Abstract
Five decades of research and practical application of computers in biomedicine has given rise to the discipline of medical informatics, which has made many advances in genomic and translational medicine possible. Developments in nanotechnology are opening up the prospects for nanomedicine and regenerative medicine where informatics and DNA computing can become the catalysts enabling health care applications at sub-molecular or atomic scales. Although nanomedicine promises a new exciting frontier for clinical practice and biomedical research, issues involving cost-effectiveness studies, clinical trials and toxicity assays, drug delivery methods, and the implementation of new personalized therapies still remain challenging. Nanoinformatics can accelerate the introduction of nano-related research and applications into clinical practice, leading to an area that could be called “translational nanoinformatics.” At the same time, DNA and RNA computing presents an entirely novel paradigm for computation. Nanoinformatics and DNA-based computing are together likely to completely change the way we model and process information in biomedicine and impact the emerging field of nanomedicine most strongly. In this article, we review work in nanoinformatics and DNA (and RNA)-based computing, including applications in nanopediatrics. We analyze their scientific foundations, current research and projects, envisioned applications and potential problems that might arise from them.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
Abbreviations
- BMI:
-
biomedical informatics
- NPO:
-
nanoparticle ontology
- NCI:
-
national cancer institute
References
Zheng G, Patolsky F, Cui Y, Wang WU, Lieber CM 2005 Multiplexed electrical detection of cancer markers with nanowire sensor arrays. Nat Biotechnol 23: 1294–1301
Papagiannaros A, Levchenko T, Hartner W, Mongayt D, Torchilin V 2009 Quantum dots encapsulated in phospholipid micelles for imaging and quantification of tumors in the near-infrared region. Nanomedicine 5: 216–224
Leary SP, Liu CY, Apuzzo ML 2006 Toward the emergence of nanoneurosurgery: part II—nanomedicine: diagnostics and imaging at the nanoscale level. Neurosurgery 58: 805–823
Jain K 2008 The Handbook of Nanomedicine. Humana Press, New Jersey, pp 161–192
Freitas RA 2005 What is nanomedicine?. Nanomedicine 1: 2–9
Iyer AK, Khaled G, Fang J, Maeda H 2006 Exploiting the enhanced permeability and retention effect for tumor targeting. Drug Discov Today 11: 812–818
De Jong WH, Borm PJ 2008 Drug delivery and nanoparticles: applications and hazards. Int J Nanomedicine 3: 133–149
Malam Y, Loizidou M, Seifalian AM 2009 Liposomes and nanoparticles: nanosized vehicles for drug delivery in cancer. Trends Pharmacol Sci 30: 592–599
Storhoff JJ, Marla SS, Bao P, Hagenow S, Mehta H, Lucas A, Garimella V, Patno T, Buckingham W, Cork W, Müller UR 2004 Gold nanoparticle-based detection of genomic DNA targets on microarrays using a novel optical detection system. Biosens Bioelectron 19: 875–883
Dufès C, Uchegbu IF, Schätzlein AG 2005 Dendrimers in gene delivery. Adv Drug Deliv Rev 57: 2177–2202
Ozdemir V, Williams-Jones B, Glatt SJ, Tsuang MT, Lohr JB, Reist C 2006 Shifting emphasis from pharmacogenomics to theragnostics. Nat Biotechnol 24: 942–946
Harisinghani MG, Barentsz J, Hahn PF, Deserno WM, Tabatabaei S, van de Kaa CH, de la Rosette J, Weissleder R 2003 Noninvasive detection of clinically occult lymph-node metastases in prostate cancer. N Engl J Med 348: 2491–2499
Gradishar WJ 2006 Albumin-bound paclitaxel: a next-generation taxane. Expert Opin Pharmacother 7: 1041–1053
Maheswaran S, Sequist LV, Nagrath S, Ulkus L, Brannigan B, Collura CV, Inserra E, Diederichs S, Iafrate AJ, Bell DW, Digumarthy S, Muzikansky A, Irimia D, Settleman J, Tompkins RG, Lynch TJ, Toner M, Haber DA 2008 Detection of mutations in EGFR in circulating lung-cancer cells. N Engl J Med 359: 366–377
Nagrath S, Sequist LV, Maheswaran S, Bell DW, Irimia D, Ulkus L, Smith MR, Kwak EL, Digumarthy S, Muzikansky A, Ryan P, Balis UJ, Tompkins RG, Haber DA, Toner M 2007 Isolation of rare circulating tumour cells in cancer patients by microchip technology. Nature 450: 1235–1239
Frey LJ, Maojo V, Mitchell JA 2007 Bioinformatics linkage of heterogeneous clinical and genomic information in support of personalized medicine. Yearb Med Inform: 98–105. Erratum in: Yearb Med Inform 2008: 19, 2007
McCabe ER 2010 nanopediatrics: enabling personalized medicine for children. Pediatr Res 67: 453–457
Marin S, Merkoci 2009 A direct electrochemical stripping detection of cystic-fibrosis-related DNA linked through cadmium sulfide quantum dots. Nanotechnology 20: 55101
Mortensen NP, Fowlkes JD, Sullivan CJ, Allison DP, Larsen NB, Molin S, Doktycz MJ 2009 Effects of colistin on surface ultrastructure and nanomechanics of Pseudomonas aeruginosa cells. Langmuir 25: 3728–3733
Dames P, Gleich B, Flemmer A, Hajek K, Seidl N, Wiekhorst F, Eberbeck D, Bittmann I, Bergemann C, Weyh T, Trahms L, Rosenecker J, Rudolph C 2007 Targeted delivery of magnetic aerosol droplets to the lung. Nat Nanotechnol 2: 495–499
Stone V, Johnston H, Clift MJ 2007 Air pollution, ultrafine and nanoparticle toxicology: cellular and molecular interactions. IEEE Trans Nanobioscience 6: 331–340
Dobson J 2007 Toxicological aspects and applications of nanoparticles in paediatric respiratory disease. Paediatr Respir Rev 8: 62–66
Service RF 2004 Nanotoxicology. Nanotechnology grows up. Science 304: 1732–1734
Anguita A, Martín L, Crespo J, Tsiknakis M 2008 An ontology-based method to solve query identifier heterogeneity in post-genomic clinical trials. Stud Health Technol Inform 136: 3–8
McCusker JP, Phillips JA, Beltrán AG, Finkelstein A, Krauthammer M 2009 Semantic web data warehousing for caGrid. BMC Bioinformatics 10: S2
Alonso-Calvo R, Maojo V, Billhardt H, Martin-Sanchez F, García-Remesal M, Perez-Rey D 2007 An agent- and ontology-based system for integrating public gene, protein, and disease databases. J Biomed Inform 40: 17–29
Perez-Rey D, Maojo V, García-Remesal M, Alonso-Calvo R, Billhardt H, Martin-Sanchez F, Sousa A 2006 ONTOFUSION: ontology-based integration of genomic and clinical databases. Comput Biol Med 36: 712–730
Tomalia DA 2009 In quest of a systematic framework for unifying and defining nanoscience. J Nanopart Res 11: 1251–1310
Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA 2009 BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 37 (Web Server issue): W170–W173
Brazas MD, Fox JA, Brown T, McMillan S, Ouellette BF 2008 Keeping pace with the data: 2008 update on the bioinformatics links directory. Nucleic Acids Res 36 (Web Server issue): W2–W4
de la Calle G, García-Remesal M, Chiesa S, de la Iglesia D, Maojo V 2009 BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature. BMC Bioinformatics 10: 320–328
Chiesa S, García-Remesal M, de la Calle G, de la Iglesia D, Bankauskaite V, Maojo V 2010 Building an index of nanomedical resources: an automatic approach based on text mining. In: Lovrek I, Howlett RJ, Jain LC (eds) Knowledge-Based Intelligent Information and Engineering Systems. Springer-Verlag, Berlin, pp 50–57
Chiesa S, De La Iglesia D, Crespo J, Martin-Sanchez F, Kern J, Potamias G, Maojo V 2009 European efforts in nanoinformatics research applied to nanomedicine. Stud Health Technol Inform 150: 757–761
Brazma A 2009 Minimum Information About a Microarray Experiment (MIAME)–successes, failures, challenges. Scientific WorldJournal 9: 420–423
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Consortium OB, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S 2007 The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25: 1251–1255
Thomas DG, Pappu RV, Baker NA 2009 Ontologies for cancer nanotechnology research. Conf Proc IEEE Eng Med Biol Soc 1: 4158–4161
Gowers T, Nielsen M 2009 Massively collaborative mathematics. Nature 461: 879–881
Roukes M 2001 Plenty of room, indeed. Sci Am 285: 48–51: 54-57
Blois MS 1994 Information and Medicine: The Nature of Medical Descriptions. University of California Press, Berkeley, CA, pp 1–37
Purnick PE, Weiss R 2009 The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10: 410–422
Endy D 2005 Foundations for engineering biology. Nature 438: 449–453
Amos M 2005 Models of molecular computation. Theoretical and Experimental DNA Computation. Springer-Verlag, Berlin, pp 45–70
Adleman LM 1994 Molecular computation of solutions to combinatorial problems. Science 266: 1021–1024
Benenson Y, Paz-Elitzur T, Adar R, Keinan E, Livneh Z, Shapiro E 2001 Programmable and autonomous computing machine made of biomolecules. Nature 414: 430–434
Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E 2004 An autonomous molecular computer for logical control of gene expression. Nature 429: 423–429
Shapiro E, Benenson Y 2006 Tapping the computing power of biological molecules gives rise to tiny machines that can speak directly to living cells. Sci Am 295: 44–51
Seelig G, Soloveichik D, Zhang DY, Winfree E 2006 Enzyme-free nucleic acid logic circuits. Science 314: 1585–1588
Zhang DY, Turberfield AJ, Yurke B, Winfree E 2007 Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318: 1121–1125
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC 1998 Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806–811
Isaacs FJ, Dwyer DJ, Collins JJ 2006 RNA synthetic biology. Nat Biotechnol 24: 545–554
Davidson EA, Ellington AD 2007 Synthetic RNA circuits. Nat Chem Biol 3: 23–28
Win MN, Smolke CD 2008 Higher-order cellular information processing with synthetic RNA devices. Science 322: 456–460
Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R, Benenson Y 2007 A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 25: 795–801
Miró Bueno JM, Rodríguez-Patón A 2009 A new model of synthetic genetic oscillator based on trans-acting repressor ribozyme. In: Omatu S, Rocha MP, Bravo J, Fernández-Riverola F, Corchado E, Bustillo A, Corchado JM (eds) Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. Springer-Verlag, Berlin, pp 1170–1177
Stojanovic MN, Stefanovic D 2003 A deoxyribozyme-based molecular automaton. Nat Biotechnol 21: 1069–1074
Weiss R, Homsy GE, Knight TF 2002 Toward in vivo digital circuits. In: Landweber LF, Winfree E (eds) Evolution as Computation: DIMACS Workshop. Springer-Verlag, Berlin, pp 275–295
Simmel FC 2007 Towards biomedical applications for nucleic acid nanodevices. Nanomedicine 2: 817–830
Benenson Y 2009 Biocomputers: from test tubes to live cells. Mol Biosyst 5: 675–685
Author information
Authors and Affiliations
Corresponding author
Additional information
Supported, in part, by the European Commission (Action-Grid project), the Ministry of Science and Innovation of Spain (COMBIOMED RETICS, FIS and the ONTOMINEBASE project), and the Comunidad de Madrid.
Rights and permissions
About this article
Cite this article
Maojo, V., Martin-Sanchez, F., Kulikowski, C. et al. Nanoinformatics and DNA-Based Computing: Catalyzing Nanomedicine. Pediatr Res 67, 481–489 (2010). https://doi.org/10.1203/PDR.0b013e3181d6245e
Received:
Accepted:
Issue date:
DOI: https://doi.org/10.1203/PDR.0b013e3181d6245e
This article is cited by
-
Nanoinformatics and biomolecular nanomodeling: a novel move en route for effective cancer treatment
Environmental Science and Pollution Research (2020)
-
High-performance biosensing based on autonomous enzyme-free DNA circuits
Topics in Current Chemistry (2020)
-
Nanoinformatics: developing new computing applications for nanomedicine
Computing (2012)
