Posts Tagged ‘hybridization’

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. 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


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.


1. Paul W. K. Rothemund. Folding DNA to create nanoscale shapes and patterns. NATURE 2006 (March 16)|Vol 440: 297-302.

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.

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).

3. Muniza Zahid, Byeonghoon Kim, Rafaqat Hussain, Rashid Amin and Sung H Park. DNA nanotechnology: a future perspective. Nanoscale Research Letters 2013, 8:119.

4.By: Cientifica Ltd 2007. The Nanotech Revolution in Drug Delivery.

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.,%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.

7. SEEMAN N.C. Nanomaterials based on DNA. Annu. Rev. Biochem. 2010;79:65–87.

8. Yin P, Choi HMT, Calvert CR, Pierce NA. Programming biomolecular self-assembly pathways. Nature.2008;451:318–323.

9. Yan Lee P, Wong KY: Nanomedicine: a new frontier in cancer therapeutics. Curr Drug Deliv 2011, 8(3):245-253. OpenURL

10. Qian, L.L., Winfree, E., and Bruck, J. Neural Network Computation with DNA Strand Displacement Cascades. Nature 2011 475, 368-372.

11. Acharya S, Dilnawaz F, Sahoo SK: Targeted epidermal growth factor receptor nanoparticle bioconjugates for breast cancer therapy. Biomaterials 2009, 30(29):5737-5750.

12. Bohunicky B, Mousa SA: Biosensors: the new wave in cancer diagnosisNanotechnology, Science and Applications 2011, 4:1-10.

13. Sanvicens N, Mannelli I, Salvador J, Valera E, Marco M: Biosensors for pharmaceuticals based on novel technologyTrends Anal Chem 2011, 30:541-553.

14. Amin R, Kulkarni A, Kim T, Park SH: DNA thin film coated optical fiber biosensorCurr Appl Phys 2011, 12(3):841-845.

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.

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.

II. By: Tilda Barliya PhD. Nanotechnology, personalized medicine and DNA sequencing.

III. By: Larry Bernstein MD FACP. DNA Sequencing Technology.

IV. By: Venkat S Karra PhD. Measuring glucose without needle pricks: nano-sized biosensors made the test easy.


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Reporter and Curator: Dr. Sudipta Saha, Ph.D.

A number of novel genes have been identified in association with a variety of endocrine phenotypes over the last few years. However, although mutations in a number of genes have been described in association with disorders such as

  • hypogonadotropic hypogonadism,
  • congenital hypopituitarism,
  • disorders of sex development, and
  • congenital hyperinsulinism,

these account for a minority of patients with these conditions, suggesting that many more genes remain to be identified.

How will these novel genes be identified? Monogenic disorders can arise as a result of genomic microdeletions or microduplications, or due to single point mutations that lead to a functional change in the relevant protein. Such disorders may also result from altered expression of a gene, and hence altered dosage of the protein. Candidate genes may be identified by utilizing naturally occurring or transgenic mouse models, and this approach has been particularly informative in the elucidation of the genetic basis of a number of disorders.

Other approaches include the identification of chromosomal rearrangements using conventional karyotyping techniques, as well as novel assays such as array comparative genomic hybridization (CGH) and single nucleotide polymorphism oligonucleotide arrays (SNP arrays). These molecular methods usually result in the identification of gross abnormalities as well as submicroscopic deletions and duplications, and eventually to the discovery of single gene defects that are associated with a particular phenotype.

However, there is no doubt that the major advances in novel gene identification will be made as a result of the sequencing of the genome of affected individuals and comparison with control data that are already available. Chip techniques allow hybridization of DNA or RNA to hundreds of thousands of probes simultaneously. Microarrays are being used for mutational analysis of human disease genes.

Complete sequencing of genomes or sequencing of exons that encode proteins (exome sequencing) is now possible, and will lead to the elucidation of the etiology of a number of human diseases in the next few years. High-throughput, high-density sequencing using microarray technology potentially offers the option of obtaining rapid, accurate, and relatively inexpensive sequence of large portions of the genome. One such technique is oligo-hybridization sequencing, which relies on the differential hybridization of target DNA to an array of oligonucleotide probes. This technique is ideally suited to the analysis of DNA from patients with defined disorders, such as disorders of sex development and retinal disease, but suffers from a relatively high false positive rate and failure to detect insertions and deletions.

It is often difficult to perform studies in humans, and so the generation of animal models may be valuable in understanding the etiology and pathogenesis of disease. A number of naturally occurring mouse models have led to the identification of corresponding candidate genes in humans, with mutations subsequently detected in human patients. More frequently, genes of interest are often deleted and lead to the generation of disease models.

In general, mouse models correlate well with human disease; however species-specific defects need to be taken into account. Additionally, the transgenic models could be used to manipulate a condition, with the potential for new therapies. The advent of conditional transgenesis has led to an exponential increase in our understanding of how the mutation of a single gene impacts on a single organ. Using technology such as inducible gene expression systems, the effect of switching on or switching off a gene at a particular stage in development can be determined.

Advances in genomics will also have a major impact on therapeutics. Micro RNAs (miRNA) are small non-coding RNAs that regulate gene expression by targeting mRNAs of protein coding genes or non-coding RNA transcripts. Micro RNAs also have an important role in developmental and physiological processes and can act as tumor suppressors or oncogenes in the ontogenesis of cancers. The use of small interfering RNA (siRNA) offers promise of novel therapies in a range of conditions, such as cystic fibrosis and Type II autosomal dominant IGHD. Elucidation of the genetic basis of disease also allows more direct targeting of therapy. For instance, children with permanent neonatal-onset diabetes mellitus (PNDM) due to mutations in SUR1 or KIR6.2 were previously treated with insulin but have now been shown to respond well to sulfonylureas, thereby allowing the cessation of insulin therapy.

Finally, we are now entering the era of pharmacogenetics when the response of an individual to various therapeutic agents may be determined by their genotype. For example, a polymorphism in the GH receptor that results in deletion of exon 3 may be associated with an improved response to GH. Thus the elucidation of the genetic basis of many disorders will aid their management, and permit the tailoring of therapy in individual patients.

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