DNA Nanostructures: Current Challenges and Opportunities for Cellular Delivery.

DNA nanotechnology has produced a wide range of self-assembled structures, offering unmatched possibilities in terms of structural design. Because of their programmable assembly and precise control of size, shape, and function, DNA particles can be used for numerous biological applications, including imaging, sensing, and drug delivery. While the biocompatibility, programmability, and ease of synthesis of nucleic acids have rapidly made them attractive building blocks, many challenges remain to be addressed before using them in biological conditions. Enzymatic hydrolysis, low cellular uptake, immune cell recognition and degradation, and unclear biodistribution profiles are yet to be solved. Rigorous methodologies are needed to study, understand, and control the fate of self-assembled DNA structures in physiological conditions. In this review, we describe the current challenges faced by the field as well as recent successes, highlighting the potential to solve biology problems or develop smart drug delivery tools. We then propose an outlook to drive the translation of DNA constructs toward preclinical design. We particularly believe that a detailed understanding of the fate of DNA nanostructures within living organisms, achieved through thorough characterization, is the next required step to reach clinical maturity.

[1]  C. Mao,et al.  Kidney-Targeted Cytosolic Delivery of siRNA Using a Small-Sized Mirror DNA Tetrahedron for Enhanced Potency , 2020, ACS central science.

[2]  J. Guan,et al.  Interrogation of Folic Acid-Functionalized Nanomedicines: The Regulatory Roles of Plasma Proteins Reexamined. , 2020, ACS nano.

[3]  H. Sleiman,et al.  Detailed cellular assessment of albumin-bound oligonucleotides: Increased stability and lower non-specific cell uptake. , 2020, Journal of controlled release : official journal of the Controlled Release Society.

[4]  Igor L. Medintz,et al.  Understanding the fate of DNA nanostructures inside the cell. , 2020, Journal of materials chemistry. B.

[5]  Veikko Linko,et al.  Challenges and Perspectives of DNA Nanostructures in Biomedicine , 2020, Angewandte Chemie.

[6]  Peixuan Guo,et al.  Ultra-thermostable RNA nanoparticles for solubilizing and high-yield loading of paclitaxel for breast cancer therapy , 2020, Nature Communications.

[7]  L. Scott Givosiran: First Approval , 2020, Drugs.

[8]  W. Alshaer,et al.  Aptamers Chemistry: Chemical Modifications and Conjugation Strategies , 2019, Molecules.

[9]  C. Mirkin,et al.  Spherical Nucleic Acids with Tailored and Active Protein Coronae , 2019, ACS central science.

[10]  M. DiFiglia,et al.  A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system , 2019, Nature Biotechnology.

[11]  J. Cornelissen,et al.  Polymorphic assembly of virus-capsid proteins around DNA and the cellular uptake of the resulting particles. , 2019, Journal of controlled release : official journal of the Controlled Release Society.

[12]  J. Kjems,et al.  Cellular uptake of covalent and non-covalent DNA nanostructures with different sizes and geometries. , 2019, Nanoscale.

[13]  Ryan L Setten,et al.  The current state and future directions of RNAi-based therapeutics , 2019, Nature Reviews Drug Discovery.

[14]  H. Sleiman,et al.  Uptake and Fate of Fluorescently Labeled DNA Nanostructures in Cellular Environments: A Cautionary Tale , 2019, ACS central science.

[15]  Christian Wiraja,et al.  Framework nucleic acids as programmable carrier for transdermal drug delivery , 2019, Nature Communications.

[16]  S. Pressé,et al.  Quantitative Mapping of Endosomal DNA Processing by Single Molecule Counting. , 2019, Angewandte Chemie.

[17]  Chad A Mirkin,et al.  Exploration of the nanomedicine-design space with high-throughput screening and machine learning , 2019, Nature Biomedical Engineering.

[18]  Yamuna Krishnan,et al.  DNA nanodevices map enzymatic activity in organelles , 2019, Nature Nanotechnology.

[19]  Hale Bila,et al.  Engineering a stable future for DNA-origami as a biomaterial. , 2019, Biomaterials science.

[20]  Aviv Regev,et al.  DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction , 2018, Cell.

[21]  Chunhai Fan,et al.  DNA Nanotechnology-Enabled Drug Delivery Systems. , 2018, Chemical reviews.

[22]  A. Saminathan,et al.  A DNA nanomachine chemically resolves lysosomes in live cells , 2018, Nature Nanotechnology.

[23]  Jiye Shi,et al.  DNA origami nanostructures can exhibit preferential renal uptake and alleviate acute kidney injury , 2018, Nature Biomedical Engineering.

[24]  Yusuke Sakai,et al.  DNA Aptamers for the Functionalisation of DNA Origami Nanostructures , 2018, Genes.

[25]  Baoquan Ding,et al.  Rationally Designed DNA‐Origami Nanomaterials for Drug Delivery In Vivo , 2018, Advanced materials.

[26]  Xiaolei Zuo,et al.  DNA Nanostructure-Programmed Like-Charge Attraction at the Cell-Membrane Interface , 2018, ACS central science.

[27]  Hendrik Dietz,et al.  Sequence-programmable covalent bonding of designed DNA assemblies , 2018, Science Advances.

[28]  A. Desideri,et al.  Entry, fate and degradation of DNA nanocages in mammalian cells: a matter of receptors. , 2018, Nanoscale.

[29]  Y. Liu,et al.  Floxuridine Homomeric Oligonucleotides "Hitchhike" with Albumin In Situ for Cancer Chemotherapy. , 2018, Angewandte Chemie.

[30]  Veikko Linko,et al.  On the Stability of DNA Origami Nanostructures in Low-Magnesium Buffers. , 2018, Angewandte Chemie.

[31]  Khalid K. Alam,et al.  Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines , 2018, Nature Communications.

[32]  Donald E Ingber,et al.  Modulation of the Cellular Uptake of DNA Origami through Control over Mass and Shape. , 2018, Nano letters.

[33]  A. Khvorova,et al.  Diverse lipid conjugates for functional extra-hepatic siRNA delivery in vivo , 2018, bioRxiv.

[34]  A. Khvorova,et al.  Hydrophobicity drives the systemic distribution of lipid-conjugated siRNAs via lipid transport pathways , 2018, bioRxiv.

[35]  Hanadi F. Sleiman,et al.  DNA Nanostructures at the Interface with Biology , 2018 .

[36]  Baoquan Ding,et al.  A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo , 2018, Nature Biotechnology.

[37]  Fangjun Wang,et al.  Multi-hierarchical profiling the structure-activity relationships of engineered nanomaterials at nano-bio interfaces , 2018, bioRxiv.

[38]  Yonggang Ke,et al.  Visualization of the Cellular Uptake and Trafficking of DNA Origami Nanostructures in Cancer Cells. , 2018, Journal of the American Chemical Society.

[39]  M. Moore,et al.  Comparison of partially and fully chemically-modified siRNA in conjugate-mediated delivery in vivo , 2018, Nucleic acids research.

[40]  Tao Zhang,et al.  Anti-inflammatory and Antioxidative Effects of Tetrahedral DNA Nanostructures via the Modulation of Macrophage Responses. , 2018, ACS applied materials & interfaces.

[41]  Peixuan Guo,et al.  The Effect of Size and Shape of RNA Nanoparticles on Biodistribution. , 2017, Molecular therapy : the journal of the American Society of Gene Therapy.

[42]  Christopher C. Griffith,et al.  Systemic Delivery of Bc12-Targeting siRNA by DNA Nanoparticles Suppresses Cancer Cell Growth. , 2017, Angewandte Chemie.

[43]  Hendrik Dietz,et al.  Biotechnological mass production of DNA origami , 2017, Nature.

[44]  C. Buske,et al.  Super-Resolution Microscopy Unveils Dynamic Heterogeneities in Nanoparticle Protein Corona. , 2017, Small.

[45]  Peixuan Guo,et al.  Size, Shape, and Sequence-Dependent Immunogenicity of RNA Nanoparticles , 2017, Molecular therapy. Nucleic acids.

[46]  John C. Chaput,et al.  Analysis of aptamer discovery and technology , 2017 .

[47]  D. Yan,et al.  DNA Trojan Horses: Self-Assembled Floxuridine-Containing DNA Polyhedra for Cancer Therapy. , 2017, Angewandte Chemie.

[48]  Kemin Wang,et al.  DNA tetrahedron nanostructures for biological applications: biosensors and drug delivery. , 2017, The Analyst.

[49]  Wei Pan,et al.  A DNA Tetrahedron Nanoprobe with Controlled Distance of Dyes for Multiple Detection in Living Cells and in Vivo. , 2017, Analytical chemistry.

[50]  Maximilian T. Strauss,et al.  Super-resolution microscopy with DNA-PAINT , 2017, Nature Protocols.

[51]  David J. Mooney,et al.  Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation , 2017, Nature Communications.

[52]  Hanadi F Sleiman,et al.  Development of DNA Nanostructures for High-Affinity Binding to Human Serum Albumin. , 2017, Journal of the American Chemical Society.

[53]  anastasia. khvorova,et al.  The chemical evolution of oligonucleotide therapies of clinical utility , 2017, Nature Biotechnology.

[54]  Eric T. Wang,et al.  Barcoded nanoparticles for high throughput in vivo discovery of targeted therapeutics , 2017, Proceedings of the National Academy of Sciences.

[55]  Jing Zhu,et al.  A DNA dual lock-and-key strategy for cell-subtype-specific siRNA delivery , 2016, Nature Communications.

[56]  John C C Hsu,et al.  Optimized DNA "Nanosuitcases" for Encapsulation and Conditional Release of siRNA. , 2016, Journal of the American Chemical Society.

[57]  Benoit Dubertret,et al.  Quantum dot-loaded monofunctionalized DNA Icosahedra for single particle tracking of endocytic pathways , 2016, Nature nanotechnology.

[58]  Joachim O. Rädler,et al.  Shape and Interhelical Spacing of DNA Origami Nanostructures Studied by Small-Angle X-ray Scattering. , 2016, Nano letters.

[59]  A. Desideri,et al.  Receptor-Mediated Entry of Pristine Octahedral DNA Nanocages in Mammalian Cells. , 2016, ACS nano.

[60]  J. Kjems,et al.  Intracellular Delivery of a Planar DNA Origami Structure by the Transferrin-Receptor Internalization Pathway. , 2016, Small.

[61]  Gang Bao,et al.  The effect of nanoparticle size on in vivo pharmacokinetics and cellular interaction. , 2016, Nanomedicine.

[62]  Ping Wang,et al.  Tumor-Penetrating Peptide-Modified DNA Tetrahedron for Targeting Drug Delivery. , 2016, Biochemistry.

[63]  Jiye Shi,et al.  Multiple-Armed Tetrahedral DNA Nanostructures for Tumor-Targeting, Dual-Modality in Vivo Imaging. , 2016, ACS applied materials & interfaces.

[64]  Kemin Wang,et al.  A DNA tetrahedron-based molecular beacon for tumor-related mRNA detection in living cells. , 2016, Chemical Communications.

[65]  J. Watts,et al.  Oligonucleotide therapeutics: chemistry, delivery and clinical progress. , 2015, Future medicinal chemistry.

[66]  Yamuna Krishnan,et al.  Designing DNA nanodevices for compatibility with the immune system of higher organisms. , 2015, Nature nanotechnology.

[67]  Pekka Orponen,et al.  DNA rendering of polyhedral meshes at the nanoscale , 2015, Nature.

[68]  Xu Zhou,et al.  Stability study of tubular DNA origami in the presence of protein crystallisation buffer , 2015 .

[69]  C. Bennett,et al.  Pharmacokinetics, biodistribution and cell uptake of antisense oligonucleotides. , 2015, Advanced drug delivery reviews.

[70]  T. Liedl,et al.  DNA nanotubes as intracellular delivery vehicles in vivo. , 2015, Biomaterials.

[71]  Chor Yong Tay,et al.  Nature-inspired DNA nanosensor for real-time in situ detection of mRNA in living cells. , 2015, ACS nano.

[72]  Xiaolei Zuo,et al.  A study of pH-dependence of shrink and stretch of tetrahedral DNA nanostructures. , 2015, Nanoscale.

[73]  S. Crooke,et al.  Identification and characterization of intracellular proteins that bind oligonucleotides with phosphorothioate linkages , 2022 .

[74]  Y. Weizmann,et al.  Enzymatic synthesis of periodic DNA nanoribbons for intracellular pH sensing and gene silencing. , 2015, Journal of the American Chemical Society.

[75]  Fritz Eckstein,et al.  Phosphorothioates, essential components of therapeutic oligonucleotides. , 2014, Nucleic acid therapeutics.

[76]  Hyojeong Kim,et al.  Stability of DNA Origami Nanostructure under Diverse Chemical Environments , 2014 .

[77]  William M. Shih,et al.  Addressing the Instability of DNA Nanostructures in Tissue Culture , 2014, ACS nano.

[78]  Jiye Shi,et al.  Single-particle tracking and modulation of cell entry pathways of a tetrahedral DNA nanostructure in live cells. , 2014, Angewandte Chemie.

[79]  Qiao Jiang,et al.  DNA origami as an in vivo drug delivery vehicle for cancer therapy. , 2014, ACS nano.

[80]  Chad A. Mirkin,et al.  Intracellular Fate of Spherical Nucleic Acid Nanoparticle Conjugates , 2014, Journal of the American Chemical Society.

[81]  J. Kjems,et al.  Quantification of cellular uptake of DNA nanostructures by qPCR. , 2014, Methods.

[82]  Paul W. Wiseman,et al.  Sequence-responsive unzipping DNA cubes with tunable cellular uptake profiles , 2014 .

[83]  H. Bermudez,et al.  Aptamer-Targeted DNA Nanostructures for Therapeutic Delivery , 2014, Molecular pharmaceutics.

[84]  William M. Shih,et al.  Virus-Inspired Membrane Encapsulation of DNA Nanostructures To Achieve In Vivo Stability , 2014, ACS nano.

[85]  H. Sleiman,et al.  Development and characterization of gene silencing DNA cages. , 2014, Biomacromolecules.

[86]  A method to study in vivo stability of DNA nanostructures☆ , 2013, Methods.

[87]  H. Sleiman,et al.  Site-specific positioning of dendritic alkyl chains on DNA cages enables their geometry-dependent self-assembly. , 2013, Nature chemistry.

[88]  Stefan Tenzer,et al.  Rapid formation of plasma protein corona critically affects nanoparticle pathophysiology. , 2013, Nature nanotechnology.

[89]  M. Hayden,et al.  Rational design of antisense oligonucleotides targeting single nucleotide polymorphisms for potent and allele selective suppression of mutant Huntingtin in the CNS , 2013, Nucleic acids research.

[90]  Byeong-Su Kim,et al.  Sentinel lymph node imaging by a fluorescently labeled DNA tetrahedron. , 2013, Biomaterials.

[91]  Weihong Tan,et al.  Self-assembled, aptamer-tethered DNA nanotrains for targeted transport of molecular drugs in cancer theranostics , 2013, Proceedings of the National Academy of Sciences.

[92]  Xiang Wang,et al.  Nanomaterial toxicity testing in the 21st century: use of a predictive toxicological approach and high-throughput screening. , 2013, Accounts of chemical research.

[93]  Hanadi F Sleiman,et al.  Simple design for DNA nanotubes from a minimal set of unmodified strands: rapid, room-temperature assembly and readily tunable structure. , 2013, ACS nano.

[94]  Ick Chan Kwon,et al.  Drug delivery by a self-assembled DNA tetrahedron for overcoming drug resistance in breast cancer cells. , 2013, Chemical communications.

[95]  H. Sleiman,et al.  DNA nanostructure serum stability: greater than the sum of its parts. , 2013, Chemical communications.

[96]  Chunhai Fan,et al.  Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors. , 2012, Angewandte Chemie.

[97]  G. Deleavey,et al.  Designing chemically modified oligonucleotides for targeted gene silencing. , 2012, Chemistry & biology.

[98]  Hao Yan,et al.  DNA origami as a carrier for circumvention of drug resistance. , 2012, Journal of the American Chemical Society.

[99]  Daniel G. Anderson,et al.  Molecularly Self-Assembled Nucleic Acid Nanoparticles for Targeted In Vivo siRNA Delivery , 2012, Nature nanotechnology.

[100]  Shawn M. Douglas,et al.  A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads , 2012, Science.

[101]  D. H. Burke Cell-penetrating RNAs: new keys to the castle. , 2012, Molecular therapy : the journal of the American Society of Gene Therapy.

[102]  Jin-Ho Ahn,et al.  Design, assembly, and activity of antisense DNA nanostructures. , 2011, Small.

[103]  Tim Liedl,et al.  Cellular immunostimulation by CpG-sequence-coated DNA origami structures. , 2011, ACS nano.

[104]  H. Pei,et al.  Self-assembled multivalent DNA nanostructures for noninvasive intracellular delivery of immunostimulatory CpG oligonucleotides. , 2011, ACS nano.

[105]  Masayuki Endo,et al.  Photo-cross-linking-assisted thermal stability of DNA origami structures and its application for higher-temperature self-assembly. , 2011, Journal of the American Chemical Society.

[106]  Dong-Ming Huang,et al.  Aptamer-conjugated DNA icosahedral nanoparticles as a carrier of doxorubicin for cancer therapy. , 2011, ACS nano.

[107]  Matthew J. A. Wood,et al.  DNA cage delivery to mammalian cells. , 2011, ACS nano.

[108]  Sandhya P Koushika,et al.  A synthetic icosahedral DNA-based host-cargo complex for functional in vivo imaging. , 2011, Nature communications.

[109]  Mark Bathe,et al.  A primer to scaffolded DNA origami , 2011, Nature Methods.

[110]  Chad A Mirkin,et al.  Scavenger receptors mediate cellular uptake of polyvalent oligonucleotide-functionalized gold nanoparticles. , 2010, Bioconjugate chemistry.

[111]  Baldomero Oliva,et al.  Multivalent antibodies: when design surpasses evolution. , 2010, Trends in biotechnology.

[112]  Jung-Won Keum,et al.  Enhanced resistance of DNA nanostructures to enzymatic digestion. , 2009, Chemical communications.

[113]  Chengde Mao,et al.  DNA nanotubes as combinatorial vehicles for cellular delivery. , 2008, Biomacromolecules.

[114]  David R Corey,et al.  Chemical modification: the key to clinical application of RNA interference? , 2007, The Journal of clinical investigation.

[115]  Chad A. Mirkin,et al.  Oligonucleotide-Modified Gold Nanoparticles for Intracellular Gene Regulation , 2006, Science.

[116]  Paul W K Rothemund,et al.  Sturdier DNA nanotubes via ligation. , 2006, Nano letters.

[117]  Jasmyn A. Dunn,et al.  Differences in Macrophage Activation by Bacterial DNA and CpG-Containing Oligonucleotides1 , 2005, The Journal of Immunology.

[118]  J. Wengel,et al.  LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. , 2004, Biochemistry.

[119]  Thomas Tuschl,et al.  Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. , 2003, Antisense & nucleic acid drug development.

[120]  P. D. Cook,et al.  In vivo fate of phosphorothioate antisense oligodeoxynucleotides: predominant uptake by scavenger receptors on endothelial liver cells. , 1997, Nucleic acids research.

[121]  R. Wagner,et al.  Intracellular disposition and metabolism of fluorescently-labeled unmodified and modified oligonucleotides microinjected into mammalian cells. , 1993, Nucleic acids research.

[122]  J. Shaw,et al.  Modified deoxyoligonucleotides stable to exonuclease degradation in serum. , 1991, Nucleic acids research.

[123]  J. Walder,et al.  Substrate specificity and kinetics of degradation of antisense oligonucleotides by a 3' exonuclease in plasma. , 1991, Antisense research and development.