By Professor Juewen
Professor Juewen Liu, Assistant Professor, Department of Chemistry,
University of Waterloo, 200 University Avenue, Waterloo, Ontario, Canada
Corresponding author: firstname.lastname@example.org
Sixty years ago, the famous structure of the DNA double helix was solved,
bringing about the birth of modern molecular biology. Since then, DNA has been
extensively studied as a genetic material. In the 1970s, solid-phase DNA
synthesis was invented, allowing one to obtain arbitrary oligonucleotide
sequences. In 1986, the invention of polymerase chain reaction (PCR) allowed an
infinite number of DNA copies to be amplified from even a single molecule. It is
these two techniques that have made it possible to explore new functions of DNA.
DNA has highly programmable structures that can be designed based on a simple
base pairing rule. For example, a field called structural DNA nanotechnology has
experienced rapid developments, manifested by the many published sophisticated
2D and 3D nanostructures. Upon these structures, various
nanoparticles have been deposited to offer other functions. Another interesting
advancement was the discovery of DNA as a catalyst (catalytic DNA) and for
molecular recognition (aptamer), making DNA a functional substitute for
proteins. Compared to proteins, DNA is much more stable, easier to perform
site-specific labeling, and easier for conjugation to various materials,
popularizing DNA as the molecule of choice in constructing functional nano- and
Nanomaterials are attractive because they possess unique size and
distance-dependent physical properties. While particle size can be well
controlled through chemical synthesis, the control of inter-particle distance
with sub-nm precision and the organization of different types of particles
remained difficult. DNA provides a unique solution to solving these problems. On
the other hand, the molecular recognition property of DNA and DNA aptamers
allows these nanomaterials to be used for biosensing and biomedical
applications.[2,3] My lab is interested in
exploring the biophysical interface between DNA and various nanomaterials to
guide the design of better biosensors, biomaterials, and drug delivery systems.
Within a persistent length of ~50 nm, double-stranded DNA can be considered
as a rigid rod with a diameter of just 2 nm. Each additional base pair
contributes to a length increase of 0.34 nm. Therefore, sub-nm control of
distance can be achieved using DNA. With the availability of a diverse range of
attachment chemistry, DNA can be linked to almost all known nanomaterials. We
are interested in studying the distance-dependent properties of various
nanomaterials, including gold nanoparticles, liposomes, magnetic nanoparticles,
quantum dots, and graphene using DNA as a linker. For example, Figure 1A shows
the assembly of DNA-functionalized gold nanoparticles using a linker DNA with a
subsequent color change from red to purple. The same idea
can be applied to the assembly of soft liposome nanoparticles (Figure 1B), as well as gold-liposome hybrid (Figure 1C). The inter-particle distance can be precisely controlled by
changing the DNA sequence. Studying these systems can provide insights into the
DNA-surface interaction as well as the coupling of physical events among the
Figure 1. Schematics of DNA-directed assembly
of gold nanoparticles (A), liposomes (B), and their hybrids (C).
representative TEM micrograph of the structure shown in (C).
Beyond a simple structural molecule, DNA can recognize a wide range of ions,
molecules, and even cells with high specificity. In the case of detecting the
highly toxic mercury, a thymine rich DNA is used. As shown in Figure 2, this DNA
can fold into a hairpin upon mercury binding where upon addition of a DNA
binding dye called SYBR Green I (SG), a green fluorescence is obtained.
Immobilizing the mercury detecting DNA to a hydrogel has a number of advantages.
The gel allows sensor drying and regeneration. More importantly, the gel can
actively adsorb mercury, increasing its concentration within the gel. Via
immobilization, we have achieved a highly selective and sensitive detection of
mercury without the use of any analytical instrument.[7,8]
Figure 2. A DNA-based biosensor immobilized on
a hydrogel for mercury detection where
SG becomes highly fluorescent upon
binding to the double-stranded region in the DNA.
Apart from the recognition of heavy metal ions, aptamers can be selected to
bind other molecules such as proteins and metabolites. This aptamer selection
process starts with a huge library of random DNA molecules where only the
sequences that bind the metabolite are retained. In Figure 3, the sequence that
can bind to ATP is shown. While this aptamer can detect ATP
effectively in pure buffer, its performance is strongly interfered by the
presence of blood serum. For blood samples, it is important to achieve detection
in a very small sample volume. We found that by attaching the aptamer-based
sensor onto a magnetic microparticle (MMP), it is possible to achieve detection
in just 10 mL of human blood serum. Because of the MMP, we could separate the
ATP binding step from the fluorescence signal detection step, allowing us to
dilute the effect of blood serum.
Figure 3. Sequence of the ATP binding aptamer and its
a MMP allowing effective ATP detection in human blood
Drug delivery applications
The same DNA selection method can also be used to target cancer cells. Many DNA aptamers have already been isolated to target many
different tumor cell lines. For example, a guanine rich sequence has entered
clinical trials. Taking advantage of nanomaterials for drug loading and imaging,
DNA-functionalized biomaterials can allow sophisticated functions to be realized
including targeted delivery and diagnosis.
In summary, DNA is a very versatile molecule with both structural and
functional properties. Interfacing DNA with various nano- and biomaterials can
significantly improve the performance of these DNA molecules in various
applications. At the same time, the structural property of DNA allows precise
assembly of nanomaterials with high precision, allowing fundamental biophysical
understandings that can fuel the further development of various
- Seeman NC. DNA in a material world. Nature 2003; 421:
- Storhoff JJ, Mirkin CA. Programmed Materials Synthesis with
DNA. Chem. Rev. 1999; 99: 1849-62.
- Liu J, Cao Z, Lu Y. Functional Nucleic Acid Sensors. Chem.
Rev. 2009; 109: 1948–98.
- Smith BD, Liu J. Assembly of DNA-Functionalized Nanoparticles
in Alcoholic Solvents Reveals Opposite Thermodynamic and Kinetic Trends for DNA
Hybridization. J. Am. Chem. Soc. 2010; 132: 6300–1.
- Dave N, Liu J. Programmable Assembly of DNA-Functionalized
Liposomes by DNA. Acs Nano 2011; 5: 1304–12.
- Dave N, Liu J. Protection and Promotion of UV
Radiation-Induced Liposome Leakage via DNA-Directed Assembly with Gold
Nanoparticles. Adv. Mater. 2011; in press.
- Dave N, Huang P-JJ, Chan MY, Smith BD, Liu J. Regenerable
DNA-Functionalized Hydrogels for Ultrasensitive, Instrument-Free Mercury(II)
Detection and Removal in Water. J. Am. Chem. Soc. 2010; 132: 12668–73.
- Joseph KA, Dave N, Liu J. Electrostatically Directed Visual
Fluorescence Response of DNA-Functionalized Monolithic Hydrogels for Highly
Sensitive Hg2+ Detection. ACS Appl. Mater. Inter. 2011; 3: 733–9.
- Huizenga DE, Szostak JW. A DNA Aptamer That Binds Adenosine
and ATP. Biochemistry 1995; 34: 656-65.
- Huang PJJ, Liu JW. Flow Cytometry-Assisted Detection of
Adenosine in Serum with an Immobilized Aptamer Sensor. Anal. Chem. 2010;
- Fang XH, Tan WH. Aptamers Generated from Cell-SELEX for
Molecular Medicine: A Chemical Biology Approach. Acc. Chem. Res. 2010;