Molecular models of DNA

About: Molecular models of DNA is a research topic. Over the lifetime, 300 publications have been published within this topic receiving 16805 citations.

Exploring the Feasibility of a DNA Computer: Design of an ALU Using Sticker-Based DNA Model

Abstract: Since its inception, DNA computing has advanced to offer an extremely powerful, energy-efficient emerging technology for solving hard computational problems with its inherent massive parallelism and extremely high data density. This would be much more powerful and general purpose when combined with other existing well-known algorithmic solutions that exist for conventional computing architectures using a suitable ALU. Thus, a specifically designed DNA Arithmetic and Logic Unit (ALU) that can address operations suitable for both domains can mitigate the gap between these two. An ALU must be able to perform all possible logic operations, including NOT, OR, AND, XOR, NOR, NAND, and XNOR; compare, shift etc., integer and floating point arithmetic operations (addition, subtraction, multiplication, and division). In this paper, design of an ALU has been proposed using sticker-based DNA model with experimental feasibility analysis. Novelties of this paper may be in manifold. First, the integer arithmetic operations performed here are 2s complement arithmetic, and the floating point operations follow the IEEE 754 floating point format, resembling closely to a conventional ALU. Also, the output of each operation can be reused for any next operation. So any algorithm or program logic that users can think of can be implemented directly on the DNA computer without any modification. Second, once the basic operations of sticker model can be automated, the implementations proposed in this paper become highly suitable to design a fully automated ALU. Third, proposed approaches are easy to implement. Finally, these approaches can work on sufficiently large binary numbers.

Cytosine, the double helix and DNA self-assembly

Abstract: DNA self-assembly has crucial implications in reading out the genetic information in the cell and in nanotechnological applications. In a recent paper, self-assembled DNA crystals displaying spectacular triangular motifs have been described (Zheng et al., 2009). The authors claimed that their data demonstrate the possibility to rationally design well-ordered macromolecular 3D DNA lattice with precise spatial control using sticky ends. However, the authors did not recognize the fundamental features that control DNA self-assembly in the lateral direction. By analysing available crystallographic data and simulating a DNA triangle, we show that the double helix geometry, sequence-specific cytosine–phosphate interactions and divalent cations are in fact responsible for the precise spatial assembly of DNA.

Macroscopic localization lengths of vibrational normal modes in a heuristic DNA model

Abstract: In this work we study the localization of vibrational modes in heuristic models for disordered DNA-like molecules. Within such approach, atomic groups are replaced by renormalized sites connected by effective springs. The oscillation amplitudes at each site are considered and the localization degree of the normal modes is analyzed by means of the participation ratio, as well as the relative fluctuation of an ensemble of disorder realizations for normal modes in different frequency ranges. The present results suggest that the dynamical properties at low frequencies are completely different for double-strand structures compared to single-strand ones. Irrespective to disorder, double-strand molecules show normal modes with macroscopic localization lengths at low frequencies, for a wide range of spring constants considered in the literature, in contrast to the strong localization in single strands.