3D fractal DNA assembly from coding, geometry and protection

Alessandra Carbone, Chengde Mao, Pamela E. Constantinou, Baoquan Ding, Jens Kopatsch, William B. Sherman, Nadrian Seeman

Research output: Contribution to journalArticle

Abstract

We present DNA components whose 3D geometry and cohesive portions are compatible with a fractal 3D assembly. DNA parallelograms have been proposed in Carbone and Seeman [(2002b) Natural Computing 1: 469-480; [(2003) Natural Computing 2: 133-151] as suitable building blocks for a 2D fractal assembly of the Sierpinski carpet. Here we use Mao 3D triangles, which are 3D geometrically trigonal molecules, to construct basic building blocks and we obtain a simplified version of the 2D assembly design. As in the previous 2D construction, we utilize the interplay of coding in the form of cohesive ends, geometrical complementarity and protection of potentially undesirable sites of r eactivity. The schema we propose works for trigonal symmetries and the Mao triangle is one example of a possible DNA trigonal tile.

Original languageEnglish (US)
Pages (from-to)235-252
Number of pages18
JournalNatural Computing
Volume3
Issue number3
DOIs
StatePublished - Aug 2004

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Fractals
DNA
Geometry
Tile
Molecules

Keywords

  • Coding of times
  • DNA 3D assembly
  • DNA molecules
  • DNA nanotechnology
  • DNA protection
  • Geometry of tiles
  • Sierpinski cube
  • Tiling

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Carbone, A., Mao, C., Constantinou, P. E., Ding, B., Kopatsch, J., Sherman, W. B., & Seeman, N. (2004). 3D fractal DNA assembly from coding, geometry and protection. Natural Computing, 3(3), 235-252. https://doi.org/10.1023/B:NACO.0000036819.42166.1a

3D fractal DNA assembly from coding, geometry and protection. / Carbone, Alessandra; Mao, Chengde; Constantinou, Pamela E.; Ding, Baoquan; Kopatsch, Jens; Sherman, William B.; Seeman, Nadrian.

In: Natural Computing, Vol. 3, No. 3, 08.2004, p. 235-252.

Research output: Contribution to journalArticle

Carbone, A, Mao, C, Constantinou, PE, Ding, B, Kopatsch, J, Sherman, WB & Seeman, N 2004, '3D fractal DNA assembly from coding, geometry and protection', Natural Computing, vol. 3, no. 3, pp. 235-252. https://doi.org/10.1023/B:NACO.0000036819.42166.1a
Carbone A, Mao C, Constantinou PE, Ding B, Kopatsch J, Sherman WB et al. 3D fractal DNA assembly from coding, geometry and protection. Natural Computing. 2004 Aug;3(3):235-252. https://doi.org/10.1023/B:NACO.0000036819.42166.1a
Carbone, Alessandra ; Mao, Chengde ; Constantinou, Pamela E. ; Ding, Baoquan ; Kopatsch, Jens ; Sherman, William B. ; Seeman, Nadrian. / 3D fractal DNA assembly from coding, geometry and protection. In: Natural Computing. 2004 ; Vol. 3, No. 3. pp. 235-252.
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