Towards biomedical applications for nucleic acid nanodevices.

DNA and RNA can be used to construct artificial nanodevices with strong potential for future biomedical applications. DNA nanodevices can function as biosensors, which detect and report the presence of proteins and naturally occurring nucleic acids, such as mRNA or microRNAs. Complex sensors can be realized by supporting DNA devices with DNA-based information processing. Artificial DNA-based reaction networks can be created that amplify molecular signals or evaluate logical functions to report the simultaneous presence of several disease-related molecules. Other applications for DNA nanodevices are found in controlled release and drug delivery. DNA can be used to build nanocontainers for drugs or switchable hydrogels, which can trap and release compounds. For in vivo applications of DNA nanodevices, techniques for efficient packaging and delivery have been developed and the first examples of intracellular RNA-based nanodevices have already been demonstrated.

[1]  R. M. Herriott,et al.  Blood Nucleases and Infectious Viral Nucleic Acids , 1961, Nature.

[2]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[3]  R. Kole,et al.  Stability of antisense DNA oligodeoxynucleotide analogs in cellular extracts and sera. , 1991, Life sciences.

[4]  N. Seeman,et al.  Synthesis from DNA of a molecule with the connectivity of a cube , 1991, Nature.

[5]  D. Bartel,et al.  Isolation of new ribozymes from a large pool of random sequences [see comment]. , 1993, Science.

[6]  A. Sachs,et al.  Messenger RNA degradation in eukaryotes , 1993, Cell.

[7]  Y. Cheng,et al.  Antisense oligonucleotides as therapeutic agents--is the bullet really magical? , 1993, Science.

[8]  N. Seeman,et al.  Construction of a DNA-Truncated Octahedron , 1994 .

[9]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[10]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[11]  F. Gage,et al.  In Vivo Gene Delivery and Stable Transduction of Nondividing Cells by a Lentiviral Vector , 1996, Science.

[12]  Sanjay Tyagi,et al.  Molecular Beacons: Probes that Fluoresce upon Hybridization , 1996, Nature Biotechnology.

[13]  Nikolaos A. Peppas,et al.  Pulsatile local delivery of thrombolytic and antithrombotic agents using poly(N-isopropylacrylamide-co-methacrylic acid) hydrogels , 1996 .

[14]  Xiaodong Wang,et al.  Induction of Apoptotic Program in Cell-Free Extracts: Requirement for dATP and Cytochrome c , 1996, Cell.

[15]  G. F. Joyce,et al.  A general purpose RNA-cleaving DNA enzyme. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J. Szostak,et al.  In vitro selection of functional nucleic acids. , 1999, Annual review of biochemistry.

[17]  K. Heider,et al.  Polycation‐based DNA complexes for tumor‐targeted gene delivery in vivo , 1999, The journal of gene medicine.

[18]  Takashi Miyata,et al.  A reversibly antigen-responsive hydrogel , 1999, Nature.

[19]  N. Seeman,et al.  A nanomechanical device based on the B–Z transition of DNA , 1999, Nature.

[20]  B Mattiasson,et al.  'Smart' polymers and what they could do in biotechnology and medicine. , 1999, Trends in biotechnology.

[21]  L. Gold,et al.  The use of aptamers in large arrays for molecular diagnostics. , 1999, Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology.

[22]  R. Pelton,et al.  Temperature-sensitive aqueous microgels. , 2000, Advances in colloid and interface science.

[23]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[24]  N. Peppas,et al.  Hydrogels in Pharmaceutical Formulations , 1999 .

[25]  M. Hughes,et al.  The cellular delivery of antisense oligonucleotides and ribozymes. , 2001, Drug discovery today.

[26]  M. Stojanović,et al.  Aptamer-based folding fluorescent sensor for cocaine. , 2001, Journal of the American Chemical Society.

[27]  P. Couvreur,et al.  Nanoparticulate systems for the delivery of antisense oligonucleotides. , 2001, Advanced drug delivery reviews.

[28]  Kinam Park,et al.  Environment-sensitive hydrogels for drug delivery , 2001 .

[29]  A. Kabanov,et al.  Evaluation of polyplexes as gene transfer agents. , 2001, Journal of controlled release : official journal of the Controlled Release Society.

[30]  A. Ellington,et al.  Aptamer beacons for the direct detection of proteins. , 2001, Analytical biochemistry.

[31]  T. Tuschl,et al.  Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells , 2001, Nature.

[32]  M. Famulok,et al.  Intramers as promising new tools in functional proteomics. , 2001, Chemistry & biology.

[33]  Volker A Erdmann,et al.  Selection of RNA aptamers to the Alzheimer's disease amyloid peptide. , 2002, Biochemical and biophysical research communications.

[34]  N. Seeman,et al.  A robust DNA mechanical device controlled by hybridization topology , 2002, Nature.

[35]  Milan N Stojanovic,et al.  Aptamer-based colorimetric probe for cocaine. , 2002, Journal of the American Chemical Society.

[36]  Weihong Tan,et al.  A Single DNA Molecule Nanomotor , 2002 .

[37]  Darko Stefanovic,et al.  Deoxyribozyme-based logic gates. , 2002, Journal of the American Chemical Society.

[38]  Michael Famulok,et al.  In vivo-applied functional RNAs as tools in proteomics and genomics research. , 2002, Trends in biotechnology.

[39]  Georg Sczakiel,et al.  Endogenous expression of a high-affinity pseudoknot RNA aptamer suppresses replication of HIV-1. , 2002, Nucleic acids research.

[40]  J Henke,et al.  Magnetofection: enhancing and targeting gene delivery by magnetic force in vitro and in vivo , 2002, Gene Therapy.

[41]  J. Olivot,et al.  Human endothelial cells selectively express large amounts of pancreatic‐type ribonuclease (RNase 1) , 2002, Journal of cellular biochemistry.

[42]  Y. Bae,et al.  Thermosensitive sol-gel reversible hydrogels. , 2002, Advanced drug delivery reviews.

[43]  N. Seeman DNA in a material world , 2003, Nature.

[44]  Nobuko Hamaguchi,et al.  Aptamer-based biosensor arrays for detection and quantification of biological macromolecules. , 2003, Analytical biochemistry.

[45]  Hermann E. Gaub,et al.  DNA: A Programmable Force Sensor , 2003, Science.

[46]  Jean-Louis Mergny,et al.  DNA duplex–quadruplex exchange as the basis for a nanomolecular machine , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[47]  D. Stefanovic,et al.  Deoxyribozyme-based half-adder. , 2003, Journal of the American Chemical Society.

[48]  Yingfu Li,et al.  Structure-switching signaling aptamers. , 2003, Journal of the American Chemical Society.

[49]  Jens Kurreck,et al.  Antisense technologies. Improvement through novel chemical modifications. , 2003, European journal of biochemistry.

[50]  Chunhai Fan,et al.  Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[51]  A. Turberfield,et al.  DNA fuel for free-running nanomachines. , 2003, Physical review letters.

[52]  Darko Stefanovic,et al.  A deoxyribozyme-based molecular automaton , 2003, Nature Biotechnology.

[53]  Andrew D Ellington,et al.  In vitro selection of molecular beacons. , 2003, Nucleic acids research.

[54]  John J Rossi,et al.  Approaches for the sequence-specific knockdown of mRNA , 2003, Nature Biotechnology.

[55]  I. Verma,et al.  Gene therapy with viral vectors. , 2003, Annual review of pharmacology and toxicology.

[56]  William M. Shih,et al.  A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron , 2004, Nature.

[57]  N. Seeman,et al.  A precisely controlled DNA biped walking device , 2004 .

[58]  Nadrian C Seeman,et al.  A protein-driven DNA device that measures the excess binding energy of proteins that distort DNA. , 2004, Angewandte Chemie.

[59]  D. C. Lin,et al.  Mechanical properties of a reversible, DNA-crosslinked polyacrylamide hydrogel. , 2004, Journal of biomechanical engineering.

[60]  Yi Lu,et al.  Adenosine-dependent assembly of aptazyme-functionalized gold nanoparticles and its application as a colorimetric biosensor. , 2004, Analytical chemistry.

[61]  J. Reif,et al.  A unidirectional DNA walker that moves autonomously along a track. , 2004, Angewandte Chemie.

[62]  Friedrich C. Simmel,et al.  Transcriptional control of DNA-based nanomachines , 2004 .

[63]  Chengde Mao,et al.  Molecular gears: a pair of DNA circles continuously rolls against each other. , 2004, Journal of the American Chemical Society.

[64]  Naftali Tishby,et al.  Stochastic computing with biomolecular automata , 2004, Proc. Natl. Acad. Sci. USA.

[65]  E. Shapiro,et al.  An autonomous molecular computer for logical control of gene expression , 2004, Nature.

[66]  N. Pierce,et al.  A synthetic DNA walker for molecular transport. , 2004, Journal of the American Chemical Society.

[67]  R. Breaker,et al.  Gene regulation by riboswitches , 2004, Nature Reviews Molecular Cell Biology.

[68]  Friedrich C Simmel,et al.  A DNA-based machine that can cyclically bind and release thrombin. , 2004, Angewandte Chemie.

[69]  Farren J. Isaacs,et al.  Engineered riboregulators enable post-transcriptional control of gene expression , 2004, Nature Biotechnology.

[70]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature reviews genetics.

[71]  A. Heeger,et al.  Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor. , 2005, Angewandte Chemie.

[72]  Razvan Nutiu,et al.  Aptamers with fluorescence-signaling properties. , 2005, Methods.

[73]  U. Gerland,et al.  DNA as a programmable viscoelastic nanoelement. , 2005, Biophysical journal.

[74]  Koji Sode,et al.  Novel electrochemical sensor system for protein using the aptamers in sandwich manner. , 2005, Biosensors & bioelectronics.

[75]  D. Endy Foundations for engineering biology , 2005, Nature.

[76]  M. Mascini,et al.  Aptamer-based biosensors for the detection of HIV-1 Tat protein. , 2005, Bioelectrochemistry.

[77]  M. Elowitz,et al.  Reconstruction of genetic circuits , 2005, Nature.

[78]  A. Schätzlein,et al.  Dendrimers in gene delivery. , 2005, Advanced drug delivery reviews.

[79]  Russell P. Goodman,et al.  Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication , 2005, Science.

[80]  Sivan Yogev,et al.  Parallel biomolecular computation on surfaces with advanced finite automata. , 2005, Journal of the American Chemical Society.

[81]  Dmitry M Kolpashchikov,et al.  Boolean control of aptamer binding states. , 2005, Journal of the American Chemical Society.

[82]  M. Levy,et al.  Quantum‐Dot Aptamer Beacons for the Detection of Proteins , 2005, Chembiochem : a European journal of chemical biology.

[83]  Juewen Liu,et al.  Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. , 2005, Angewandte Chemie.

[84]  J. Hadgraft,et al.  The use of colloidal microgels as a (trans)dermal drug delivery system. , 2005, International journal of pharmaceutics.

[85]  Tibor Hianik,et al.  Detection of aptamer-protein interactions using QCM and electrochemical indicator methods. , 2005, Bioorganic & medicinal chemistry letters.

[86]  A. Turberfield,et al.  A free-running DNA motor powered by a nicking enzyme. , 2005, Angewandte Chemie.

[87]  Itamar Willner,et al.  Endonuclease-based logic gates and sensors using magnetic force-amplified readout of DNA scission on cantilevers. , 2005, Journal of the American Chemical Society.

[88]  Eun Jeong Cho,et al.  Production and processing of aptamer microarrays. , 2005, Methods.

[89]  Razvan Nutiu,et al.  A DNA-protein nanoengine for "on-demand" release and precise delivery of molecules. , 2005, Angewandte Chemie.

[90]  Travis S. Bayer,et al.  Programmable ligand-controlled riboregulators of eukaryotic gene expression , 2005, Nature Biotechnology.

[91]  Kevin W Plaxco,et al.  A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement. , 2005, Journal of the American Chemical Society.

[92]  Joachim O Rädler,et al.  Using gene regulation to program DNA-based molecular devices. , 2005, Small.

[93]  N. Seeman From genes to machines: DNA nanomechanical devices. , 2005, Trends in biochemical sciences.

[94]  D. Guyer,et al.  Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease , 2006, Nature Reviews Drug Discovery.

[95]  Tim Liedl,et al.  A surface-bound DNA switch driven by a chemical oscillator. , 2006, Angewandte Chemie.

[96]  P. Rothemund Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[97]  Soong Ho Um,et al.  Enzyme-catalysed assembly of DNA hydrogel , 2006, Nature materials.

[98]  S. Balasubramanian,et al.  A reversible pH-driven DNA nanoswitch array. , 2006, Journal of the American Chemical Society.

[99]  Itamar Willner,et al.  A virus spotlighted by an autonomous DNA machine. , 2006, Angewandte Chemie.

[100]  N. Sugimoto,et al.  DNA logic gates based on structural polymorphism of telomere DNA molecules responding to chemical input signals. , 2006, Angewandte Chemie.

[101]  E. Winfree,et al.  Construction of an in vitro bistable circuit from synthetic transcriptional switches , 2006, Molecular systems biology.

[102]  Andrew J Turberfield,et al.  Single-molecule protein encapsulation in a rigid DNA cage. , 2006, Angewandte Chemie.

[103]  J. Hoheisel Microarray technology: beyond transcript profiling and genotype analysis , 2006, Nature Reviews Microbiology.

[104]  Farren J. Isaacs,et al.  RNA synthetic biology , 2006, Nature Biotechnology.

[105]  D. H. Burke,et al.  HIV-1 inactivation by nucleic acid aptamers. , 2006, Frontiers in bioscience : a journal and virtual library.

[106]  Itamar Willner,et al.  Concatenated logic gates using four coupled biocatalysts operating in series , 2006, Proceedings of the National Academy of Sciences.

[107]  Chengde Mao,et al.  Antibody Nanoarrays with a Pitch of ∼20 Nanometers , 2006 .

[108]  A. Keefe,et al.  Properties of Therapeutic Aptamers , 2006 .

[109]  Juewen Liu,et al.  Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. , 2006, Current opinion in biotechnology.

[110]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .

[111]  Hao Yan,et al.  Self-assembled signaling aptamer DNA arrays for protein detection. , 2006, Angewandte Chemie.

[112]  Andrew J Turberfield,et al.  DNA hairpins: fuel for autonomous DNA devices. , 2006, Biophysical journal.

[113]  Erik Winfree,et al.  Catalyzed relaxation of a metastable DNA fuel. , 2006, Journal of the American Chemical Society.

[114]  Paul W. K. Rothemund,et al.  Rothemund, P.W.K.: Folding DNA to create nanoscale shapes and patterns. Nature 440, 297-302 , 2006 .

[115]  D. Bunka,et al.  Aptamers come of age – at last , 2006, Nature Reviews Microbiology.

[116]  Intramers for Protein Function Analysis and Drug Discovery , 2006 .

[117]  Friedrich C. Simmel,et al.  A modular DNA signal translator for the controlled release of a protein by an aptamer , 2006, Nucleic acids research.

[118]  Anne Condon,et al.  Designed DNA molecules: principles and applications of molecular nanotechnology , 2006, Nature Reviews Genetics.

[119]  Itamar Willner,et al.  Autonomous fueled mechanical replication of nucleic acid templates for the amplified optical detection of DNA. , 2006, Angewandte Chemie.

[120]  Nadrian C Seeman,et al.  RNA used to control a DNA rotary nanomachine. , 2006, Nano letters.

[121]  Itamar Willner,et al.  DNA-based machines. , 2006, Organic & biomolecular chemistry.

[122]  F. Simmel,et al.  Controlled trapping and release of quantum dots in a DNA-switchable hydrogel. , 2007, Small.

[123]  Chunhai Fan,et al.  A target-responsive electrochemical aptamer switch (TREAS) for reagentless detection of nanomolar ATP. , 2007, Journal of the American Chemical Society.

[124]  Ehud Keinan,et al.  A Programmable Biomolecular Computing Machine with Bacterial Phenotype Output , 2007, Chembiochem : a European journal of chemical biology.

[125]  R. Weiss,et al.  A universal RNAi-based logic evaluator that operates in mammalian cells , 2007, Nature Biotechnology.

[126]  Friedrich C Simmel,et al.  Controlling DNA Polymerization with a Switchable Aptamer , 2007, Chembiochem : a European journal of chemical biology.

[127]  I. Willner,et al.  Amplified analysis of low-molecular-weight substrates or proteins by the self-assembly of DNAzyme-aptamer conjugates. , 2007, Journal of the American Chemical Society.

[128]  Itamar Willner,et al.  The aggregation of Au nanoparticles by an autonomous DNA machine detects viruses. , 2007, Small.

[129]  Itamar Willner,et al.  Spotlighting of cocaine by an autonomous aptamer-based machine. , 2007, Journal of the American Chemical Society.

[130]  Natasa Jonoska,et al.  Trends in computing with DNA , 2008, Journal of Computer Science and Technology.