Biomod/2011/PSU/BlueGenes/lit

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Home     ::: Overview     :::     Methods     :::     Results     :::     Application     :::     Literature     :::     Team

Literature

Here we list the papers that have helped us get to where we are with the project.

DNA Origami

Before we could begin our project, we had to first learn about DNA origami. These are the papers have helped us learn more about the research in this innovative field.

  • Nadrian Seeman. Nucleic Acid Junctions and Lattices.
Journal of Theoretical Biology 99: 237-247. 1982. [1]
  • Paul Rothemund. Folding DNA to create nanoscale shapes and patterns.
Nature 440: 297-302. 2006. [2]
  • Hendrik Dietz, Shawn Douglas and William Shih. 2009. Folding DNA into Twisted and Curved Nanoscale Shapes.
Science 325(5941): 725-730.
  • Carlos Castro, Fabian Kilchherr, Do-Nyun Kim, Enrique Shiao, Tobias Wauer, Philipp Wortmann, Mark Bathe, and Hendrik Dietz. A primer to scaffolded DNA origami.
Nature Methods 8(3): 221-229. 2011. [3]
  • Yonggang Ke, Jaswinder Sharma, Minghui Liu, Kasper Jahn, Yan Liu and Hao Yan. Scaffolded DNA origami of a DNA tetrahedron molecular container.
Nano Letters 9(6): 2445-2447. 2009. [4]
  • Ebbe S. Andersen, Mingdong Dong, Morten M. Nielsen, Kasper Jahn, Allan Lind-Thomsen, Wael Mamdouh, Kurt V. Gothelf, Flemming Besenbacher and Jørgen Kjems. DNA Origami Design of Dolphin-Shaped Structures with Flexible Tails.
ACS Nano 2(6): 1213-1218. 2008. [5]


Mathematics

These papers helped us understand the mathematics.

  • Timothy Lezon and Ivet Bahar. Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology.
PLoS Computational Biology 6(6): e1000816. 2010. [6]
  • Ivet Bahar, Ali Rana Atilgan, Melik C. Demirel, and Burak Erma. Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability.
Physical Review Letters 80: 2733-2736. 1998. [7]
  • Melik Demirel, Ali Rana Atilgan, Robert L. Jernigan, Burak Erman, and Ivet Bahar. Identification of kinetically hot residues in proteins.
Protein Science 7: 2522-2532. 1998.[8]


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