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DNA: Not Merely the Secret of Life
Bio-Inspired Bottom-Up Nanoscale Control of the Structure of Matter
Nadrian C. Seeman
Department of ChemistryNew York University
New York, NY 10003, [email protected]
Workshop on the Computational
World View and the SciencesPrinceton UniversityDecember 11, 2006
DNA BASE PAIRS
C C
N
C
C
O
NH
O R
H
CH3
T
H
CC
NC
N C
N
N N
H
HC
H
R
A
O
C C
N
N
C
C
R
H
HN
H
H
CC
NC
C
N
N
C
OC
H
NR
H
N H
H
G
3.4 Å
~20 Å
10-10.5Pairs/Turn
B-DNA
Reciprocal Exchange:A Theoretical Tool To Generate
New DNA Motifs
Seeman, N.C. (2001), NanoLett. 1, 22-26.
R e cip roc a lE x ch an ge
R e s o lve
Reciprocal Exchange in aDouble Helical Context
Seeman, N.C. (2001), NanoLett. 1, 22-26.
+
+
S t r a n d
P o l a r i t y
I d e n t i c a l
S t r a n d
P o l a r i t y
O p p o s i te R e s o l v e
R e c i p r o c a l
E x c h a n g e
R e s o l v e
R e c i p r o c a l
E x c h a n g e
D S + D S H J
Seeman, N.C. (1982), J. Theor.Biol. 99, 237-247.
Design of Immobile Branched Junctions:Minimize Sequence Symmetry
IIACTCGTGC
TGAGCACG••••••••
A
T
C
G A
T A
T A
T
C
G
C
G C
G• • • • • • • •
3322
11 44
C G
C G
CG
A T
A T
AT
CG
C G
•
•
•
•
•
•
•
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IV
I
III
C GCG
C G
A T
A TAT
C G
••
•
••
•
•
C G•
Sticky-Ended Cohesion: Smart Affinity
Qiu, H., Dewan, J.C. & Seeman, N.C. (1997) J. Mol. Biol. 267, 881-898.
Sticky-Ended Cohesion: Structure
Seeman, N.C. (1982), J. Theor.Biol. 99, 237-247.
The Central Concept of Structural DNA Nanotechnology:Combine Branched DNA with Sticky Ends to
Make Objects, Lattices and Devices
AB'
B
A'A
B' B'
B
A
A'
A'
B
OBJECTIVES AND APPLICATIONSFOR OUR LABORATORY
ARCHITECTURAL CONTROL AND SCAFFOLDING
[1] MACROMOLECULAR CRYSTALLIZATION (PERIODIC IN 2D AND 3D).[2] NANOELECTRONICS ORGANIZATION (PERIODIC IN 2D AND 3D).[3] DNA-BASED COMPUTATION (APERIODIC IN 2D OR 3D).[4] CONTROL OF POLYMER AND MATERIALS COMPOSITION & TOPOLOGY.
[1] NANOROBOTICS.[2] NANOFABRICATION.
NANOMECHANICAL DEVICES
NO
CRYSTALS?PRAY FOR CRYSTALSSET UP CRYSTALS
GUESS NEW CONDITIONS
GUESS CONDITIONS
CHANGE DEITIES
DO CRYSTALLOGRAPHY
YES
CURRENT CRYSTALLIZATION PROTOCOL
Seeman, N.C. (1982), J. Theor.Biol. 99, 237-247.
A New Suggestion for Producing Macromolecular Crystals
Robinson, B.H. & Seeman, N.C. (1987), Protein Eng. 1, 295-300..
A Method for Organizing Nano-Electronic Components
Why DNA?Predictable Intermolecular Interactions:Both Affinity and Structure.
Can Design Shape by Selecting Sequence:Robust Branched Motifs Programmable by Sequence.
Convenient Automated Chemistry:Both Vanilla DNA and Useful Derivatives.
Convenient Modifying Enzymes: Ligases, Exonucleases, Restriction Enzymes, Topoisomerases.
Locally A Stiff Polymer:
Persistence Length ~500 Å; Stiff Branched Motifs Have Been Developed.
Robust Molecule:Can Heat Individual Strands without Doing Damage.
Amenable to Molecular Biology and Biotechnology Techniques:Gels, Autoradiography, PCR.
Externally Readable Code when Paired:Different Points in a Lattice Can be Addressed.
High Functional Group Density:Every 3.4 Å Nucleotide Separation.
Prototype for Many Derivatives:The Gene Therapy Enterprise Has Generated Hundreds of Analogs
Potentially Self-Replicable and Selectable:May be Able to Make and Improve Constructs Inexpensively.
