Molecular quantum spin network controlled by a single qubit

Scalable quantum technologies will require an unprecedented combination of precision and complexity for designing stable structures of well-controllable quantum systems. It is a challenging task to find a suitable elementary building block, of which a quantum network can be comprised in a scalable way. Here we present the working principle of such a basic unit, engineered using molecular chemistry, whose control and readout are executed using a nitrogen vacancy (NV) center in diamond. The basic unit we investigate is a synthetic polyproline with electron spins localized on attached molecular sidegroups separated by a few nanometers. We demonstrate the readout and coherent manipulation of very few ($\leq 6$) of these $S=1/2$ electronic spin systems and access their direct dipolar coupling tensor. Our results show, that it is feasible to use spin-labeled peptides as a resource for a molecular-qubit based network, while at the same time providing simple optical readout of single quantum states through NV-magnetometry. This work lays the foundation for building arbitrary quantum networks using well-established chemistry methods, which has many applications ranging from mapping distances in single molecules to quantum information processing.Comment: Author name typ

In-cell approaches in electron paramagnetic resonance spectroscopy to study conformations of DNA G-quadruplexes

The current work deals with the development of EPR for biological applications. Based on existing in vitro techniques, in-cell approaches for determination of distance constraints by double electron-electron resonance (DEER) were established. After proof-of-principle experiments on rigid model systems, in-cell DEER has been applied to study formation of G-quadruplexes adopted by human telomeric DNA oligomers upon their microinjection into living cells.Distances between two spin labels are derived from a DEER experiment. Their incorporation into DNA oligomers was achieved by inserting nitroxide-modified 2′-deoxyuridines at places of thymidines during solid-phase synthesis. By means of CD spectroscopy it was shown that nitroxides incorporated in this way in loop regions of G-quadruplexes do not disturb their initial structures. In spite of the inherent flexibility of loops, measured interspin distances are characteristic: they vary significantly for different G-quadruplex topologies providing a criterion for identification of those topologies. The most probable interspin distance can be predicted from existing high-resolution structural data and compared with reference measurements of known structures allowing for allocation to a certain structure. Even several conformations can be identified within a single experiment if the difference between the most probable interspin distances exceeds 0.3 nm. In the ion-dependent folding of the d[AGGG(TTAGGG)3] the antiparallel-basket topology was found for Na+ (in agreement with high-resolution NMR structure) and for the first time a 1:1 mixture of the antiparallel-basket and the parallel-propeller in the presence of K+ ions was identified.G-quadruplexes may alter folding topology if they are formed one after another within a long DNA sequence. This influence of neighboring G-quadruplexes was studied in a sequence with three G-quadruplex-forming blocks where one of them – in the middle or at the side – was selectively labeled with nitroxides. Consequent distance measurements allowed for conclusion on topologies adopted solely by the middle or the terminal part of the DNA sequence and thus allowed for building models for the folded human telomeric DNA in solution.The intracellular environment is known to reduce nitroxides to EPR-silent hydroxylamines. Therefore, prior to novel in-cell distance measurements free nitroxides were deposited into cells via microinjection. Here, the reduction kinetics of two types of nitroxides was described within Michaelis-Menten formalism for enzymatic processes. Thus, an enzymatic origin of reduction in cellulo was proposed. It was found that inside X. laevis oocytes and in their extract the five member ring nitroxides (like PCA) are reduced much slower than their six member ring analogs. In principle, both six and five member ring nitroxides are suitable for in-cell DEER if no long incubation time is required. However, five member ring nitroxides are preferable due to longer half-life and thus easier handling.Conformations of the d[AGGG(TTAGGG)3] inside oocytes where nucleus-like conditions preside were studied after incubating the unfolded sequence for 15 min after injection. Two conformations at 1:1 ratio were found inside cells. These were the antiparallel-basket and the parallel-propeller. This result is the same as found in K+-containing buffer. Thus, a dominant role of K+ in in-cell folding of the human telomeric oligonucleotide was established. This result was also confirmed by in-extract measurement providing an alternative way to study conformations in cellulo. A time-dependent experiment allowed monitoring of the folding process.DEER was shown to be applicable for structural identification goals of biological objects under their native conditions. In-cell DEER can provide means to analyze conformations and folding of nucleic acid structures inside living cells which has hitherto been unachievable

Temperature Determination by EPR at 275 GHz and the Detection of Temperature Jumps in Aqueous Samples

Second-moment analysis along two dimensions of continuous-wave EPR spectra of nitroxides enables EPR thermometry in a broad temperature range. Simulations show that the temperature can be derived in both the slow-motion and the fast-motion regime, which is experimentally verified at 275 GHz for H₂O/glycerol (50/50% by volume) and pure water. We demonstrate that this tool allows the calibration of temperature jumps induced by infrared laser irradiation of a submicroliter sample in the single-mode cavity of a 275 GHz spectrometer, which prepares for kinetic studies of processes involving paramagnetic species

Conformations of individual quadruplex units studied in the context of extended human telomeric DNA

G-quadruplex conformations within a sequence of three quadruplex units of human telomeric DNA were studied by two-frequency pulsed electron paramagnetic resonance (EPR) spectroscopy. In contrast to some individual G quadruplexes, within the higher-order human telomeric sequence a (3+1) hybrid structure is formed

Untersuchung von Quadruplex-Konformationen der humanen Telomerensequenz mit Puls-EPR

Unter physiologischen Bedingungen nehmen Telomersequenzen unterschiedliche Quadruplexkonformationen ein, deren genaue Strukturen jedoch noch nicht zweifelsfrei bekannt sind. Doppelt spinmarkierte Oligonucleotide, die aus G-reichen Telomerabschnitten bestehen, wurden synthetisiert und mithilfe von Puls-EPR charakterisiert. In K+-haltiger Lösung liegen die Propeller- und die Korbform als 1:1-Mischung nebeneinander vor

Evaluation of spin labels for in-cell EPR by analysis of nitroxide reduction in cell extract of Xenopus laevis oocytes

Spin-label electron paramagnetic resonance (SL-EPR) spectroscopy has become a powerful and useful tool for studying structure and dynamics of biomacromolecules. However, utilizing these methods at physiological temperatures for in-cell studies is hampered by reduction of the nitroxide spin labels and thus short half-lives in the cellular environment. Consequently, reduction kinetics of two structurally different nitroxides was investigated in cell extracts of Xenopus laevis oocytes using rapid-scan cw-exper- iments at X-band. The five member heterocyclic ring nitroxide PCA (3-carboxy-2,2,5,5-tetramethylpyrro- lidinyl-1-oxy) under investigation features much higher stability against intracellular reduction than the six member ring analog TOAC (2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxilic acid) and is therefore a suitable spin label type for in-cell EPR. The kinetic data can be described according to the Michaelis–Menten model and thus suggest an enzymatic or enzyme-mediated reduction process

Evaluation of Copper(II) Transfer between Amyloid-beta Peptides by Relaxation-Induced Dipolar Modulation Enhancement (RIDME)

Stehle J, Hülsmann M, Godt A, Drescher M, Azarkh M. Evaluation of Copper(II) Transfer between Amyloid-beta Peptides by Relaxation-Induced Dipolar Modulation Enhancement (RIDME). ChemPhysChem . 2024.In the brains of Alzheimer's disease patients, fibrillar aggregates containing amyloid-beta (Abeta) peptides are found, along with elevated concentrations of Cu(II) ions. The aggregation pathways of Abeta peptides can be modulated by Cu(II) ions and determined by the formation and nature of the Cu(II)-Abeta complex. If spin-labeled, the Cu(II)-Abeta complex contains two dipolar coupled paramagnetic centers, the spin label and the Cu(II) ion. Measurement of the dipolar coupling between these paramagnetic centers by relaxation-induced dipolar modulation enhancement (RIDME) allows to monitor the complex formation and thus opens a way to follow the Cu(II) transfer between peptides if a mixture of wild-type and spin-labeled ones is used. We evaluate this approach for a specific Cu(II)-Abeta complex, the aggregation-inert Component II. The kinetics of the Cu(II) transfer can be resolved by performing RIDME in a time-dependent manner. A temporal resolution of seconds has been achieved, with the potential to reach milliseconds, using a rapid-freeze quench device to stop the Cu(II) transfer in solution after defined incubation times. © 2024 Wiley-VCH GmbH

How accurately defined are the overtone coefficients in Gd(III)-Gd(III) RIDME?

Azarkh M, Keller K, Qi M, Godt A, Yulikov M. How accurately defined are the overtone coefficients in Gd(III)-Gd(III) RIDME? Journal of magnetic resonance . 2022;339: 107217.Relaxation-induced dipolar modulation enhancement (RIDME) is a pulse EPR technique that is particularly suitable to determine distances between paramagnetic centers with a broad EPR spectrum, e.g. metal-ion-based ones. As far as high-spin systems (S > ) are concerned, the RIDME experiment provides not only the basic dipolar frequency but also its overtones, which complicates the determination of interspin distances. Here, we present and discuss in a step-by-step fashion an r.m.s.d.-based approach for the calibration of the overtone coefficients for a series of molecular rulers doubly labeled with Gd(III)-PyMTA tags. The constructed 2D total-penalty diagrams help revealing that there is no unique set of overtone coefficients but rather a certain pool, which can be used to extract distance distributions between high-spin paramagnetic centers, as determined from the RIDME experiment. This is of particular importance for comparing RIDME overtone calibration and distance distributions obtained in different labs. Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved