Dependence of Distance Distributions Derived from Double Electron–Electron Resonance Pulsed EPR Spectroscopy on Pulse‐Sequence Time

Pulsed double electron–electron resonance (DEER) provides pairwise P(r) distance distributions in doubly spin labeled proteins. We report that in protonated proteins, P(r) is dependent on the length of the second echo period T owing to local environmental effects on the spin‐label phase memory relaxation time T_m. For the protein ABD, this effect results in a 1.4 Å increase in the P(r) maximum from T=6 to 20 μs. Protein A has a bimodal P(r) distribution, and the relative height of the shorter distance peak at T=10 μs, the shortest value required to obtain a reliable P(r), is reduced by 40 % relative to that found by extrapolation to T=0. Our results indicate that data at a series of T values are essential for quantitative interpretation of DEER to determine the extent of the T dependence and to extrapolate the results to T=0. Complete deuteration (99 %) of the protein was accompanied by a significant increase in T_m and effectively abolished the P(r) dependence on T.     

The Double‐Histidine Cu2+‐Binding Motif: A Highly Rigid,Site‐Specific Spin Probe for Electron Spin Resonance Distance Measurements

The development of ESR methods that measure long‐range distance distributions has advanced biophysical research. However, the spin labels commonly employed are highly flexible, which leads to ambiguity in relating ESR measurements to protein‐backbone structure. Herein we present the double‐histidine (dHis) Cu²⁺‐binding motif as a rigid spin probe for double electron–electron resonance (DEER) distance measurements. The spin label is assembled in situ from natural amino acid residues and a metal salt, requires no postexpression synthetic modification, and provides distance distributions that are dramatically narrower than those found with the commonly used protein spin label. Simple molecular modeling based on an X‐ray crystal structure of an unlabeled protein led to a predicted most probable distance within 0.5 Å of the experimental value. Cu²⁺ DEER with the dHis motif shows great promise for the resolution of precise, unambiguous distance constraints that relate directly to protein‐backbone structure and flexibility.     

The Double‐Histidine Cu2+‐Binding Motif: A Highly Rigid,Site‐Specific Spin Probe for Electron Spin Resonance Distance Measurements

The development of ESR methods that measure long‐range distance distributions has advanced biophysical research. However, the spin labels commonly employed are highly flexible, which leads to ambiguity in relating ESR measurements to protein‐backbone structure. Herein we present the double‐histidine (dHis) Cu²⁺‐binding motif as a rigid spin probe for double electron–electron resonance (DEER) distance measurements. The spin label is assembled in situ from natural amino acid residues and a metal salt, requires no postexpression synthetic modification, and provides distance distributions that are dramatically narrower than those found with the commonly used protein spin label. Simple molecular modeling based on an X‐ray crystal structure of an unlabeled protein led to a predicted most probable distance within 0.5 Å of the experimental value. Cu²⁺ DEER with the dHis motif shows great promise for the resolution of precise, unambiguous distance constraints that relate directly to protein‐backbone structure and flexibility.     

Relative Orientation of Rigid Nitroxides by PELDOR: Beyond Distance Measurements in Nucleic Acids

Show me your angle : Incorporation of the rigid spin label Ç allows determination of both distance and orientation of two nitroxide spin labels in DNA by PELDOR experiments at common X‐band frequencies. The orientational information is obtained by varying the position of the detection pulses over the nitroxide spectrum. Simulation of the set of time traces yields very precise distances and angles.

     

Spin–Spin Artificial DNA Intercalated with Silver Cations: Theoretical Prediction

The indirect nuclear spin–spin coupling constants of Ag⁺ cation intercalated between imidazole rings in DNA chains are calculated by means of DFT with relativistic effects taken into account by the use of the zeroth‐order regular approximation Hamiltonian (DFT‐ZORA). The calculations model how the ¹J(¹⁵N,¹⁰⁹Ag) coupling constant is affected by different types of geometry deformations and by the presence of water, which is simulated by means of the polarizable continuum model and explicitly present water molecules. Calculations for systems containing two and three imidazole pairs are also carried out to model the influence of stacking interactions. The computed ¹J(¹⁵N,¹⁰⁹Ag) spin–spin coupling constant is in the range of 85–105 Hz (depending on the computational model) and is in good agreement with the experimental value (ca. 92 Hz). This coupling constant is very little affected by the presence of solvent, stacking interactions, and geometry deformations. Such behavior is explained by visualization of the coupling path by means of coupling energy density (CED). Bigger models allow the coupling constant between two adjacent silver ions to be computed, and give a value of approximately 1 Hz, which is probably too small to be of practical interest. The ²J(¹⁵N,¹⁵N) value is calculated to be about 2.5 Hz, and is therefore of measurable magnitude.     

Site‐Directed Spin‐Labeling of DNA by the Azide–Alkyne ‘Click’ Reaction: Nanometer Distance Measurements on 7‐Deaza‐2′‐deoxyadenosine and 2′‐Deoxyuridine Nitroxide Conjugates Spatially Separated or Linked to a ‘dA‐dT’ Base Pair

Nucleobase‐directed spin‐labeling by the azide‐alkyne ‘click’ (CuAAC) reaction has been performed for the first time with oligonucleotides. 7‐Deaza‐7‐ethynyl‐2′‐deoxyadenosine ( 1 ) and 5‐ethynyl‐2′‐deoxyuridine ( 2 ) were chosen to incorporate terminal triple bonds into DNA. Oligonucleotides containing 1 or 2 were synthesized on a solid phase and spin labeling with 4‐azido‐2,2,6,6‐tetramethylpiperidine 1‐oxyl (4‐azido‐TEMPO, 3 ) was performed by post‐modification in solution. Two spin labels ( 3 ) were incorporated with high efficiency into the DNA duplex at spatially separated positions or into a ‘dA‐dT’ base pair. Modification at the 5‐position of the pyrimidine base or at the 7‐position of the 7‐deazapurine residue gave steric freedom to the spin label in the major groove of duplex DNA. By applying cw and pulse EPR spectroscopy, very accurate distances between spin labels, within the range of 1–2 nm, were measured. The spin–spin distance was 1.8±0.2 nm for DNA duplex 17 ( dA*^7,10 ) ?11 containing two spin labels that are separated by two nucleotides within one individual strand. A distance of 1.4±0.2 nm was found for the spin‐labeled ‘dA‐dT’ base pair 15 ( dA*⁷ ) ?16 ( dT*⁶ ). The ‘click’ approach has the potential to be applied to all four constituents of DNA, which indicates the universal applicability of the method. New insights into the structural changes of canonical or modified DNA are expected to provide additional information on novel DNA structures, protein interaction, DNA architecture, and synthetic biology.     

Sequence‐Specific DNA Recognition by Cyclic Pyrrole–Imidazole Cysteine‐Derived Polyamide Dimers

Pyrrole–imidazole (PI) polyamides bind to the minor groove of the DNA duplex in a sequence‐specific manner and thus have the potential to regulate gene expression. To date, various types of PI polyamides have been designed as sequence‐specific DNA binding ligands. One of these, cysteine cyclic PI polyamides containing two β‐alanine molecules, were designed to recognize a 7 bp DNA sequence with high binding affinity. In this study, an efficient cyclization reaction between a cysteine and a chloroacetyl residue was used for dimerization in the synthesis of a unit that recognizes symmetrical DNA sequences. To evaluate specific DNA binding properties, dimeric PI polyamide binding was measured by using a surface plasmon resonance (SPR) method. Extending this molecular design, we synthesized a large dimeric PI polyamide that can recognize a 14 bp region in duplex DNA.     

Nucleotide‐Independent Copper(II)‐Based Distance Measurements in DNA by Pulsed ESR Spectroscopy

A site‐specific Cu²⁺ binding motif within a DNA duplex for distance measurements by ESR spectroscopy is reported. This motif utilizes a commercially available 2,2′‐dipicolylamine (DPA) phosphormadite easily incorporated into any DNA oligonucleotide during initial DNA synthesis. The method only requires the simple post‐synthetic addition of Cu²⁺ without the need for further chemical modification. Notably, the label is positioned within the DNA duplex, as opposed to outside the helical perimeter, for an accurate measurement of duplex distance. A distance of 2.7 nm was measured on a doubly Cu²⁺‐labeled DNA sequence, which is in exact agreement with the expected distance from both DNA modeling and molecular dynamic simulations. This result suggests that with this labeling strategy the ESR measured distance directly reports on backbone DNA distance, without the need for further modeling. Furthermore, the labeling strategy is structure‐ and nucleotide‐independent.     

High‐Field Pulsed EPR Spectroscopy for the Speciation of the Reduced [PV2Mo10O40]6− Polyoxometalate Catalyst Used in Electron‐Transfer Oxidations

An in‐depth spectroscopic EPR investigation of a key intermediate, formally notated as [PV^IVV^VMo₁₀O₄₀]^6? and formed in known electron‐transfer and electron‐transfer/oxygen‐transfer reactions catalyzed by H₅PV₂Mo₁₀O₄₀, has been carried out. Pulsed EPR spectroscopy have been utilized: specifically, W‐band electron–electron double resonance (ELDOR)‐detected NMR and two‐dimensional (2D) hyperfine sub‐level correlation (HYSCORE) measurements, which resolved ⁹⁵Mo and ¹⁷O hyperfine interactions, and electron–nuclear double resonance (ENDOR), which gave the weak ⁵¹V and ³¹P interactions. In this way, two paramagnetic species related to [PV^IVV^VMo₁₀O₄₀]^6? were identified. The first species (30–35 %) has a vanadyl (VO²⁺)‐like EPR spectrum and is not situated within the polyoxometalate cluster. Here the VO²⁺ was suggested to be supported on the Keggin cluster and can be represented as an ion pair, [PV^VMo₁₀O₃₉]^8?[V^IVO²⁺]. This species originates from the parent H₅PV₂Mo₁₀O₄₀ in which the vanadium atoms are nearest neighbors and it is suggested that this isomer is more likely to be reactive in electron‐transfer/oxygen‐transfer reaction oxidation reactions. In the second (70–65 %) species, the V^IV remains embedded within the polyoxometalate framework and originates from reduction of distal H₅PV₂Mo₁₀O₄₀ isomers to yield an intact cluster, [PV^IVV^VMo₁₀O₄₀]^6?.     

Spin Crossover in Nitrito‐Myoglobin as Revealed by Resonance Raman Spectroscopy

The myoglobin (Mb) heme Fe‐O‐N=O and heme Fe‐O‐N=O/2‐nitrovinyl species have been characterized by resonance Raman spectroscopy. In the heme Fe‐O‐N=O species, the bound nitrite ligand is removed by solvent exchange, thus reforming metmyoglobin (metMb). The high‐spin heme Fe‐O‐N=O unit is converted into a low‐spin heme Fe‐O‐N=O/2‐nitrovinyl species that can be reversibly switched between a low‐ and a high‐spin state without removing the bound nitrite ligand, as observed in the case of the heme Fe‐O‐N=O species. This spin‐state change is likely to be accompanied by a general structural rearrangement in the protein‐binding pocket. This example is the first of a globin protein that can reversibly change its metal spin state through an internal perturbation. These findings provide a basis for understanding the structure–function relationship of the spin cross found in other metalloenzymes and Fe^III–porphyrin complexes.     

Synthesis and Conformational Characterisation of Hexameric β‐Peptide Foldamers by Using Double POAC Spin Labelling and cw‐EPR

A selected set of terminally protected β‐hexapeptides, each containing two nitroxide‐based (3R,4R)‐4‐amino‐1‐oxyl‐2,2,5,5‐tetramethylpyrrolidine‐3‐carboxylic acid (POAC) residues combined with four (1S,2S)‐2‐aminocyclopentane‐1‐carboxylic acid (ACPC) residues, was synthesised by using solution methods and was fully characterised. The two POAC residues are separated in the sequences by different numbers of intervening ACPC residues. The conformational features of the doubly spin‐labelled β‐hexapeptides were examined in chloroform by FTIR absorption and continuous‐wave electron paramagnetic resonance spectroscopic techniques. In particular, the biradical exchange coupling (J) between two POAC residues within each peptide indicates unambiguously that the secondary structure overwhelmingly adopted is the 12‐helix. Taken together, these results support the view that POAC is an excellent β‐amino acid for exploring this type of helical conformation in doubly labelled β‐peptides.     

An Isolable Diphosphene Radical Cation Stabilized by Three‐Center Three‐Electron π‐Bonding with Chromium: End‐On versus Side‐On Coordination

Two salts ( 2 and 4 ) containing the radical cations of complexed diphosphenes have been isolated and characterized by electron paramagnetic resonance (EPR) spectroscopy, IR spectroscopy, and single‐crystal X‐ray diffraction. The P?P bond is coordinated to the Cr center either in an end‐on (in 2 ) or a side‐on (in 4 ) fashion. The spin density of the radical is delocalized over the Cr atom and the two P atoms in 2 whereas the unpaired electron is mainly localized on the Cr atom in 4 . This work provides the first example of a complexed diphosphene radical ( 2 ) featuring novel three‐center three‐electron (3c‐3e) π‐bonding in the Cr‐P‐P unit, and the first example of a 17 e Cr radical with a side‐on π‐bonded ligand ( 4 ).