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Posts Tagged ‘DNA nanotechnology’


9:20AM 11/12/2014 – 10th Annual Personalized Medicine Conference at the Harvard Medical School, Boston

REAL TIME Coverage of this Conference by Dr. Aviva Lev-Ari, PhD, RN – Director and Founder of LEADERS in PHARMACEUTICAL BUSINESS INTELLIGENCE, Boston http://pharmaceuticalintelligence.com

9:20 a.m. Panel Discussion – Genomic Technologies

Genomic Technologies

The greatest impetus for personalized medicine is the initial sequencing of the human genome at the beginning of this Century. As we began to recognize the importance of genetic factors in human health and disease, efforts to understand genetic variation and its impact on health have accelerated. It was estimated that it cost more than two billion dollars to sequence the first human genome and reduction in the cost of sequence became an imperative to apply this technology to many facets of risk assessment, diagnosis, prognosis and therapeutic intervention. This panel will take a brief historical look back at how the technologies have evolved over the last 15 years and what the future holds and how these technologies are being applied to patient care.

Genomic Technologies

Opening Speaker and Moderator:

George Church, Ph.D.
Professor of Genetics, Harvard Medical School; Director, Personal Genomics

Genomic Technologies and Sequencing

  • highly predictive, preventative
  • non predictive

Shareable Human Genomes Omics Standards

$800 Human Genome Sequence – Moore’s Law does not account for the rapid decrease in cost of Genome Sequencing

Genome Technologies and Applications

  • Genia nanopore – battery operated device
  • RNA & protein traffic
  • Molecular Stratification Methods – more than one read, sequence ties
  • Brain Atlas  – transcriptome of mouse brains
  • Multigenics – 700 genes: hGH therapies

Therapies

  • vaccine
  • hygiene
  • age

~1970 Gene Therapy in Clinical Trials

Is Omic technologies — a Commodity?

  • Some practices will have protocols
  • other will never become a commodity

 

Panelists:

Sam Hanash, M.D., Ph.D. @MDAndersonNews

Director, Red & Charline McCombs Institute for Early Detection & Treatment of Cancer MD Anderson Cancer Center

Heterogeneity among Cancer cells. Data analysis and interpretation is very difficult, back up technology

Proteins and Peptides before analysis with spectrometry:

  • PM  – Immunotherapy approaches need be combined with other techniques
  • How modification in protein type affects disease
  • amplification of an aberrant protein – when that happens cancer developed. Modeling on a CHip of peptide synthesizer

Mark Stevenson @servingscience

Executive Vice President and President, Life Sciences Solutions
Thermo Fisher Scientific

Issues of a Diagnostics Developer:

  • FDA regulation, need to test on several tissues
  • computational environment
  • PCR, qPCR – cost effective
  • BGI – competitiveness

Robert Green, MD @BrighamWomens

Partners, Health Care Personalized Medicine — >>Disclosure: Illumina and three Pharmas

Innovative Clinical Trial: Alzheimer’s Disease, integration of sequencing with drug development

  • Population based screening with diagnosis
  • Cancer predisposition: Cost, Value, BRCA
  • epigenomics technologies to be integrated
  • Real-time diagnostics
  • Screening makes assumption on Predisposition
  • Public Health view: Phenotypes in the Framingham Studies: 64% pathogenic genes were prevalent – complication based in sequencing.

Questions from the Podium:

  • Variants analysis
  • Metastasis different than solid tumor itself – Genomics will not answer issues related to tumor in special tissues variability

 

 

 

 

– See more at: http://personalizedmedicine.partners.org/Education/Personalized-Medicine-Conference/Program.aspx#sthash.qGbGZXXf.dpuf

@HarvardPMConf

#PMConf

@SachsAssociates

 

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Author: Tilda Barliya PhD

The field of DNA and RNA nanotechnologies  are considered one of the most dynamic research areas in the field of drug delivery in molecular medicine. Both DNA and RNA have a wide aspect of medical application including: drug deliveries, for genetic immunization, for metabolite and nucleic acid detection, gene regulation, siRNA delivery for cancer treatment (I), and even analytical and therapeutic applications.

Seeman (6,7) pioneered the concept 30 years ago of using DNA as a material for creating nanostructures; this has led to an explosion of knowledge in the now well-established field of DNA nanotechnology. The unique properties in terms of free energy, folding, noncanonical base-pairing, base-stacking, in vivo transcription and processing that distinguish RNA from DNA provides sufficient rationale to regard RNA nanotechnology as its own technological discipline. Herein, we will discuss the advantages of DNA nanotechnology and it’s use in medicine.

So What is the rational of using DNA nanotechnology(3)?

  • Genetic studies – its application in various biological fields like biomedicine, cancer research, medical devices  and genetic engineering.
  • Its unique properties of structural stability, programmability of sequences, and predictable self-assembly.
DNA origami

Structures made from DNA using the DNA-origami method (Rothemund, 2006)

Structural DNA nanotechnology rests on three pillars: [1] Hybridization; [2] Stably branched DNA; and [3] Convenient synthesis of designed sequences.

Hybridization

Hybridization. The self-association (self=assembly) of complementary nucleic acid molecules or parts of molecules, is implicit in all aspects of structural DNA nanotechnology. Individual motifs are formed by the hybridization of strands designed to produce particular topological species. A key aspect of hybridization is the use of sticky ended cohesion to combine pieces of linear duplex DNA; this has been a fundamental component of genetic engineering for over 35 years (7). Not only is hybridization critical to the formation of structure, but it is deeply involved in almost all the sequence-dependent nanomechanical devices that have been constructed, and it is central to many attempts to build structural motifs in a sequential fashion (7,8 ).

Stably Branched DNA

branched DNA molecules are central to DNA nanotechnology. It is the combination of in vitro hybridization and synthetic branched DNA that leads to the ability to use DNA as a construction material. Such branched DNA is thought to be intermediates in genetic recombination (such as Holliday junctions).

Convenient Synthesis of Designed Sequences

Biologically derived branched DNA molecules, such as Holliday junctions, are inherently unstable, because they exhibit sequence symmetry; i.e., the four strands actually consist of two pairs of strands with the same sequence. This symmetry enables an isomerization known as branch migration that allows the branch point to relocate.  DNA nanotechnology entailed sequence design that attempted to minimize sequence symmetry in every way possible.

One of the most remarkable innovations in structural DNA-nanotechnology in recent years is DNA origami, which was invented in 2006 by Paul Rothemund (1) (see Fig above). DNA origami utilizes the genome from a virus together with a large number of shorter DNA strands to enable the creation of numerous DNA-based structures (Figure 1). The shorter DNA strands forces the long viral DNA to fold into a pattern that is defined by the interaction between the long and the short DNA strands (1,2).

Rothemund believes that an  application of patterned DNA origami would be the creation of a ‘nanobreadboard’, to which diverse components could be added. The attachment of proteins23, for example, might allow novel biological experiments aimed at modelling complex protein assemblies and examining the effects of spatial organization, whereas molecular electronic or plasmonic circuits might be created by attaching nanowires, carbon nanotubes or gold nanoparticles (1).

DNA nanotechnology and Biological Application

The physical and chemical properties of nanomaterials such as polymers, semiconductors, and metals present diverse advantages for various in vivo applications (3,9 ). For example:

  • Therapeutics – In cancer for example, nanosystems that are designed from biological materials such as DNA and RNA are ‘programmed’ to be able to evade most, if not all, drug-resistance mechanisms. Based on these properties, most nanosystems are able to deliver high concentrations of drugs to cancer cells while curtailing damage to surrounding healthy cells (2b, 3, 9, 11, 15).
  • Biosensors – capable of picking up very specific biological signals and converting them into electrical outputs that can be analyzed for identification. Biosensors are efficient as they have a high ratio of surface area to volume as well as adjustable electronic, magnetic, optical, and biological properties (3, 12, 13, 14).
  • **Amin and colleagues have developed a biotinylated DNA thin film-coated fiber optic reflectance biosensor for the detection of streptavidin aerosols. DNA thin films were prepared by dropping DNA samples into a polymer optical fiber which responded quickly to the specific biomolecules in the atmosphere. This approach of coating optical fibers with DNA nanostructures could be very useful in the future for detecting atmospheric bio-aerosols with high sensitivity and specificity (3, 14)
  • Computing – Another aspect uses the programmability of DNA to create devices that are capable of computing. Here, the structure of the assembled DNA is not of primary interest. Instead, control of the DNA sequence is used in the creation of computational algorithms, like e.g. artificial neural networks. Qian et al for example, built on the richness of DNA computing and strand displacement circuitry, they showed how molecular systems can exhibit autonomous brain-like behaviours. Using a simple DNA gate architecture that allows experimental scale-up of multilayer digital circuits, they systematically transform arbitrary linear threshold circuits (an artificial neural network model) into DNA strand displacement cascades that function as small neural networks (3, 10).
  • Additional features: 3rd generation DNA sequencers (II), Biomimetic systems, Energy transfer and photonics etc

Summary:

DNA nanotechnology is an evolving field that affects medicine, computation, material sciences, and physics. DNA nanostructures offer unprecedented control over shape, size, mechanical flexibility and anisotropic surface  modification. Clearly, proper control over these aspects can increase  circulation times by orders of magnitude, as can be seen for longcirculating particles such as erythrocytes and various pathogenic particles evolved to overcome this issue.  The use of DNA in DNA/protein-based matrices makes these structures inherently amenable to structural tunability. More research in this direction  will certainly be developed, making DNA a promising biomaterial  in tissue engineering. future development of novel ways in which DNA would be utilized to have a much more comprehensive role in biological computation and data storage is envisaged.

REFERENCES

1. Paul W. K. Rothemund. Folding DNA to create nanoscale shapes and patterns. NATURE 2006 (March 16)|Vol 440: 297-302. http://www.nature.com/nature/journal/v440/n7082/full/nature04586.html

http://www.dna.caltech.edu/Papers/DNAorigami-nature.pdf

2. Andre V. Pinheiro, Dongran Han, William M. Shih and Hao Yan. Challenges and opportunities for structural DNA nanotechnology. Nature Nanotechnology 2011 Dec | VOL 6: 763-772.  http://www.nature.com/nnano/journal/v6/n12/pdf/nnano.2011.187.pdf

2b. Thi Huyen La, Thi Thu Thuy Nguyen, Van Phuc Pham, Thi Minh Huyen Nguyen and Quang Huan Le.  Using DNA nanotechnology to produce a drug delivery system. Adv. Nat. Sci.: Nanosci. Nanotechnol. 4 (2013) 015002 (7pp). http://iopscience.iop.org/2043-6262/4/1/015002http://iopscience.iop.org/2043-6262/4/1/015002/pdf/2043-6262_4_1_015002.pdf

3. Muniza Zahid, Byeonghoon Kim, Rafaqat Hussain, Rashid Amin and Sung H Park. DNA nanotechnology: a future perspective. Nanoscale Research Letters 2013, 8:119. http://www.nanoscalereslett.com/content/8/1/119

4.By: Cientifica Ltd 2007. The Nanotech Revolution in Drug Delivery.  http://www.cientifica.com/WhitePapers/054_Drug%20Delivery%20White%20Paper.pdf

5. Gemma Campbell. Nanotechnology and its implications for the health of the E.U citizen: Diagnostics, drug discovery and drug delivery. Institute of Nanotechnology and Nanoforum. http://www.nano.org.uk/nanomednet/images/stories/Reports/diagnostics,%20drug%20discovery%20and%20drug%20delivery.pdf

6.Peixuan Guo., Haque F., Brent Hallahan, Randall Reif and Hui Li. Uniqueness, Advantages, Challenges, Solutions, and Perspectives in Therapeutics Applying RNA Nanotechnology. Nucleic Acid Ther. 2012 August; 22(4): 226–245. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426230/

7. SEEMAN N.C. Nanomaterials based on DNA. Annu. Rev. Biochem. 2010;79:65–87. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3454582/

8. Yin P, Choi HMT, Calvert CR, Pierce NA. Programming biomolecular self-assembly pathways. Nature.2008;451:318–323.  http://www.ncbi.nlm.nih.gov/pubmed/18202654

9. Yan Lee P, Wong KY: Nanomedicine: a new frontier in cancer therapeutics. Curr Drug Deliv 2011, 8(3):245-253. OpenURLhttp://www.eurekaselect.com/73728/article

10. Qian, L.L., Winfree, E., and Bruck, J. Neural Network Computation with DNA Strand Displacement Cascades. Nature 2011 475, 368-372.  http://www.nature.com/nature/journal/v475/n7356/full/nature10262.html

11. Acharya S, Dilnawaz F, Sahoo SK: Targeted epidermal growth factor receptor nanoparticle bioconjugates for breast cancer therapy. Biomaterials 2009, 30(29):5737-5750. http://www.sciencedirect.com/science/article/pii/S0142961209006929

12. Bohunicky B, Mousa SA: Biosensors: the new wave in cancer diagnosisNanotechnology, Science and Applications 2011, 4:1-10. http://www.dovepress.com/biosensors-the-new-wave-in-cancer-diagnosis-peer-reviewed-article-NSA-recommendation1

13. Sanvicens N, Mannelli I, Salvador J, Valera E, Marco M: Biosensors for pharmaceuticals based on novel technologyTrends Anal Chem 2011, 30:541-553. http://www.sciencedirect.com/science/article/pii/S016599361100015X

14. Amin R, Kulkarni A, Kim T, Park SH: DNA thin film coated optical fiber biosensorCurr Appl Phys 2011, 12(3):841-845. http://www.sciencedirect.com/science/article/pii/S1567173911005888

15. Choi, Y.; Baker, J. R. Targeting Cancer Cells with DNA Assembled Dendrimers: A Mix and Match Strategy for Cancer. Cell Cycle 2005, 4, 669–671. http://www.ncbi.nlm.nih.gov/pubmed/15846063  http://www.landesbioscience.com/journals/cc/article/1684/

Other related articles on this Open Access Online Scientific Journal include the following

I. By: Ziv Raviv PhD. The Development of siRNA-Based Therapies for Cancer. https://pharmaceuticalintelligence.com/2013/05/09/the-development-of-sirna-based-therapies-for-cancer/

II. By: Tilda Barliya PhD. Nanotechnology, personalized medicine and DNA sequencing. https://pharmaceuticalintelligence.com/2013/01/09/nanotechnology-personalized-medicine-and-dna-sequencing/

III. By: Larry Bernstein MD FACP. DNA Sequencing Technology. https://pharmaceuticalintelligence.com/2013/03/03/dna-sequencing-technology/

IV. By: Venkat S Karra PhD. Measuring glucose without needle pricks: nano-sized biosensors made the test easy. https://pharmaceuticalintelligence.com/2012/09/04/measuring-glucose-without-needle-pricks-nano-sized-biosensors-made-the-test-easy/

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