1. DNA a modifiable tool
Abstract:
DNA has many bonding capabilities that allow this molecule to form “machines”.
These structures are created by the interactions of different DNA sequences that help in
the process of synthesis and even in the process of gene silencing. Another template
used in the synthesis of these macromolecular structures is branched DNA or bDNA,
which later leaves the option of simply bonding bDNA to synthesize lattices, or other
structures (Teller et. al 2010). Uridine is also used to synthesize bDNA (Chandra et. al
2007). Another way to unite two strands of DNA is by the integration of oligomers
(Dolinnaya et. al 2001). Bonding can be assured, by observing changes in fluorescence.
It is given off as energy after applying a special dye that allows the light to be viewed
(Yurke et.al 2000). DNAzymes are oligomers that are used to silence genes (Dass et. al
2008). This process can help with the eradication of hereditary diseases.
Introduction:
DNA is an astonishing molecule representative of the continuity and diversification of
organisms. Continuity is represented, because during cell division, the molecule is also
replicated to continue playing a major role in protein synthesis necessary for the survival
and development of species. Diversification is represented, because when it comes to
reproduction, gametes produced by meiosis contain different combinations of parent
DNA.
Not only is the DNA structure; the double helix, made for its own synthesis, but now it
is integrated into the investigation of nanotechnology. Some properties of the molecule,
such as the bonding of nucleotide sequences, and the nucleotides themselves, add to
the list of things DNA is capable of doing. Furthermore, DNA is being bonded to itself to
create structures that can function according to the shape of the structures.
other types of structures. DNAzymes
are DNA structures that serve as
Binding DNA: catalysts in reactions. They are created
due to specific conditions that bind the
DNA comes with instructions for all of
molecules in certain places to create
its major processes. Researchers (Teller
shapes. As authors indicate, structure
et. al 2010) show that certain nucleotide
determines the function of the molecule.
sequences serve as a locator for binding
sites. Here, crossing over occurs, similar Bonding is also possible due to certain
to the differentiation process in meiosis. ending sequences or telomeres that
Ionic bonds also occur due to polarity in have a sticky characteristic. Literally
the molecule that promotes shaping to DNA sequences are cut and bonded by
these ends to create the nanostructure
made from DNA.
Depending on the type of bond, the
difficulty of structuring is equally
proportional. If the bond is dependent on

2. charges, sequences that have the uracil and the sugar ribose in the
opposite charge have to be located. backbone of the DNA molecule forming
This causes these opposite charges to this glycosidic linkage. Other DNA
attract to form a bond, and subsequently molecules can be added to these
a shape. linkages to create new branches to the
original structure. This results in the
They further indicate that when DNA is formation of bDNA.
exposed to a magnetic field, it reacts by
curling and bending itself, by the Structures Made from DNA and
repulsive and attractive forces. After the their applications:
magnetic field is either removed or shut
down, the molecule had reacted to The shorter the structure, the stronger
these fields. It ends up all curled and it will be. This is why nanotechnology is
bonded with its own backbone; it being incorporated into many
becomes adhered this way, forming a investigations today.
very strong structure.
Tweezer shaped DNA is used for
Furthermore, shapes like tweezers ultrasensitive sensing. The reactions the
from DNA can be created. Lattices can molecules have when exposed to either
be synthesized by the bonding of many polar fields can help determine the
molecules of bDNA. Another way that environment. When DNA molecules are
DNA is applied to nanotechnological exposed to an environment with varying
research is the incorporation of pH, the reaction can be recorded and
DNAzymes. This involves the usage of analyzed. The results can be used to
the oligomers, or single stranded DNA determine how DNA reacts to these
to take part in the process of gene changes in pH. These are called DNA
silencing. machines. These molecular machines
are stimulated to open and close by the
Branching in DNA called bDNA, addition of DNA molecules. This
occurs naturally. Bonding these process is called hybridization (Yurke
molecules is possible with the use of et.al 2000). A dye that emits
single stranded DNA fragments called fluorescence is added so it can later be
oligomers. Water soluble reagents are quantified. In this case, fluorescence is
used to ligate the oligomers to bDNA measured as a form of energy released.
(Dolinnaya et. al 2001). Branched DNA A proportion was established because
is more efficiently bonded by the use of when the level of fluorescence is high,
double stranded oligomers. They are the “tweezers” are closed, on the
bonded by their phosphate backbone, in contrary, if these levels are low, then the
an overlapping pattern, with a “locking in molecules is said to be opened. When
place bond” to the other DNA strands. there is opening of the tweezers, energy
This procedure is a type of chemical is being used up, so there is evidence of
ligation. a reaction occurring.
However, bDNA can also be DNAzymes are types of DNA that
synthesized more efficiently with the catalyze chemical reactions (Dass et. al
integration of uridine (Chandra et. al 2008). They can function as enzymes,
2007). Uridine is a branching monomer acquiring the denomination. They are
that is created by the combination of introduced into a cell to then be

3. transported into the nucleus. Most some molecules that once they take part
DNAzymes are light activated. They in the process, they stimulate the
become active in terms of mobility inside activation of others to completely
the nucleus. DNAzymes catalyze a replicate a DNA molecule. However,
specific synthesis of DNA by cleaving the phenomenon of bDNA occurs
into RNA and causing gene silencing. In naturally with the bonding of the sticky
this way the origin of a genetic disease ends with another strand of DNA.
is eradicated by simply eliminating a
certain gene or causing the synthesis of Oligomers or single stranded DNA are
another. This process requires the extracted as DNA replication takes
integration of oligomers, that bond to place. These oligomers also occur
their corresponding RNA sequences naturally but require the process of
and silences the gene (Dass et. al extraction.
2008).
DNA nanotubes are a combination of
a DNA molecule wrapped around a
carbon nanotube. This structure can
then be applied for sensing of
complimentary DNA. When bonding of
the complimentary strand occurs to the
strand in the carbon nanotube, the
fluorescence is altered giving off a
reading that confirms bonding is taking
place between oligomers.
DNA lattices are used to enclose
materials. This combination can add
magnetism and even increase or even
add efficiency to the material’s catalytic
properties. These lattices can also be
used as cell compartments. Cells
adhere to the molecular structures,
where they can be studied or observed
and are Perfect for “In Vitro ” testing.
The environment can be controlled by
adding substances that react to maintain
desired conditions. As these cells
replicate, they are contained in these
lattices for further studies.
Replication of the Structures:
The replication of the tweezer like
DNA, and the lattice composed of DNA
has not yet been achieved perhaps
because DNA is replicated in a specific
process that requires the integration of

4. Conclusions:
The integration of DNA to nanotechnology enhances the nanotechnology that already
exists. The example of the wrapping of the DNA strand to detect complimentary strands
serves as an application for carbon nanotubes. DNA machines are also a great example
of nanotechnological advances and can be applied to many tests and experiments.
Oligomers can silence genes, meaning that the expression of a disease can be
silenced. This can lead to the elimination of possible hereditary diseases that might be
expressed. For example, for a tumor to start, it needs epithelial proteins, that help these
masses adhere. The single stranded DNA can be used to silence the gene that can be
translated into this protein, thus avoiding adherence of the tumors. Another possible
application of these DNA machines can be on lab testing. Changes in pH or other
factors can affect the structure of DNA. Lab tests can be revised and these factors can
be observed to help determine their healthy levels in the blood serum. This can help
maintain the structure of DNA and maybe avoid the damaging of it. This damaging of
the structure might lead to wrongful synthesis of certain proteins, thus causing diseases
or even mutations.

5. References:
1.Chandra Madhavaiah, Keller Sascha, Luo Yan and Marx Andreas. 2007. A modified Uridine for the
synthesis of branched DNA, Tetrahedron. Volume 63, issue 35: pages 8576-8580.
2.Dass Crispin R., Choong Peter F.M. and Khachigian Levon M., DNAzyme technology and cancer
therapy: cleave and let die, Department of Orthopedics, St. Vincent’s Hospital Melbourne, Fitzroy, Victoria,
Australia; Bone and Soft Tissue Sarcoma Service, Peter MacCallum Cancer Centre, Melbourne, Australia;
and Centre for Vascular Research, Department of Pathology, School of Medical Sciences, The University of
New South Wales and Department of Hematology, Prince of Wales Hospital, Sydney, Australia.
3.Dolinnaya Nina, Gryaznov Sergei, Ahle David, Chang Chu-An, Shabarova Zoe A., Ureda Mickey S. and
Horn Thomas, 2001. Construction of branched DNA (bDNA) molecules by chemical ligation, Lynx
Pharmaceuticals, Foster City, CA 94404, USA.
4. Teller Carsten and Willner Itamar. 2010. Functional nucleic acid nanostructures and DNA machines,
Institute of Chemistry, the Hebrew University of Jerusalem, 91904 Jerusalem, Israel.
5.Yurke Bernard, Turbereld Andrew J., Mills Allen P. Jr , Simmel Friedrich C. & Neumann Jennifer L., A
DNA-fuelled molecular machine made of DNA, Bell Laboratories, Lucent Technologies, 600 Mountain
Avenue, Murray Hill, New Jersey 07974, USA Department of Physics, University of Oxford, Clarendon
Laboratory, Parks Road, Oxford OX1 3PU, UK.
6.Science Direct- investigation listings, PDF
7.Nature- magazine
8.Proquest- Website