in today’s lecture, we will cover: what is bionanotechnology? · pdf filein...
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In today’s lecture, we will cover:
What is bionanotechnology?
How can DNA be used in nanotechnology?
What are aptamers?
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What is bionanotechnology?
ATP synthase
Nano “motor”
Bionanotechnology is nanotechnology that uses biological starting materials, biological design principles or has biological or medical applications.
Ribosome
Nano “factory”
Using ATP synthase for a rotor• Ni nanopropellor attached to ATP synthase, then attached to a surface.
• Rotation powered by 2 mM ATP
Ricky K. Soong, et al. Powering an Inorganic Nanodevice with a BiomolecularMotor Science 290, 1555 (2000)
Mimicking the ATP synthase nanorotor
• www.youtube.com/watch?v=P3Df2UqRPoQ
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Molecular assembler mimicking the ribosome
Science 11 January 2013: Vol. 339 no. 6116 pp. 189‐193
https://www.newscientist.com/article/dn23065-nanomachine-mimics-natures-protein-factory/
How can DNA be used in nanotechnology?
DNA’s unique properties make it well‐suited for nanotechnology
• Size/Shape
• Diameter of about 2.5 nm
• Helical pitch of 3.4 nm (10 base pairs)
• Persistence length of 50 nm
DNA’s unique properties make it well‐suited for nanotechnology
• Recognition
• A binds to T
• G binds to C
• Shape of DNA is programmable and predictable
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DNA’s unique properties make it well‐suited for nanotechnology
• Can be chemically synthesized• PCR to make many copies
DNA nanoscaffolds
DNA nanomachines
DNA nanosensors
DNA as a nanoscaffold• One approach uses “sticky ends” and DNA tiles
Seeman et al Nature 1991, 350, 631
DNA as a nanoscaffold• Very complicated tiles can make interesting patterns
Seeman JACS, 2004, 126, 10230.
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How can this be useful?
• Can use the DNA patterns as a scaffold or a template for other nanocomponents
Nano Lett. 2006 Vol. 6, No. 7, 1502‐1504
How can this be useful?
• Can use the DNA patterns as a scaffold or a template for other nanocomponents
Nano Lett. 2006 Vol. 6, No. 7, 1502‐1504
DNA can access complex patterns
Sharma et al Science 2009 112 ‐ 116
A newer approach is called “DNA origami”
• A long piece of viral DNA is folded by a computer program into a certain pattern
• Short “staple” DNA are designed to hold the folds in place
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“DNA Origami” can make complex patterns
Rothemund, P.W.K. Nature 2006, 440, 297‐302.
“DNA Origami” can make complex 2D and 3D patterns
Rothemund, P.W.K. Nature 2006, 440, 297‐302.
3D box made with DNA origami
• AFM images of the sheets (a), the folded box (b), and the box with the lid open (c).
19Andersen et al. “Self-assembly of a nanoscale DNA box with a controllable lid” Nature2009, 459, 73-77.
You can make your own!
• http://cando‐dna‐origami.org/
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DNA as a nanomachine
• We are probably years away from DNA machines that can do complex tasks
• Current nano‐machines are very simple
A DNA‐based molecular assembler
Seeman, “A proximity‐based programmable DNA nanoscale assembly line” Nature Volume: 465, Pages: 202–205
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Seeman, “A proximity-based programmable DNA nanoscale assembly line” Nature Volume: 465, Pages: 202–205 23
A DNA‐based molecular assembler
• UV light excites a molecule to release an electron
• Electron reacts and breaks DNA
• DNA releases and “walks” along a track
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UV‐powered DNA “walker”
http://pubs.acs.org/doi/full/10.1021/acs.nanolett.5b02502
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• UV light excites a molecule to release an electron
• Electron reacts and breaks DNA
• DNA releases and “walks” along a track
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UV‐powered DNA “walker”
http://pubs.acs.org/doi/full/10.1021/acs.nanolett.5b02502
DNA as a nanosensor (cont’d)
• DNA recognition is not limited to its complementary sequence
• Certain type of DNA can also recognize and bind to other molecules
• These molecules are known as Aptamers
– Aptus: to fit
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• Aptamers are synthetic stretches of DNA or RNA that can fold into nanosized shapes capable of binding to molecular targets
–bind targets (small molecules, proteins) with high affinity
• Kd values in the micromolar to sub‐nanomolar range
What are Aptamers?• Aptamers are synthetic stretches of DNA or RNA that can fold into nanosized shapes capable of binding to molecular targets
– remarkable selectivity
• Theophyline aptamer: difference of a single methyl group leads to 10 000 times weaker binding
What are Aptamers?
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Aptamers are discovered by the SELEX screening procedure
Tuerk, C., Gold, L. Science 1990; Ellington, A.D., Szostak, J.W. Nature 1990
target
Random region
Fixed regions
PCR
Clone, sequence,
characterize
SELEX explained: Science Magazine’s Dance your Ph.D
Can aptamers make fertilizers “smart”?
“ You cannot feed 6B people today (2007) and 9B in 2050 without judicious use of chemical fertilizers."
Dr. Jacques Diouf, Director‐General of the FAO.
The efficiency of current fertilizer technology is very low
• 50‐70% of fertilizer applied to crops is lost to air, water and other processes
• >$1B a year for Canadian farmers
• Major environmental impact (runoff and greenhouse gas emissions)
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Can aptamers make fertilizers “smart”?
Y. Sultan and M. C. DeRosaSmall 2011, 7, 1219‐1226.
Preparation of hollow capsules with aptamer‐loaded walls
• Film deposition by Layer‐by‐Layer approach on sacrificial templates
Y. Sultan and M. C. DeRosaSmall 2011, 7, 1219‐1226.
Preparation of hollow capsules with aptamer‐loaded walls
Aptamer capsules specific for a root exudate show increased dye
permeability
Target molecule Diffusion coefficient (µm2/s)
Aptamer film with Exudate 0.113± 0.043Aptamer film with Negative control
0.051± 0.008
Sultan and DeRosa