Molecular Ruler Research Articles

Geometry of Hydrogen Bonds in Liquid Ethanol Probed by Proton NMR Experiments.

Quantitative information of hydrogen bonding is crucial to our understanding of the structure and properties of associated liquids. Here, we outline a simple procedure to establish the geometry of hydrogen bonds in liquid ethanol using proton nuclear magnetic resonance (NMR) spectroscopy. We do so by exploiting differences in proton chemical shift values, that originate from the secondary isotope effect, to distinguish the methyl and hydroxyl group protons of CH3CH2OH from those of the deuterated CH3CD2OH in the 1H NMR spectra of mixtures of the two. This has allowed us to measure the ratios of the inter- to intramolecular distances between methyl to hydroxyl and methylene to hydroxyl protons using one-dimensional (1D) transient nuclear Overhauser effect NMR measurements as a molecular ruler. We model liquid ethanol by ab initio molecular dynamics simulations and identify all possible pairs of ethanol molecules in the ensemble that satisfied the NMR-determined inter- to intramolecular distance ratio criteria. For these pairs of ethanol molecules, we find the mean value of the hydrogen bonding distance, rOH···O, to be 1.93 Å and the value of the ∠HO···O angle to be 13.3°, thus effectively establishing the geometry of hydrogen bonds in liquid ethanol. An interesting observation that emerges from our study is the linear correlation between hydrogen bond distances and angles in ethanol.

Diverse anion exchange of pliable [X2@Pd3L4]4+ double cages: a molecular ruler for recognition of polyatomic anions.

Reaction of Pd(BF4)2 with L (L = bis(pyridin-3-yl-propyl)pyridine-3,5-dicarboxylate) in the 1 : 2 mole ratio gives rise to a spiro-type [PdL2]·(BF4)2·2C6H6·2CH3CN, and further self-assembly of [PdL2]·(BF4)2·2C6H6·2CH3CN with Pd(NO3)2 in the 2 : 1 mole ratio in Me2SO at 90 °C produces a uniquely pliable double cage of [(NO3)2(H2O)2@Pd3L4](BF4)4·6C3H7NO. Both the encapsulated NO3- and the outside BF4- anions are exchanged by X- to form [(X)2@Pd3L4](X')4 (X- = PF6-, ClO4-, and/or NO3-; X'- = BF4-, PF6-, ClO4-, and NO3-) with all-inclusive pure or mixed anions. The pliable and characteristic properties of the double cages were confirmed by anion exchange of the nestled or outside anions in the present study. This system can be used as a ruler for recognition of ubiquitous polyatomic anions.

Accessing distributions of exchange and dipolar couplings in stiff molecular rulers with Cu(II) centres.

Determining distributed exchange couplings is important for understanding the properties of synthetic magnetic molecules. Such distributions can be determined from pulsed dipolar spectroscopy (PDS) data, but this is challenging due to the similar influence of both exchange and dipolar couplings on such data. In this work we introduce two models that aim to identify these two contributions to the spin-spin couplings from frequency-domain PDS data of shape-persistent molecules having either two Cu(ii) ions, or a Cu(ii) ion and a nitroxide radical as the paramagnetic moieties. The first model assumes correlated Lorentzian or Gaussian exchange and dipole-dipole coupling distributions whose parameters are the model's unknowns. The second model relies on prior knowledge of the distance distribution and by performing Tikhonov regularization along the exchange coupling dimension yields the latter distribution model-free. Both models were able to differentiate between the absence and the presence of exchange interaction, to determine the coupling regime (ferro- or antiferromagnetic) and to estimate the distribution shape. In contrast, calculations within the exchange resilient model of the neural network analysis implemented in DeerAnalysis2018 were not able for our data to identify exchange couplings and return correct distance distributions. However, the generic model was able to identify and separate the strongly curved intermolecular background in the relaxation-induced dipolar modulation enhancement (RIDME) experiments. Our analysis revealed that in such systems exchange coupling may be present up to at least 3.3 nm in π-conjugated systems involving Cu(ii)-PyMTA, while it is negligible for distances r ≥ 4.5 nm between Cu(ii) ions and r ≥ 3.8 nm between a Cu(ii) ion and an unpaired electron of a nitroxide radical. Disruption of the π-conjugation between the ligand of the Cu(ii) complex and the nitroxide leads to negligible exchange coupling at distances r ≥ 2.6 nm in the corresponding [Cu(ii)-TAHA]-nitroxide ruler. Overall, for cases with known distance distributions, the presented analysis techniques allow to determine distributions of exchange couplings from PDS data.

Exosomes-mediated synthetic Dicer substrates delivery for intracellular Dicer imaging detection

Ribonuclease Dicer initiates gene-silencing process by cleaving exogenously long RNA duplexes into small interfering RNA (siRNA) or endogenous precursor microRNAs (pre-miRNAs) into mature miRNAs. It holds great promise in cancer diagnosis and therapeutics due to its molecular ruler role. However, the intracellular Dicer detection remains a key challenge and Dicer related gene therapy has never been explored. In this study, we design a fluorescent labeling Dicer substrate and effectively deliver it into cell by exosomes derived from the target parent cells for intracellular Dicer expression level monitor and gene therapy. Using pre-miRNA let-7a as a model, the Dicer substrates with two terminals labeled with fluorescent and quencher group respectively was obtained by T4 RNA mediated ligase reaction from two short RNA sequences. Then, the substrate was packaged into exosomes by electroporation and delivered to target cells for intracellular dicer imaging detection. After packaging substrates into exosomes with little immunogenicity and good innate biocompatibility by electroporation and delivered to target cells, the Dicer mediated substrate cleavage was effectively monitored by the fluorescence recovery, providing a powerful tool for Dicer analysis. Importantly, the cleaved product exhibited significant suppression toward tumor cell growth and regulated cancer cells cycle. This work might open a new avenue for Dicer analysis and Dicer-related clinical application.

Measurement of Accurate Interfluorine Distances in Crystalline Organic Solids: A High-Frequency Magic Angle Spinning NMR Approach.

Long-range interatomic distance restraints are critical for the determination of molecular structures by NMR spectroscopy, both in solution and in the solid state. Fluorine is a powerful NMR probe in a wide variety of contexts, owing to its favorable magnetic properties, ease of incorporation into biological molecules, and ubiquitous use in synthetic organic molecules designed for diverse applications. Because of the large gyromagnetic ratio of the 100% naturally abundant 19F isotope, interfluorine distances as long as 20 Å are accessible in magic-angle spinning (MAS) dipolar recoupling experiments. Herein, we present an approach for the determination of accurate interfluorine distances in multispin systems, using the finite pulse radio frequency driven recoupling (fpRFDR) at high MAS frequencies of 40-60 kHz. We use a series of crystalline "molecular ruler" solids, difluorobenzoic acids and 7F-L-tryptophan, for which the intra- and intermolecular interfluorine distances are known. We describe the optimal experimental conditions for accurate distance determinations, including the choice of a phase cycle, the relative advantages of selective inversion one-dimensional versus two-dimensional correlation experiments, and the appropriate numerical simulation protocols. An optimal strategy for the analysis of RFDR exchange curves in organic solids with extended spin interaction networks is presented, which, even in the absence of crystal structures, can be potentially incorporated into NMR structure determination.

A CRISPR RNA Is Closely Related With the Size of the Cascade Nucleoprotein Complex.

The currently known prokaryotic adaptive immune system against mobile genetic elements is based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR-associated (Cas) proteins and the transcribed short CRISPR RNA (crRNA) molecule form a heterologous ribonucleoprotein complex that neutralizes invading foreign nucleic acids, wherein the crRNA molecule base-pairs with the exogenous genetic elements. In the ribonucleoprotein complexes of the type I CRISPR system, a helical backbone of six identical subunits is commonly found. However, it is not clear how this ribonucleoprotein complex is assembled and what is the determinant factor for its size. We elucidated the crystal structure of the Csy3 subunit of the type I-F ribonucleoprotein complex from Zymomonas mobilis (ZmCsy3), in which seven ZmCsy3 protomers in the asymmetric unit form a molecular helix that is part of a filamentous structure in the entire crystal system. This ZmCsy3 helical structure is remarkably similar to the crRNA-bound hexameric Csy3 backbone from Pseudomonas aeruginosa, with conserved interactions between neighboring subunits. The monomeric ZmCsy3 in solution is transformed into different oligomeric states depending on the added crRNAs. These results suggest that a crRNA and Csy3 subunit play a determinant role in the stepwise formation of the functional Cascade ribonucleoprotein complex and the recruitment of other subunits, and crRNA functions as a molecular ruler for determining the size of the Cascade silencing complex.

Molecular affinity rulers: systematic evaluation of DNA aptamers for their applicabilities in ELISA.

Many nucleic acid aptamers that bind to target molecules have been reported as antibody alternatives. However, while the affinities of aptamers vary widely, little is known about the relationship between the affinities and their applicabilities for practical use. Here, we developed molecular affinity rulers: a series of DNA aptamers with different affinities that bind to the same area of target molecules, to measure the aptamer and its device applicabilities. For the ruler preparation, we used high-affinity DNA aptamers containing a hydrophobic unnatural base (Ds) as the fifth base. By replacing Ds bases with A bases in Ds-DNA aptamers targeting VEGF165 and interferon-γ, we prepared two sets of DNA aptamers with dissociation constants (KD) ranging from 10−12 to 10−8 M. Using these molecular affinity rulers, we evaluated the sensitivity of DNA aptamers in ELISA (enzyme-linked immunosorbent assay), which showed the clear relationship between aptamer affinities and their detection sensitivities. In sandwich-type ELISA using combinations of aptamers and antibodies, aptamers with KD values lower than ∼10−9 M were required for sufficient sensitivities (limit of detection (LOD) < 10 pM) and signal intensities, but optimizations improved the lower-affinity aptamers’ applicabilities. These aptamer affinity rulers could be useful for evaluating and improving aptamer applicabilities.

Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution.

Histones are basic protein monomers capable of interacting with DNA, providing the mechanism of DNA compaction inside the cell nucleus. The well-ordered assembly process of histone and DNA is a potential candidate as the approach for building DNA-protein nanostructures. Here, utilizing the sequence-independent histone-DNA interaction, we present an approach to self-assemble histones and single-stranded DNA (ssDNA) to form well-defined histone-DNA (sHD) nanoparticles and their multidimensional cross-linked complexes (cHD). By using various molecular biology and microscopy techniques, we elucidate the structure of these complexes, and we show that they are formed at carefully controlled conditions of temperature, ionic strength, concentration, and incubation time. We also demonstrate using a set of ssDNA molecular rulers and a geometric accommodation model that the assembly of sHD and cHD particles proceeds with precise geometry so that the number of ssDNA in these particles can be programmed by the length of ssDNA. We further show that the formation of cHD amplifies the effect of the length of ssDNA on the self-assembly, allowing for distinguishing ssDNA of different lengths at single nucleotide resolution. We envision that our geometry-directed approach of self-assembling histone-DNA nanostructures and the fundamental insights can serve as a structural platform to advance building precisely ordered DNA-protein nanostructures.

Ion-Pair Dynamics upon Photoinduced Electron Transfer Monitored by Pump-Pump-Probe Spectroscopy.

The excited-state dynamics of the radical anion of perylene (Pe) generated upon bimolecular photoinduced electron transfer (PET) with a donor was investigated using broadband pump-pump-probe spectroscopy. It was found to depend on the age of the anion, that is, on the time interval between the first pump pulse that triggers PET and the second one that excites the ensuing Pe anion (Pe•-). These differences, observed in acetonitrile but not in tetrahydrofuran, report on the evolution of the PET product from an ion pair to free ions. Two photoinduced charge recombination pathways of the ion pair to the neutral Pe*(S1) + donor state were identified: one occurring in a few picoseconds fromPe•-*(D1) and one taking place within 100-200 fs fromPe•-*(D n>1). Both processes are sensitive to the interionic distance over different length scales and thus serve as molecular rulers.

Nitration of Tyrosine Channels Photoenergy through a Conical Intersection in Water.

Nitration of tyrosine occurs under oxidative stress in vivo. The product, 3-nitrotyrosine (3NY), has a dramatically decreased quantum yield and can be used as a molecular ruler. In this study, femtosecond transient absorption spectroscopy and quantum calculations were implemented to elucidate the photoinduced relaxation processes of anionic 3NY in water. Upon 400 nm excitation into an excited electronic state with notable charge-transfer (CT) character, a barrierless nitro-twisting motion rapidly (<100 fs) guides the chromophore into an adjacent twisted intramolecular CT state, therein reaching a sloped S1/S0 conical intersection on the ∼100 fs time scale. Once in the hot ground state, excess energy is further released through vibrational cooling with biexponential time constants of ∼140 and 680 fs in water. Nitro back-twisting occurs on longer time scales (∼1.1 and 9 ps in water), returning the system to original ground state. Systematic evaluations of excited-state potential energies of anionic 3NY were performed by density functional theory (DFT) and time-dependent DFT calculations, showing that intersystem crossing (ISC) from the first singlet state (S1) to the first or second triplet state (T1 or T2) is unlikely. Inclusion of an explicit water molecule in calculations leads to improved mapping of the excited-state energy ordering of the second singlet state (S2) and T2, further diminishing ISC probability from S1 and favoring an ultrafast internal conversion to S0. These results provide deep insights into the highly efficient nonradiative decay of anionic 3NY in aqueous solution, with nitro-site-specific information that can help infer the characterization and potential optogenetic control of 3NY in protein environment.

Bioinformatics analysis of diversity in bacterial glycan chain-termination chemistry and organization of carbohydrate-binding modules linked to ABC transporters.

The structures of bacterial cell surface glycans are remarkably diverse. In spite of this diversity, the general strategies used for their assembly are limited. In one of the major processes, found in both Gram-positive and Gram-negative bacteria, the glycan is polymerized in the cytoplasm on a polyprenol lipid carrier and exported from the cytoplasm by an ATP-binding cassette (ABC) transporter. The ABC transporter actively participates in determining the chain length of the glycan substrate, which impacts functional properties of the glycoconjugate products. A subset of these systems employs an additional elaborate glycan capping strategy that dictates the size distribution of the products. The hallmarks of prototypical capped glycan systems are a chain-terminating enzyme possessing a coiled-coil molecular ruler and an ABC transporter possessing a carbohydrate-binding module, which recognizes the glycan cap. To date, detailed investigations are limited to a small number of prototypes, and here, we used our current understanding of these processes for a bioinformatics census of other examples in available genome sequences. This study not only revealed additional instances of existing terminators but also predicted new chemistries as well as systems that diverge from the established prototypes. These analyses enable some new functional hypotheses and offer a roadmap for future research.

Carbon Nanotube-Inorganic Hybrid Systems and Devices

We present different strategies for the generation of multifunctional nanomaterials employing single-walled carbon nanotubes (SWCNTs). In particular, we will discuss the formation of nanohybrids via the in-solution assembly of inorganic nanomaterials to SWCNTs, employed as nanoelectrodes or as nanoscale vector templates. Notably, both static and dynamic heterostructures were assembled, as well as nanoscale electronic devices; this allowed us to study and tailor various systems for different applications. We will first discuss the in-solution assembly of organic-inorganic heterostructures consisting of single Quantum Dots (QDs) univocally linked at the terminal ends of individual SWCNTs. Monofunctionalized SWCNT-QD heterostructures were obtained and photophysical investigations at the single nanohybrid level showed evidence of electronic coupling [1]. Additionally, DNA linkers of differing lengths were used as molecular rulers to control the distance, and hence tune the energy/charge transfer between the two nanostructures in these SWCNT-QD nanohybrids.[2] A dynamic SWCNT-QD hybrid was also designed and assembled using a G-quadruplex DNA aptamer linker, so that the distance between the SWCNT and QD could be dynamically modulated by the introduction and removal of potassium ions (K+);[2] the system was further found to be sensitive to K+ concentrations between 1pM and 25mM. By and large, this approach opens the possibility of assembling tailored optoelectronic and light harvesting systems with single-particle control. Finally, we will present the direct synthesis of multiplexed metal nanowire based devices using carbon nanotubes as vector templates. SWCNTs were filled with specifically designed metal precursors and dispersed in aqueous solution, enabling solution processability. The filled SWNTs were immobilized from solution onto different pre-patterned electrodes via a low-cost dielectrophoresis methodology. Metal nanowires were then grown by a facile and low temperature annealing treatment, while the nanotubes were removed using an oxygen plasma once immobilized in a device configuration. Electrical characterizations demonstrated the successful fabrication of metal nanowire electronic devices (no gate dependence).[3] Overall the strategy presented allows for a facile, low-cost and direct synthesis of multiple metal nanowire based devices for nanoelectronic applications. [1] Small, 2017,13, 1603042 [2] Advanced Science, 2018, 5, 1800596 [3] Submitted

Gd(III)-Gd(III) Relaxation-Induced Dipolar Modulation Enhancement for In-Cell Electron Paramagnetic Resonance Distance Determination.

In-cell distance determination by electron paramagnetic resonance (EPR) spectroscopy reveals essential structural information about biomacromolecules under native conditions. We demonstrate that the pulsed EPR technique RIDME (relaxation induced dipolar modulation enhancement) can be utilized for such distance determination. The performance of in-cell RIDME has been assessed at Q-band using stiff molecular rulers labeled with Gd(III)-PyMTA and microinjected into Xenopus laevis oocytes. The overtone coefficients are determined to be the same for protonated aqueous solutions and inside cells. As compared to in-cell DEER (double electron–electron resonance, also abbreviated as PELDOR), in-cell RIDME features approximately 5 times larger modulation depth and does not show artificial broadening in the distance distributions due to the effect of pseudosecular terms.

Twin-FRET: A New Molecular Ruler for Biomolecules

Conformational changes in biomolecules underpin all biological processes and being able to quantify these structural changes in solution is crucial to understand biological function. By carefully positioning two fluorophores within the biomolecule, it is possible to use fluorescence resonance energy transfer (FRET) as a molecular ruler to measure the desired distance. In current FRET assays, the biomolecule needs to be labelled with two different chemical fluorophores acting as a donor-acceptor FRET pair. Incorporation of these two chemically different species at specific positions within the biomolecule is challenging due to limited chemical labelling strategies. Here, we present a radically different strategy for measuring distances in biomolecules. We have developed the concept of TWIN-FRET which removes the need for two different fluorophores attached to the biomolecule by chemically encoding the FRET pair within the structure of the fluorophore itself. We have designed and synthesised a fluorescent molecule to prove this concept. The fluorophore (FH) has an acid-base equilibrium with a ground state pKa∼8.9. We have derivatized the fluorophore to its succinimide ester, and used this derivative, to label a duplex DNA with two molecules of the same fluorophore at specific positions. Our results demonstrate the transfer of non-radiative energy from the neutral (FH) to the anionic (F−) state of the fluorescent molecule. We further demonstrate the use of TWIN-FRET to measure nanometer-size distances within the DNA duplex, and we obtained distance values similar to those obtained using a conventional FRET pair (Alexa488-Cy3). By removing the need to introduce two different chemical structures within the biomolecule, we greatly simplified the methodology to measure nanometer-size distances in biomolecules. We expect this technique to be widely used in structural and biophysical studies of nucleic acids, proteins and interactions between them.

Microfluidic DNA combing for parallel single-molecule analysis

DNA combing is a widely used method for stretching and immobilising DNA molecules on a surface. Fluorescent labelling of genomic information enables high-resolution optical analysis of DNA at the single-molecule level. Despite its simplicity, the application of DNA combing in diagnostic workflows is still limited, mainly due to difficulties in analysing multiple small-volume DNA samples in parallel. Here, we report a simple and versatile microfluidic DNA combing technology (μDC), which allows manipulating, stretching and imaging of multiple, microliter scale DNA samples by employing a manifold of parallel microfluidic channels. Using DNA molecules with repetitive units as molecular rulers, we demonstrate that the μDC technology allows uniform stretching of DNA molecules. The stretching ratio remains consistent along individual molecules as well as between different molecules in the various channels, allowing simultaneous quantitative analysis of different samples loaded into parallel channels. Furthermore, we demonstrate the application of μDC to characterise UVB-induced DNA damage levels in human embryonic kidney cells and the spatial correlation between DNA damage sites. Our results point out the potential application of μDC for quantitative and comparative single-molecule studies of genomic features. The extremely simple design of μDC makes it suitable for integration into other microfluidic platforms to facilitate high-throughput DNA analysis in biological research and medical point-of-care applications.

Dynamic Single Molecular Rulers: Toward Quantitative Detection of MicroRNA-21 in Living Cells.

Innovative techniques to measure microRNA (miRNA) in vivo could greatly improve the fundamental understanding of complex cellular processes. Herein, we report a novel method for real-time, quantitative miRNA detection inside living cells based on core-satellite plasmon rulers (PRs). This approach allows for the statistical analysis of single hybridization event caused by target miRNA. We investigated hundreds of satellite leaving events and found that the distribution of the time range for one strand displacement event is miRNA concentration-dependent, which obeyed Poisson statistics. Probing several such PRs under dark-field microscopy would provide precise determination of miRNA in vitro and in living cells, without photobleaching or blinking of the fluorophores. We believe the simple and practical approach on the basis of dynamic PRs with single-molecule sensitivity combined with statistical analysis hold promising potential to visualize native nucleic acids with short sequence and low-abundance.

Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy: Concepts and Applications.

We review the basic concepts and recent applications of two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS), which is the extension of fluorescence correlation spectroscopy (FCS) to analyze the correlation of fluorescence lifetime in addition to fluorescence intensity. Fluorescence lifetime is sensitive to the microenvironment and can be a “molecular ruler” when combined with FRET. Utilization of fluorescence lifetime in 2D FLCS thus enables us to quantify the inhomogeneity of the system and the interconversion dynamics among different species with a higher time resolution than other single-molecule techniques. Recent applications of 2D FLCS to various biological systems demonstrate that 2D FLCS is a unique and promising tool to quantitatively analyze the microsecond conformational dynamics of macromolecules at the single-molecule level.

Model-Free Estimation of Energy-Transfer Timescales in a Closely Emitting CdSe/ZnS Quantum Dot and Rhodamine 6G FRET Couple.

Analysis of Förster resonance energy transfer (FRET) in nanoparticles is often complicated by a number of factors, such as close emission band positions of the donor and acceptor, the presence of simultaneous photoinduced electron transfer, fluorescence blinking, and natural excited-state decay processes. To address these concerns, mostly from materials chemists and biologists, herein, a state-of-the-art FRET analysis method that utilizes the bright green emission of a CdSe/ZnS core/shell quantum dot (QD) is proposed. The uniqueness of this model-free FRET analysis demonstrates the potential of these QDs to be part of an efficient FRET assay in molecular ruler applications. Molecular distance calculations relying on the proposed FRET analysis complement nicely with the expected donor-to-acceptor separation distances; the QD, as a photoluminescent marker, is electrostatically attached to a compatible fluorescent dye, rhodamine 6G. The beneficial aspects of the model-free FRET analysis provide many possibilities, including the use of low cytotoxicity QD-based FRET assays as a next-generation molecular ruler for the accurate estimation of distances inside a biological system.

Coupling the Structural and Functional Assembly of Synaptic Release Sites.

Information processing in our brains depends on the exact timing of calcium (Ca2+)-activated exocytosis of synaptic vesicles (SVs) from unique release sites embedded within the presynaptic active zones (AZs). While AZ scaffolding proteins obviously provide an efficient environment for release site function, the molecular design creating such release sites had remained unknown for a long time. Recent advances in visualizing the ultrastructure and topology of presynaptic protein architectures have started to elucidate how scaffold proteins establish “nanodomains” that connect voltage-gated Ca2+ channels (VGCCs) physically and functionally with release-ready SVs. Scaffold proteins here seem to operate as “molecular rulers or spacers,” regulating SV-VGCC physical distances within tens of nanometers and, thus, influence the probability and plasticity of SV release. A number of recent studies at Drosophila and mammalian synapses show that the stable positioning of discrete clusters of obligate release factor (M)Unc13 defines the position of SV release sites, and the differential expression of (M)Unc13 isoforms at synapses can regulate SV-VGCC coupling. We here review the organization of matured AZ scaffolds concerning their intrinsic organization and role for release site formation. Moreover, we also discuss insights into the developmental sequence of AZ assembly, which often entails a tightening between VGCCs and SV release sites. The findings discussed here are retrieved from vertebrate and invertebrate preparations and include a spectrum of methods ranging from cell biology, super-resolution light and electron microscopy to biophysical and electrophysiological analysis. Our understanding of how the structural and functional organization of presynaptic AZs are coupled has matured, as these processes are crucial for the understanding of synapse maturation and plasticity, and, thus, accurate information transfer and storage at chemical synapses.

Electronic energy transfer in biomacromolecules

Electronic energy transfer is widely used as a molecular ruler to interrogate the structure of biomacromolecules, and performs a key task in photosynthesis by transferring collected energy through specialized pigment–protein complexes. Förster theory, introduced over 70 years ago, allows linking transfer rates to simple structural and spectroscopic properties of the energy‐transferring molecules. In biosystems, however, significant deviations from Förster behavior often arise due to breakdown of the ideal dipole approximation, dielectric screening effects due to the biological environment, or departure from the weak‐coupling regime. In this review, we provide a concise overview of advances in simulations of energy transfer in biomacromolecules that allow overcoming the main limitations of Förster theory. We first discuss advances in quantum chemical methods to compute electronic couplings, their extension to multiscale formulations to include screening effects, and strategies to treat the interplay between coupling fluctuations and energy transfer dynamics. We then examine the spectral overlap term, and how this quantity can be estimated from simulations of the spectral density of exciton–phonon coupling. Finally, we discuss rate theories that can describe energy transfers in situations where strong coupling leads to delocalized excitions, a common situation found in closely packed multichromophoric systems such as photosynthetic complexes and nucleic acids.This article is categorized under: Structure and Mechanism &gt; Computational Biochemistry and Biophysics Theoretical and Physical Chemistry &gt; Spectroscopy