of broadband pulses. There are several families of broadband pulses, which are different in general pulse shape and the parameters that define them. Here, we compare the most common broadband pulses. When broadband pulses lead to a larger modulation depth, they also increase the background decay of the DEER trace. Depending on the dipolar evolution time, this can significantly increase the noise level towards the end of the form factor and limit the potential increase in the modulation-to-noise ratio (MNR). We found asymmetric hyperbolic secant (HS{1,6}) pulses to perform best for short DEER traces, leading to a MNR improvement of up to 86 % compared to rectangular pulses. For longer traces we found symmetric hyperbolic secant (HS{1,1}) pulses to perform best; however, the increase compared to rectangular pulses goes down to 43 %.

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Optimising broadband pulses for DEER depends on concentration and distance range of interest

10.5194/mr-2020-5 ◽

2020 ◽

Author(s):

Andreas Scherer ◽

Sonja Tischlik ◽

Sabrina Weickert ◽

Valentin Wittmann ◽

Malte Drescher

Keyword(s):

Form Factor ◽

Noise Level ◽

Pulse Shape ◽

Modulation Depth ◽

Distance Determination ◽

Distance Range ◽

Double Electron ◽

Common Technique ◽

Arbitrary Waveform ◽

Double Electron Electron Resonance

Abstract. EPR distance determination in the nanometre region has become an important tool for studying the structure and interaction of macromolecules. Arbitrary waveform generators (AWGs), which have recently become commercially available for EPR spectrometers, have the potential to increase the sensitivity of the most common technique double electron-electron resonance (DEER, also called PELDOR), as they allow the generation of broadband pulses. There are several families of broadband pulses, which are different in general pulse shape and the parameters that define them. Here, we compare the most common broadband pulses. When broadband pulses lead to a larger modulation depth they also increase the background decay of the DEER trace. Depending on the dipolar evolution time this can significantly increase the noise level towards the end of the form factor and limit the potential increase of the modulation to noise ratio (MNR). We found asymmetric hyperbolic secant (HS{1,6}) pulses to perform best for short DEER traces leading to a MNR improvement of up to 86 % compared to rectangular pulses. For longer traces we found symmetric hyperbolic secant (HS{1,1}) pulses to perform best, however, the increase compared to rectangular pulses goes down to 43 %.

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Distance Determination in Proteins insideXenopus laevisOocytes by Double Electron−Electron Resonance Experiments

Journal of the American Chemical Society ◽

10.1021/ja906104e ◽

2010 ◽

Vol 132 (24) ◽

pp. 8228-8229 ◽

Cited By ~ 84

Author(s):

Ryuji Igarashi ◽

Tomomi Sakai ◽

Hideyuki Hara ◽

Takeshi Tenno ◽

Toshiaki Tanaka ◽

...

Keyword(s):

Distance Determination ◽

Electron Resonance ◽

Double Electron ◽

Double Electron Electron Resonance

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Distance Determination in Multimeric Membrane Protein by Symmetry Constrained Analysis of Double Electron-Electron Resonance Spectroscopy

Biophysical Journal ◽

10.1016/j.bpj.2011.11.2212 ◽

2012 ◽

Vol 102 (3) ◽

pp. 405a

Author(s):

Olivier Dalmas ◽

H. Clark Hyde ◽

Eduardo Perozo

Keyword(s):

Membrane Protein ◽

Resonance Spectroscopy ◽

Distance Determination ◽

Electron Resonance ◽

Double Electron ◽

Double Electron Electron Resonance

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Distance determination in human ubiquitin by pulsed double electron–electron resonance and double quantum coherence ESR methods

Journal of Magnetic Resonance ◽

10.1016/j.jmr.2006.09.017 ◽

2007 ◽

Vol 184 (1) ◽

pp. 78-84 ◽

Cited By ~ 9

Author(s):

H. Hara ◽

T. Tenno ◽

M. Shirakawa

Keyword(s):

Quantum Coherence ◽

Double Quantum ◽

Distance Determination ◽

Electron Resonance ◽

Human Ubiquitin ◽

Double Electron ◽

Double Electron Electron Resonance

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Interresidual Distance Determination by Four-Pulse Double Electron-Electron Resonance in an Integral Membrane Protein: The Na+/Proline Transporter PutP of Escherichia coli

Biophysical Journal ◽

10.1016/s0006-3495(04)74310-6 ◽

2004 ◽

Vol 86 (4) ◽

pp. 2551-2557 ◽

Cited By ~ 56

Author(s):

Gunnar Jeschke ◽

Christoph Wegener ◽

Monika Nietschke ◽

Heinrich Jung ◽

Heinz-Jürgen Steinhoff

Keyword(s):

Escherichia Coli ◽

Membrane Protein ◽

Integral Membrane Protein ◽

Distance Determination ◽

Electron Resonance ◽

Double Electron ◽

Double Electron Electron Resonance

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rDEER: A Modified DEER Sequence for Distance Measurements Using Shaped Pulses

Magnetochemistry ◽

10.3390/magnetochemistry5010020 ◽

2019 ◽

Vol 5 (1) ◽

pp. 20 ◽

Cited By ~ 8

Author(s):

Thorsten Bahrenberg ◽

Yin Yang ◽

Daniella Goldfarb ◽

Akiva Feintuch

Keyword(s):

Modulation Depth ◽

Signal To Noise Ratio ◽

Dipolar Interaction ◽

Multidrug Transporter ◽

Distance Measurements ◽

Distance Information ◽

W Band ◽

Chirped Pulses ◽

Double Electron ◽

Double Electron Electron Resonance

The DEER (double electron-electron resonance, also called PELDOR) experiment, which probes the dipolar interaction between two spins and thus reveals distance information, is an important tool for structural studies. In recent years, shaped pump pulses have become a valuable addition to the DEER experiment. Shaped pulses offer an increased excitation bandwidth and the possibility to precisely adjust pulse parameters, which is beneficial especially for demanding biological samples. We have noticed that on our home built W-band spectrometer, the dead-time free 4-pulse DEER sequence with chirped pump pulses suffers from distortions at the end of the DEER trace. Although minor, these are crucial for Gd(III)-Gd(III) DEER where the modulation depth is on the order of a few percent. Here we present a modified DEER sequence—referred to as reversed DEER (rDEER)—that circumvents the coherence pathway which gives rise to the distortion. We compare the rDEER (with two chirped pump pulses) performance values to regular 4-pulse DEER with one monochromatic as well as two chirped pulses and investigate the source of the distortion. We demonstrate the applicability and effectivity of rDEER on three systems, ubiquitin labeled with Gd(III)-DOTA-maleimide (DOTA, 1,4,7,10-Tetraazacyclododecane-1,4,7,10-tetraacetic acid) or with Gd(III)-DO3A (DO3A, 1,4,7,10-Tetraazacyclododecane-1,4,7-triyl) triacetic acid) and the multidrug transporter MdfA, labeled with a Gd(III)-C2 tag, and report an increase in the signal-to-noise ratio in the range of 3 to 7 when comparing the rDEER with two chirped pump pulses to standard 4-pulse DEER.

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Direct Observation of Chain Lengths and Conformations in Oligofluorene Distributions from Controlled Polymerization by Double Electron-Electron Resonance

10.26434/chemrxiv.10002785 ◽

2019 ◽

Author(s):

Dennis Bücker ◽

Annika Sickinger ◽

Julian D. Ruiz Perez ◽

Manuel Oestringer ◽

Stefan Mecking ◽

...

Keyword(s):

Chain Length ◽

Length Distribution ◽

Catalyst System ◽

Chain Conformation ◽

Controlled Polymerization ◽

Chain Length Distribution ◽

Electron Resonance ◽

Double Electron ◽

The Individual ◽

Double Electron Electron Resonance

Synthetic polymers are mixtures of different length chains, and their chain length and chain conformation is often experimentally characterized by ensemble averages. We demonstrate that Double-Electron-Electron-Resonance (DEER) spectroscopy can reveal the chain length distribution, and chain conformation and flexibility of the individual n-mers in oligo-(9,9-dioctylfluorene) from controlled Suzuki-Miyaura Coupling Polymerization (cSMCP). The required spin-labeled chain ends were introduced efficiently via a TEMPO-substituted initiator and chain terminating agent, respectively, with an in situ catalyst system. Individual precise chain length oligomers as reference materials were obtained by a stepwise approach. Chain length distribution, chain conformation and flexibility can also be accessed within poly(fluorene) nanoparticles.

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