Molecular Recognition Interactions Research Articles

Study of stereoelectronic effects in saturated heterocycles containing nitrogen and their relation with intermolecular and intramolecular interactions

This study describes the synthesis of imidazolidines, hexahydropyrimidines, and 1,5-diazabicyclo[3.2.1]octane. These compounds are used as models to study the hyperconjugation using nuclear magnetic resonance (NMR) spectroscopy through the 13C–1H one-bond coupling constants (1JC,H) and the 1H chemical shifts. The molecular structures are corroborated by single-crystal X-ray diffraction, and the electron distribution is studied through electron mapping obtained by using Hirshfeld surface analysis to determine intermolecular and intramolecular interactions. The NMR data show that the 1JC,Hax are lower than 1JC,Heq as a consequence of the nN→σ*C–H interaction, while the 1JC,Hax are very similar to 1JC,Heq in the β-carbon to the nitrogen. This is mainly due to the stabilization energy (Eint 18–19.2 kJ/mol) by the hyperconjugative σCβ–Heq→σ*C–N interactions. This effect is marked in the chemical shift of 1H, where Heq shifts to a lower frequency than Hax. Finally, the Hirshfeld surface analysis shows that the atoms involved in hyperconjugation play an important role in the intermolecular and intramolecular interactions. The obtained results can support new study models that would afford an accurate determination of interactions in molecular recognition and predict interactions between drugs and proteins, which in turn will help the design and development of new drugs.

Impact of Halogen Bonds on Protein-Peptide Binding and Protein Structural Stability Revealed by Computational Approaches.

Halogen bonds (XBs) are essential noncovalent interactions in molecular recognition and drug design. Current studies on XBs in drug design mainly focus on the interactions between halogenated ligands and target proteins, lacking a systematic study of naturally existing and artificially prepared halogenated residue XBs (hr_XBs) and their characteristics. Here, we conducted a computational study on the potential hr_XBs in proteins/peptides using database searching, quantum mechanics calculations, and molecular dynamics simulations. XBs at the protein-peptide interaction interfaces are found to enhance their binding affinity. Additionally, the formation of intramolecular XBs (intra_XBs) within proteins may significantly contribute to the structural stability of structurally flexible proteins while having a minor impact on proteins with inherently high structural rigidity. Impressively, introducing halogens without the formation of intra_XBs may lead to a decrease in the protein structural stability. This study enriches our understanding of the roles and effects of halogenated residue XBs in biological systems.

Dual-Responsive Supramolecular Polymeric Nanomedicine for Self-Cascade Amplified Cancer Immunotherapy.

Insufficient tumor immunogenicity and immune escape from tumors remain common problems in all tumor immunotherapies. Recent studies have shown that pyroptosis, a form of programmed cell death that is accompanied by immune checkpoint inhibitors, can induce effective immunogenic cell death and long-term immune activation. Therapeutic strategies to jointly induce pyroptosis and reverse immunosuppressive tumor microenvironments are promising for cancer immunotherapy. In this regard, a dual-responsive supramolecular polymeric nanomedicine (NCSNPs) to self-cascade amplify the benefits of cancer immunotherapy is designed. The NCSNPs are formulated by β-cyclodextrin coupling nitric oxide (NO) donor, a pyroptosis activator, and NLG919, an indoleamine 2,3-dioxygenase (IDO) inhibitor, and self-assembled through host-guest molecular recognition and hydrophobic interaction to obtain nanoparticles. NCSNPs possess excellent tumor accumulation and bioavailability attributed to ingenious supramolecular engineering. The study not only confirms the occurrence of NO-triggered pyroptosis in tumors for the first time but also reverses the immunosuppressive microenvironment in tumor sites via an IDO inhibitor by enhancing the infiltration of cytotoxic T lymphocytes, to achieve remarkable inhibition of tumor proliferation. Thus, this study provides a novel strategy for cancer immunotherapy.

Contributions of London Dispersion Forces to Solution-Phase Association Processes.

ConspectusDespite their ubiquity and early discovery, London dispersion forces are often overlooked. This is due, in part, to the difficulty in assessing their contributions to molecular and polymeric structure, stability, properties, and reactivities. However, recent advances in modeling have revealed that dispersion interactions play an important role in many important chemical and biological processes. Experimental confirmation of their impact in solution has been challenging, leading to controversies about their relative importance.In the course of studying noncovalent interactions using molecular devices, our understanding and appreciation for the importance of dispersion interactions have evolved. This Account follows this intellectual journey by using examples from the literature. The goals are twofold: to describe recent advances in understanding the interaction and to provide guidance to researchers studying weak noncovalent interactions. However, first, the experimental methods for measuring the effects of dispersion interactions and the strategies for isolating their influence are described. These include the design of molecular devices to measure these weak noncovalent interactions and the strategies to disentangle the solvation, solvophobic, and dispersion components of the resulting equilibria.The literature examples are organized around five fundamental questions. (1) Do dispersion interactions have a measurable effect on solution equilibria? (2) To what extent do solvents attenuate or compensate for dispersion interactions? (3) To what extent do the solvation and solvophobic terms influence the dispersion equilibria? (4) Can we predict whether a system will form attractive dispersion or repulsive steric interactions? (5) Can the dispersion term be isolated and interrogated? We were often surprised by the answers to these questions. In each case, we describe how the systems were designed to address these questions and discuss possible interpretations of the results.While dispersion interactions in solution were weak (usually <1 kcal/mol), their influence on complexation and conformational equilibria can be observed and measured. This underscores the significance of these interactions in molecular recognition, coordination chemistry, reaction design, and catalysis. The solvent components of the dispersion equilibria can also be significant. Therefore, the isolation of the dispersion contributions from the solvation and solvophobic effects represents an ongoing challenge. The experimental studies also provide important benchmarks and offer valuable insights to help refine the next generation of computational solvent models.

"Single-pole dual-control" competing mode in plants.

Plant development and pattern formation depend on diffusible signals and location cues. These developmental signals and cues activate intracellular downstream components through cell surface receptors that direct cells to adopt specific fates for optimal function and establish biological fitness. There may be a single-pole dual-control competing mode in controlling plant development and microbial infection. In plant development, paracrine signaling molecules compete with autocrine signaling molecules to bind receptors or receptor complexes, turn on antagonistic molecular mechanisms, and precisely regulate developmental processes. In the process of microbial infection, two different signaling molecules, competing receptors or receptor complexes, form their respective signaling complexes, trigger opposite signaling pathways, establish symbiosis or immunity, and achieve biological adaptation. We reviewed several "single-pole dual-control" competing modes, focusing on analyzing the competitive commonality and characterization of "single-pole dual-control" molecular mechanisms. We suggest it might be an economical protective mechanism for plants' sequentially and iteratively programmed developmental events. This mechanism may also be a paradigm for reducing internal friction in the struggle and coexistence with microbes. It provides extraordinary insights into molecular recognition, cell-to-cell communication, and protein-protein interactions. A detailed understanding of the "single-pole dual-control" competing mode will contribute to the discovery of more receptors or antagonistic peptides, and lay the foundation for food, biofuel production, and crop improvement.

Vibrational Solvatochromism Study of the C-H···O Improper Hydrogen Bond.

The improper C-H···O hydrogen bond is an important weak interaction, with broad implications for protein and nucleic acid structure, molecular recognition, enzyme catalysis, and drug interaction. Despite its wide identification in crystal structures, the general existence of C-H···O hydrogen bonds remains elusive especially for natural C-H groups in bulk aqueous solutions at room temperature. Vibrational spectroscopy is a promising methodology to tackle this challenge, as formation of C-H···O hydrogen bonds usually causes shifts of the C-H stretch frequency. Yet, prior observations are inconclusive, as they are all based on a simple blue-shift in aqueous solution and cannot distinguish if it is an effect caused by solvent reorganization or a specific hydrogen-bonding interaction. In this work, we used vibrational solvatochromism as a calibration of the solvent reorganization effect and identified a specific H-bonding interaction. We performed vibrational solvatochromism study of C-H(D) of multiple alcohol molecules including the CH mode of CD3CH(OH)CD3 and the CD3 modes of CD3OH, CD3CH2OH, and CD3CH(OH)CD3 in a series of solvents. We found an abnormal blue-shift of the Raman frequency of the C-H and C-D bonds at both the Cα and Cβ positions of alcohols in water, which lies in an opposite direction to the expected trend due to vibrational solvatochromism. This experimental evidence supports that the improper C-H···O hydrogen bonds might generally exist between nonpolarized C-H and water in liquid solutions at room temperature.

Separation performance of the calix[8]arene functionalized with polyethylene glycol units for capillary gas chromatography.

In this paper, an amphiphilic calix[8]arene with polyethylene glycol unit branches (C8A-PEG) was synthesized and applied for capillary gas chromatography (GC). The C8A-PEG was coated on the inner wall of a capillary column by a static method with the column efficiency of 3165 plates/m and polar nature. As demonstrated, the C8A-PEG column has excellent physicochemical properties and separation performance since it has π-electron-rich 3D cavity which combines with polar PEG units. Compared with two columns corresponding to the construction units C8A and PEG, the C8A-PEG column shows distinctly advantageous performance for the mixture of 22 components with diverse types. Impressively, it shows satisfactory resolution for positional isomers and cis-/trans- isomers, especially the challenging isomers of toluidine and dimethylaniline. The outstanding distinguishing capability of the C8A-PEG stationary phase is mainly attributed to the abundant molecular recognition interactions, including van der Waals, dipole-dipole, H-bonding and π-π stacking interactions. This work has proved that the new GC stationary phases constructed by different units can complement each other's advantages, improve their physicochemical properties and separation performance, and have broad application prospects in chromatographic analysis.

Evolution of Br⋯Br contacts in enantioselective molecular recognition during chiral 2D crystallization

Halogen-mediated interactions play an important role in molecular recognition and crystallization in many chemical and biological systems, whereas their effect on homochiral versus heterochiral recognition and crystallization has rarely been explored. Here we demonstrate the evolution of Br⋯Br contacts in chiral recognition during 2D crystallization. On Ag(100), type I contacts prevail at low coverage and lead to homochiral recognition and the formation of 2D conglomerates; whereas type II contacts mediating heterochiral recognition are suppressed at medium coverage and appear in the racemates induced by structural transitions at high coverage. On Ag(111), type I contacts dominate the 2D crystallization and generate 2D conglomerates exclusively. DFT calculations suggest that the energy difference between type I and type II contacts is reversed upon adsorption due to the substrate induced mismatch energy penalty. This result provides fundamental understanding of halogen-mediated interactions in molecular recognition and crystallization on surface.

Insight into Substrate Recognition by Urea-Based Helical Foldamer Catalysts Using a DFT Global Optimization Approach.

Peptides and foldamers have recently gained increasing attention as chiral catalysts to achieve challenging (asymmetric) transformations. We previously reported that short helically folded aliphatic oligoureas in combination with achiral Brønsted bases are effective H-bonding catalysts for C-C bond-forming reactions─i.e., the conjugate addition of 1,3-dicarbonyl pronucleophiles to nitroalkenes─with high reactivity and selectivity and at remarkably low chiral catalyst/substrate molar ratios. This theoretical investigation at the density functional theory level of theory, aims to both analyze how the substrates of the reaction interact with the foldamer catalyst and rationalize a chain-length dependence effect on the catalytic properties. We confirm that the first two ureas are the only H-bond donors available to interact with external molecules. Moreover, each urea site interacts with one of the two reactants allowing a short distance between the two reacting carbons, thus facilitating the conjugated addition. Additionally, it was observed that the molecular recognition and catalyst-substrate interactions are mainly governed by electrostatic interactions but not orbital interactions (see from NBO if this is finally true). On these grounds, an electrostatic potential (ESP) analysis showed an important internal charge separation in the catalyst, the positive ESP region being concentrated around the first two ureas, with its area extending as the number of residues increases.

Synthesis, Crystal Structure and Separation Performance of p-tert-butyl(tetradecyloxy)calix[6]arene.

This work describes the investigation of separation performance of the p-tert-butyl(tetradecyloxy)calix[6]arene (C6A-C10-OH) as stationary phase for gas chromatography (GC) separations. Its structure was characterized by IR, 1H NMR, 13C NMR, MS and single-crystal X-ray diffraction analysis. The C6A-C10-OH column shows good separation capacity for aliphatic, aromatic and cis-/trans- isomers. Especially, it exhibits multiple molecular recognition interactions for the analytes with a wide range of polarity, including dispersion, π-π, H-bonding and dipole-dipole interactions. The present work provides experimental and theoretical basis for the designing of the new calixarene stationary phases in GC analyses.

Unraveling individual host-guest interactions in molecular recognition from first principles quantum mechanics: Insights into the nature of nicotinic acetylcholine receptor agonist binding.

Drug binding to a protein target is governed by a complex pattern of noncovalent interactions between the ligand and the residues in the protein's binding pocket. Here we introduce a generally applicable, parameter-free, computational method that allows for the identification, quantification, and analysis of the key ligand-residue interactions responsible for molecular recognition. Our strategy relies on Local Energy Decomposition analysis at the "gold-standard" coupled cluster DLPNO-CCSD(T) level. In the study case shown in this paper, nicotine and imidacloprid binding to the nicotinic acetylcholine receptor, our approach provides new insights into how individual amino acids in the active site determine sensitivity and selectivity of the ligands, extending and refining classical pharmacophore hypotheses. By inference, the method is applicable to any kind of host/guest interactions with potential applications in industrial biocatalysis and protein engineering.

Mechanistic Roles of Electrostatic Interactions in the Molecular Recognition of Intrinsically Disordered Proteins

Electrostatic interactions could play important roles in the molecular recognition process of intrinsically disordered proteins (IDPs) as many IDPs and the recognition elements contain charged residues. Previous studies have demonstrated that electrostatic forces could accelerate the encounter process via electrostatic steering effect and increase the efficiency of binding upon encounter for several IDPs. To further investigate the universal role of electrostatic interactions in IDPs molecular recognition, we collected the experimentally determined binding kinetics of IDPs. For many studied IDPs, the association rate constants are reduced for about ten folds when the salt concentration increases from low (~50 mM) to high (~500 mM), indicating the presence of favorable electrostatic interactions. We further performed molecular dynamics simulations using structure‐based coarse‐grained models. Simulations predicted that long‐range electrostatic interactions accelerate the binding rate in a range consistent with experimental results. Simulations also revealed that electrostatic forces generally enhance the binding kinetics by increasing the encounter rate and by enhancing the evolving efficiency. Correlating the charge density with binding kinetics revealed that the overall charge density is relate with enhancement of the capture rate constant and the charge distribution affects both the evolution rate constant and escape rate constant. Analysis of the transition path times showed that electrostatic interactions stabilize the intermediate state along the binding process. Besides affecting the binding kinetics, electrostatic interactions also redistributed the flux among multiple parallel binding transition paths. As a summary, our results suggest that favorable electrostatic interactions are present in many IDPs recognition processes. Under physiological salt concentrations, electrostatic interactions are expected to enhance the binding rate constant by several folds.Support or Funding InformationThis work was supported by Hubei University of Technology

Rational design of affinity ligands for bioseparation

Affinity adsorbents have been the cornerstone in protein purification. The selective nature of the molecular recognition interactions established between an affinity ligands and its target provide the basis for efficient capture and isolation of proteins. The plethora of affinity adsorbents available in the market reflects the importance of affinity chromatography in the bioseparation industry. Ligand discovery relies on the implementation of rational design techniques, which provides the foundation for the engineering of novel affinity ligands. The main goal for the design of affinity ligands is to discover or improve functionality, such as increased stability or selectivity. However, the methodologies must adapt to the current needs, namely to the number and diversity of biologicals being developed, and the availability of new tools for big data analysis and artificial intelligence. In this review, we offer an overview on the development of affinity ligands for bioseparation, including the evolution of rational design techniques, dating back to the years of early discovery up to the current and future trends in the field.

Auto-affitech: an automated ligand binding affinity evaluation platform using digital microfluidics with a bidirectional magnetic separation method.

The dissociation constant (Kd) is a crucial parameter for characterizing binding affinity in molecular recognition, including antigen-antibody, DNA-protein, and receptor-ligand interactions. However, conventional methods for Kd characterization usually involve a multi-step process and time-consuming operations for incubation, washing, and detection, thus causing problems, such as time delays, microbead loss, degradation of sensitive molecules, and personal errors. Here we demonstrate an automated ligand binding affinity evaluation platform (Auto-affitech) using digital microfluidics (DMF), with individual droplets at the microliter level, programmed to rapidly perform the incubation and separation of target-beads and binding ligands. Because the loss of the beads influences the detection results, we propose a new strategy for magnetic bead separation using DMF, termed the bidirectional separation method. By splitting one droplet into two asymmetric droplets, high bead retention efficiency (89.57% ± 0.05%) and high washing efficiency (99.59% ± 0.17%, with four washings) were obtained. We demonstrate the determination of Kd of an aptamer-protein system (EpCAM and its corresponding aptamer SYL3C) and an antigen-antibody system (H5N1 antigen and antibody), proving the capability and universality of Auto-affitech in various receptor-ligand systems. Integrating all the sample processing procedures, the Auto-affitech not only saves manual labor and minimizes personal errors, but also conserves samples and shortens analysis time. Overall, this platform successfully demonstrates to be an automated approach for dissociation constant evaluation and exhibits great potential for highly efficient screening of ligands.

Multi-functional self-assembled nanoparticles for pVEGF-shRNA loading and anti-tumor targeted therapy.

Although RNA interference (RNAi) technology shows great potential in cancer treatment, the tumor target delivery and sufficient cytosolic transport of RNAi agents are still the main obstacles for its clinical applications. Herein, we report a functional supramolecular self-assembled nanoparticle vector for RNAi agent loading and tumor target therapy. Molecular block adamantane-grafted poly(ethylene glycol) (Ad-PEG) was modified with epidermal growth factor receptor (EGFR)-specific binding ligand GE11 or pH-sensitive fusogenic peptide GALA and then used for self-assembly with cyclodextrin-grafted branched polyethylenimine (CD-PEI), adamantane-grafted polyamidoamine dendrimer (Ad-PAMAM), and plasmid DNA containing a small hairpin RNA expression cassette against vascular endothelial growth factor (VEGF) into functional DNA-loaded supramolecular nanoparticles (GE11&GALA-pshVEGF@SNPs) based on molecular recognition and charge interaction. These functional peptides facilitated the target cell binding, internalization, and endosomal escape of GE11&GALA-pshVEGF@SNPs, resulting in increased reporter gene expression and efficient targeted gene silencing. The systemic delivery of the GE11&GALA-pshVEGF@SNPs can efficiently downregulate the intratumoral VEGF protein levels, reduce blood vessel formation, and significantly inhibit A549 xenograft tumor growth. These results reveal the potential of these multifunctional self-assembled nanoparticles as a nucleic acid drug delivery system for the treatment of lung cancer.

One-step and green strategy for exfoliation and stabilization of graphene by phosphate pillar[6]arene and its application for fluorescence sensing of paraquat

A one-step, safe, and green approach is reported for the synthesis of 2D graphene nanosheet in water phase exfoliated by the water-soluble phosphate pillar[6]arene (PP6). Compared with the conventional method that the graphite is firstly oxidized, exfoliated to graphene oxide and then reduced to graphene sheets, the present proposed method is directly exfoliated from graphite by one-step process without using any strong oxidizing agents, such as H2SO4 or KMnO4. More importantly, the graphene obtained by this environmentally friendly method possesses excellent crystalline structure. Besides, the prepared graphene could be stabilized through π-π stacking interaction between graphene and the hydrophobic segments of benzene rings in PP6, and PP6 functionalized graphene (PP6@graphene) simultaneously combines the fluorescence quenching property of graphene and molecular recognition capability of PP6. Therefore, we construct a competitive fluorescence assay based on the molecular recognition interaction between PP6@graphene and acridine orange (AO) for determination of paraquat (PQ), a nonselective herbicide with high toxicity to humans. The fluorescence of AO is completely quenched by fluorescence resonance energy transfer (FRET) interaction between AO and PP6@graphene, and the quenched fluorescence recovers upon the successive addition of PQ, because the inclusion capability of PP6 towards PQ is stronger than that of AO. Linear response ranges of 0.2–2 μM and 2–18 μM are obtained for determination of PQ and the detection limit is 0.06 μM (S/N = 3). The constructed sensing platform is also used to detect PQ in three water samples with satisfying results, which indicates that the competitive host-guest supermolecular recognition method has potential application in practical environmental risk assessment of PQ.

Self-Assembly of an Aptamer-Decorated, DNA–Protein Hybrid Nanogel: A Biocompatible Nanocarrier for Targeted Cancer Therapy

Nanocarrier-based chemotherapy is one of the most efficient approaches for the treatment of cancer, and hence, the design of new nanocarriers is very important. Herein, the design of a new class of physically cross-linked nanoparticles (nanogel) solely made of biomolecules including DNA, protein, and biotin as a nanocarrier for the targeted cancer therapy is reported. A specific molecular recognition interaction between biotin and streptavidin is explored for the cross-linking of a DNA nanostructure for the crafting of a nanogel. The most unique structural features of nanogels include the following: (i) excellent biocompatibility, (ii) decoration of the nanogel surface with biotin and streptavidin randomly that allowed the integration of aptamer DNA onto the surface of the nanostructure through the biotin-streptavidin interaction, (iii) high doxorubicin encapsulation efficacy through the intercalation of doxorubicin inside the DNA duplex, and (iv) stimuli responsiveness. The selective uptake of a doxorubicin-loaded nanogel by aptamer-receptor-positive cell lines (CCRF-CEM and HeLa) and its delivery inside the target cells are demonstrated. The selective uptake of the nanogel by CCRF-CEM and HeLa cells is attributed to the specific interaction between the aptamer DNA decorated on the surface of the nanogel with the PTK7 receptor overexpressed on CCRF-CEM and HeLa cell lines. These results imply that the nanogel obtained from the self-assembly of biomolecules would be ideal for the crafting of nanocarriers for targeted cargo delivery applications.

Electrostatic Assemblies of Single-Walled Carbon Nanotubes and Sequence-Tunable Peptoid Polymers Detect a Lectin Protein and Its Target Sugars.

A primary limitation to real-time imaging of metabolites and proteins has been the selective detection of biomolecules that have no naturally occurring or stable molecular recognition counterparts. We present developments in the design of synthetic near-infrared fluorescent nanosensors based on the fluorescence modulation of single-walled carbon nanotubes (SWNTs) with select sequences of surface-adsorbed N-substituted glycine peptoid polymers. We assess the stability of the peptoid-SWNT nanosensor candidates under variable ionic strengths, protease exposure, and cell culture media conditions and find that the stability of peptoid-SWNTs depends on the composition and length of the peptoid polymer. From our library, we identify a peptoid-SWNT assembly that can detect lectin protein wheat germ agglutinin (WGA) with a sensitivity comparable to the concentration of serum proteins. To demonstrate the retention of nanosensor-bound protein activity, we show that WGA on the nanosensor produces an additional fluorescent signal modulation upon exposure to the lectin's target sugars, suggesting the lectin protein remains active and selectively binds its target sugars through ternary molecular recognition interactions relayed to the nanosensor. Our results inform design considerations for developing synthetic molecular recognition elements by assembling peptoid polymers on SWNTs and also demonstrate these assemblies can serve as optical nanosensors for lectin proteins and their target sugars. Together, these data suggest certain peptoid sequences can be assembled with SWNTs to serve as versatile optical probes to detect proteins and their molecular substrates.

Towards A New Approach for the Description of Cyclo⁻2,4-Dihydroxybenzoate, A Substance Which Effectively Mimics Zearalenone in Imprinted Polymers Designed for Analyzing Selected Mycotoxins in Urine.

A method of purifying cyclododecyl 2,4-dihydroxybenzoate as a potential replacement template molecule for preparation of molecularly-imprinted polymers for isolation of zearalenone in urine was developed. Full physicochemical characteristics of cyclododecyl 2,4-dihydroxybenzoate for the first time included crystallographic analysis and molecular modelling, which made possible the determination of the similarity between the cyclododecyl 2,4-dihydroxybenzoate and zearalenone molecules. The obtained molecularly-imprinted polymers show very high in vitro selectivity towards zearalenone due to specific interactions (e.g., hydrogen bonding, molecular recognition interaction). The achieved extraction recovery exceeds 94% at the tested concentration levels (20–500 ng·mL−1) with a relative standard deviation below 2%. Immunosorbents were found to have lower recoveries (below 92.5%) and RSD value between 2 and 4% for higher concentrations of the studied substance (400 ng·mL−1).

Toward Precise Manipulation of DNA-Protein Hybrid Nanoarchitectures.

Nucleic acids and proteins are the two primary building materials of living organisms. Over the past decade, artificial DNA-protein hybrid structures have been pursued for a wide range of applications. DNA nanotechnology, in particular, has dramatically expanded nanoscale molecule engineering and contributed to the spatial arrangement of protein components. Strategies for designing site-specific coupling of DNA oligomers to proteins are needed in order to allow for precise control over stoichiometry and position. Efforts have also been focused on coassembly of protein-DNA complexes by engineering their fundamental molecular recognition interactions. This Concept focuses on the precise manipulation of DNA-protein nanoarchitectures. Particular attention is paid to site-selectivity within DNA-protein conjugates, regulation of protein orientation using DNA scaffolds, and coassembly principles upon unique structural motifs. Current challenges and future directions are also discussed in the design and application of DNA-protein nanoarchitectures.