Group S2
Chris Heflin
Mike Jones
Rachael Houk
NANOTECHNOLOGY IN GENOMICS
WHAT IS GENOMICS?
Genomics is the study of all the genes of a cell,
or tissue, at the DNA, mRNA, or protein levels.
 The topic focuses on determining the entire
DNA sequence of an organism and mapping
the genetic material on a fine scale.
 The application of nanotechnology in genomics
is sometimes called “nanobiomics” in medical
fields.

WHY IS GENOMICS IMPORTANT?

Virtually every human ailment has some basis
in genes.
 Cancer,
birth defects, and vulnerabilities to other
diseases all can be transferred genetically.

Through a meticulous understanding of
genomics, efforts can be made toward
removing the propensity for these ailments,
and thus make them less common.
GENOMICS V. GENETICS

How is genomics different than genetics?
 Both
deal with genetic material, but genetics
focuses on one gene at a time.
 Genomics focuses on the entirety of the organisms
genetic material rather than an isolated gene.
APPLICATIONS OF NANOTECHNOLOGY IN
GENOMICS

Pharmaceuticals:
 Targeted
drug
development, allowing for
more localized treatment.
 While most diagnoses are
made by analyzing a
blood sample,
nanobiomics makes it
possible to analyze a
single cell.
http://mcmannes.files.wordpress.com/2009/1
1/adhd-drugs-pharmaceutical-774231.jpg
APPLICATIONS OF NANOTECHNOLOGY IN
GENOMICS

Forensics
 Allows
for more specific DNA
identification even when
using miniscule traces of
genetic material.
http://www.legaljuice.com/dna.jpg
APPLICATIONS OF NANOTECHNOLOGY IN
GENOMICS

Computing

Nanotechnology allows us to
create biomolecular devices
that are programmable and
autonomous.
 Programmable
meaning the
tasks executed can be modified
without redesigning the
structure.
 Autonomous meaning steps are
executed and self sustaining.
http://farm3.static.flickr.com/2073/2532729582_07
52f41cc2.jpg
APPLICATIONS OF NANOTECHNOLOGY IN
GENOMICS

DNA as a template
DNA is a naturally stable
structure. That stability can
be harnessed and used to
make synthetic molecules.
 Nanodevices allow for the
construction of molecules by
making changes to the DNA
template in order to produce
the desired properties.

http://www.chrismadden.co.uk/genetics/geneprinter.gif
PAPER 1
Nanotechnology and the Double Helix
By Nadrian Seeman
GOAL OF THE WORK
Develop a way of organizing DNA so that it can
be used as a tool, like for nano-machines, or as
a structure on which to build crystals for a
specific shape
 Chose DNA because it is very programmable
and predictable, simple to synthesize and
manipulate, potentially capable of selfreplication

BACKGROUND

DNA structure




Energetically favored right
spiral double helix (BDNA)
Less favorable left spiral
Organized spine of
phosphate and sugar
groups
The “rungs” of the ladder
are one of 4 base pairs
B-DNA
Z-DNA
BEGINNING WORK
From paper


http://www.flickr.com/photos/tstadler/1415613305/
Strands of DNA were
combined with specific
endcaps, which could
combine with other strands
to form simple structures,
similar to marshmallows
and toothpicks.
These connections were
weak and would not make a
good structure for
crystallization work or scaleup to the macro world
BASIC SHAPES
From paper
• Began with work done on
DNA barcodes with 5
programmable spaces
• DNA strands paired with
a double-crossover to
make blocks

Arranged
these
blocks to
make
sturdier2-D
structures
MOTION ADDED
Using programmable end-caps, two strands of
DNA can be arranged into something that
moves when a condition changes
 Potential application for nano-tweezers and
other simple nano-machines


Can use different triggers
for different locations to
get a variety of controlled
movements.
From paper
DRAWBACKS AND FUTURE WORK

Drawbacks
DNA must be worked with in aqueous solutions, so the
addition of some functional groups is challenging
 Current difficulty in promoting self-replication


Potential future
Moving from 2-D to 3-D
 Enhance self-replication to reduce manufacturing costs
 Integration with nano-electroncics

PAPER 2
DNA Nanotechnology and its Biological
Applications
By John H. Relf and Thomas H. LaBean
PAPER OVERVIEW
This paper overviews the emerging research
area of DNA nanostructures and biomolecular
devices.
 Particularly emphasized are molecular devices
that are programmable and autonomous.

http://www.svtc.org/images/content/pa
gebuilder/14163.gif
http://www.shoulderdoc.co.uk/images/upl
oaded/nanobot1.jpg
http://www.twine.com/_b/120ln
27953vf/b0kw7kcd088fsf
CAPABILITIES

Various programmable molecular-scale devices
are achievable with various capabilities,
including:
Computation
 2D Patterning
 Amplified Sensing
 Molecular Transport

Links to Pictures are in Notes
MANIPULATION OF DNA

There are a wide variety of known enzymes and other
proteins used for manipulation of DNA nanostructures that
have predictable effects.

Restriction Enzymes


Ligase Enzymes


These can cut [double helix break] or nick [single strand break] a DNA
backbone at specific locations determined by short base sequences.
They are able to heal or repair DNA nicks by forming covalent bonds in
the sugar-phosphate backbone.
Polymerase

Polymerase can extend a single strand DNA by coupling complementary
bases, thus forming a longer sequence of double strand DNA.
→
Links to Pictures are in Notes
MANIPULATION OF DNA



The previous listed reactions, together with
hybridization, are often used to execute and control DNA
computations and DNA molecular robotic operations.
The restriction enzyme reactions are programmable in
the sense that they are site specific, only executed as
determined by the appropriate DNA base sequence.
The latter two reactions, using ligase and polymerase,
require the expenditure of energy via consumption of
ATP molecules, and thus can be controlled by ATP
concentration.
+
http://comps.fotosearch.com/
comtech-robot_~ca_46_4.jpg
Link in Notes
http://www.hhs.gov/ocr/images/dnast
rand.jpg
DNA NANOSTRUCTURE

DNA nanostructures
are a multi-molecular
complex consisting of
a number of single
strand DNA that have
partially hybridized
along their subsegments.
John Relf, Thomas LeBean, DNA Nanotechnology and its Applications,
chapter 13 in Bio-Inspired and Nano-scale Integrated Computing. Wiley,
USA (2007)
DNA NANOSTRUCTURES

John Relf, Thomas LeBean, DNA Nanotechnology and its Applications,
chapter 13 in Bio-Inspired and Nano-scale Integrated Computing. Wiley,
USA (2007)

Figure A illustrates a stem-loop,
where single strand DNA loops
back to hybridize on itself (that is,
one segment of the single strand
DNA (near the 5’ end) hybridizes
with another segment further along
(nearer the 3’ end) on the same
single strand DNA strand).
The shown stem consists of the double strand DNA
region with sequence CACGGTGC on the bottom
strand. The loop in this case consists of the single
strand DNA region with sequence TTTT. Stem-loops
are often used as markers for visualizing
programmed patterning on DNA nanostructures.
DNA NANOSTRUCTURES

John Relf, Thomas LeBean, DNA Nanotechnology and its Applications,
chapter 13 in Bio-Inspired and Nano-scale Integrated Computing. Wiley,
USA (2007)

Figure B illustrates a sticky end,
where unhybridized single DNA
protrudes from the end of a
double helix. The sticky end
shown (ATCG) protrudes from
double strandDNA (CACG on the
bottom strand).
Sticky ends are often used to combine two DNA
nanostructures together via hybridization of their
complementary single strand DNA. The Figure
shows the antiparallel nature of double strand DNA
with the 5’ end of each strand pointing toward the
3’ end of its partner strand.
DNA NANOSTRUCTURES

DNA nanostructures have some unique
advantages among nanostructures:
They are relatively easy to design
 Fairly predictable in their geometric structures
 And have been experimentally implemented in a
growing number of labs around the world

They are constructed primarily of synthetic DNA
 A key principle in the study of DNA nanostructures
is the use of self-assembly processes to actuate
the molecular assembly.

John Relf, Thomas LeBean, DNA Nanotechnology and its Applications, chapter 13 in Bio-Inspired and Nano-scale Integrated Computing. Wiley, USA (2007)
FUTURE DEVELOPMENT

There are a number of key challenges still
confronting this emerging field on DNA
nanostructures, including:
The need for error-correction
 and the challenge and applications of constructing
three dimensional DNA lattices.

CONCLUSION #2

Overviewed were a number of methods for
assembling computational patterns within the
molecular fabric of DNA lattices. Surveyed were
the varied interdisciplinary techniques for carefully
designing and controlling these self assembly
processes. Many of these self-assembly processes
are computational based and programmable and
it seems likely that interdisciplinary techniques will
be essential to other emerging subfields of
nanoscience and biomolecular computation.
WORK CITED




John Relf, Thomas LeBean, DNA Nanotechnology and its
Applications, chapter 13 in Bio-Inspired and Nano-scale
Integrated Computing. Wiley, USA (2007)
Zhaoxiang Deng, Yi Chen, Ye Tian, Chengde Mao, A fresh
look at DNA 40 nanotechnology, chapter in Nanotechnology:
Science and Computation (eds. J.Chen; N. Jonoska & G.
Rozenberg), Springer, pp 23-34, (2006).
Nadrian C. Seeman, Nanotechnology and the Double Helix;
Scientific American, 290 (6), 64-75 (June 2004).
Paul W. K. Rothemund, Folding DNA to create nanoscale
shapes andpatterns, Nature 440, 297-302 (16 March
2006).
S2
Rebuttal: Applications of Genomics
Please Prepare a Rebuttal
(MISSING)
S1
Rebuttal: Applications of Genomics
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By Group S3:
Michael Koetting
Bradford Lamb
James Kancewick
REVIEW OF S2—NANOTECHNOLOGY IN
GENOMICS
THINGS DONE WELL!





Very good flow of information. Had a smooth transition
between the introductory slides and the more detailed slides
on the research.
Consistent slide formatting makes for an aesthetically
pleasing presentation.
Captions explaining images are very useful in understanding
the figures presented.
The text is very detailed—perfect for a slideshow with no
physical presentation.
Conclusions of each paper’s discussion and identification of
challenges were very helpful in understanding the level of
progress made in the papers with respect to long-term goals.
AREAS FOR IMPROVEMENT





Too many slides without images. Images are necessary to help
keep the audience entertained.
Some of the images in the slideshow are too small to read
easily. Larger images with text could be placed on their own
slide to maximize the image size/readability.
The “Conclusion #2” slide needs to be broken up into bullet
points rather than being one paragraph. This would make it
easier to read and would highlight the important points better.
Furthermore, the “Conclusion #2” slide’s title seems out of
place since there was never a slide titled “Conclusion #1.”
All of the citations for images should be placed in the
presentation.
Danielle Miller
Josh Moreno
Scott Marwil
Things Done Well
 Slides looked very professional.
 Punctuation was fairly consistent, much better than
most presentations. Slides 14, 24 and 25 had a couple
inconsistencies.
 Nice pictures. A lot of them were vibrant.
Things to Improve On
 A lot of text. There are a bunch of long paragraphs on
slides. Try to break concepts down for audience.
 The shadow on the titles of the slides looks cool, but it
is very distracting.
 Make sure your titles fit within the area your slide
design has designated for titles. Don’t let them cross
the horizontal line.
Things to Improve On
 Words and pictures overlapping.
 Use consistent placement for your citations.
 Slide 13 needs some work with regard to aesthetics.
 Don’t capitalize ‘Figure’ unless it is part of a name (i.e.
Figure 3).
 Some words too small.
S5
Rebuttal: Applications of Genomics
Please Prepare a Rebuttal
(MISSING)