Artificial DNA lattice fabrication by noncomplementarity and geometrical incompatibility

ACS Nano

Volumn 5, Issue 6, 2011, Pages 5175-5179

  Shin, Jihoon ^a   Kim, Junghoon ^b   Amin, Rashid ^a   Kim, Seungjae ^b   Kwon, Young Hun ^c   Park, Sung Ha ^a,b  

^a Sungkyunkwan University   (South Korea)

^b Sungkyunkwan University   (South Korea)

^c Hanyang University   (South Korea)

Author keywords

base pairing; complementarity; DNA; geometry; lattice

Indexed keywords

BASE PAIRING; BASE SEQUENCES; BASE-PAIRING RULES; COMPLEMENTARITY; DNA NANOSTRUCTURES; DNA OLIGONUCLEOTIDES; DNA STRUCTURE; LATTICE; LATTICE SIZE;

DNA; FABRICATION; NANOSTRUCTURES; OLIGONUCLEOTIDES; SELF ASSEMBLY;

DNA SEQUENCES;

DNA; NANOCOMPOSITE; OLIGONUCLEOTIDE;

ALGORITHM; ARTICLE; ATOMIC FORCE MICROSCOPY; BIOCHEMISTRY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; MATERIALS TESTING; METHODOLOGY; NANOTECHNOLOGY; THEORETICAL MODEL;

ALGORITHMS; BIOCHEMISTRY; DNA; MATERIALS TESTING; MICROSCOPY, ATOMIC FORCE; MODELS, MOLECULAR; MODELS, THEORETICAL; MOLECULAR CONFORMATION; NANOCOMPOSITES; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES;

EID: 79959803113     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn201312g     Document Type: Article

References (21)

1. Seeman, N. C. DNA Nanotechnology: Novel DNA Constructions Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 225-248 (Pubitemid 28286015)
2. Seeman, N. C. DNA in a Material World Nature 2003, 421, 427-431 (Pubitemid 36157949)
3. Mao, C.; Sun, W.; Seeman, N. C. Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy J. Am. Chem. Soc. 1999, 121, 5437-5443
4. Park, S. H.; Yin, P.; Liu, Y.; Reif, J. H.; LaBean, T. H.; Yan, H. Programmable DNA Self-Assemblies for Nanoscale Organization of Ligands and Proteins Nano Lett. 2005, 5, 729-733 (Pubitemid 40609749)
5. Winfree, E.; Liu, F.; Wenzler, L. A.; Seeman, N. C. Design and Self-Assembly of Two-Dimensional DNA Crystals Nature 1998, 394, 539-544 (Pubitemid 28366820)
6. Yan, H.; Park, S. H.; Finkelstein, G.; Reif, J. H.; LaBean, T. H. DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires Science 2003, 301, 1882-1884 (Pubitemid 37221388)
7. Shih, W. M.; Quispe, J. D.; Joyce, G. F. A 1.7-Kilobase Single-Stranded DNA That Folds Into a Nanoscale Octahedron Nature 2004, 427, 618-621 (Pubitemid 38248477)
8. Goodman, R. P.; Schaap, I. A. T.; Tardin, C. F.; Erben, C. M.; Berry, R. M.; Schmidt, C. F.; Turberfield, A. J. Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication Science 2005, 310, 1661-1665 (Pubitemid 41780784)
9. Yin, P.; Hariadi, R. F.; Sahu, S.; Choi, H. M.; Park, S. H.; Labean, T. H.; Reif, J. H. Programming DNA Tube Circumferences Science 2008, 321, 824-826
10. Fujibayashi, K.; Hariadi, R.; Park, S. H.; Winfree, E.; Murata, S. Toward Reliable Algorithmic Self-Assembly of DNA Tiles: A Fixed-Width Cellular Automaton Pattern Nano Lett. 2007, 8, 1791-1797
11. Rothemund, P. W. K.; Papadakis, N.; Winfree, E. Algorithmic Self-Assembly of DNA Sierpinski Triangles PLoS Biol. 2004, 2, 2041-2053
12. Mao, C.; LaBean, T. H.; Relf, J. H.; Seeman, N. C. Logical Computation Using Algorithmic Self-Assembly of DNA Triple-Crossover Molecules Nature 2000, 407, 493-496
13. Lee, J. Y.; Shin, S.-Y.; Park, T. H.; Zhang, B.-T. Solving Traveling Salesman Problems with DNA Molecules Encoding Numerical Values Biosystems 2004, 78, 39-47 (Pubitemid 39536131)
14. Fu, T.-J.; Seeman, N. C. DNA Double-Crossover Molecules Biochemistry 1993, 32, 3211-3220 (Pubitemid 23126886)
15. Barish, R. D.; Rothemund, P. W. K.; Winfree, E. Two Computational Primitives for Algorithmic Self-Assembly: Copying and Counting Nano Lett. 2005, 5, 2586-2592 (Pubitemid 43088917)
16. One can calculate the degree of noncomplementarity of sticky end base pairs. In the case of STLs (i. e., STL(X,O) and STL(X,X)), the number of different possible sticky end binding sets (e. g., c1?+c1?, c2+c3?, c3?+c4) is 10. Out of these, 5 binding sets (c1?+c4, c2+c2, c2+c4, c3?+c3?, and c4+c4) have 5 out of 5 noncomplementary sticky end base pairs, 2 binding sets (c1?+c2 and c1?+c4) have 4 out of 5 noncomplementary sticky end base pairs, and 3 binding sets (c1?+c1?, c2+c3?, and c3?+c4) have 3 out of 5 noncomplementary sticky end base pairs (Figures 13S and 19S). In the same manner, for DTL(X,O) and DTL(X,X), there are 36 possible sticky end binding sets. Besides the 2 common sets, which have 5 complementary sticky end base pairs, 12 binding sets have 5 out of 5 noncomplementary sticky end base pairs, another 12 binding sets have 4 out of 5 noncomplementary sticky end base pairs, and 10 binding sets have 3 out of 5 noncomplementary sticky end base pairs (Figures 29S and 31S).
17. Reif, J. H.; Sahu, S.; Yin, P. Compact Error-Resilient Computational DNA Tiling Assemblies. DNA Computing 10 LNCS 2005, 3384, 293-307 (Pubitemid 41231405)
18. Fujibayashi, K.; Murata, S. A Method of Error Suppression for Self-Assembling DNA Tiles. DNA Computing 10 LNCS 2005, 3384, 113-127 (Pubitemid 41231389)
19. Winfree, E.; Bekbolatov, R. Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly. DNA Computing 9 LNCS 2004, 2943, 126-144
20. Kolachure, V.; Jin, H.-C. Fabrication of P3HT/PCBM Bulk Heterojunction Solar Cells with DNA Complex Layer Conf. Rec. IEEE Photovoltaic Spec. Conf. 2008, 1-5
21. Heckman, E. M.; Yaney, P. P.; Grote, J. G.; Hopkins, F. K. Performance of an Electro-Optic Waveguide Modulator Fabricated Using a Deoxyribonucleic-Acid- Based Biopolymer Appl. Phys. Lett. 2006, 89, 181116-1-181116-3