DNA by Design: De novo Computational Framework for DNA Sequence Design and Nanotechnology

De novo enzymes by computational design.

Computational enzyme design has emerged as a promising tool for generating made-to-order biocatalysts. In addition to improving the reliability of the design cycle, current efforts in this area are focusing on expanding the set of catalyzed reactions and investigating the structure and mechanism of individual designs. Although the activities of de novo enzymes are typically low, they can be sig...

De novo design of protein mimics of B-DNA.

Structural mimicry of DNA is utilized in nature as a strategy to evade molecular defences mounted by host organisms. One such example is the protein Ocr - the first translation product to be expressed as the bacteriophage T7 infects E. coli. The structure of Ocr reveals an intricate and deliberate arrangement of negative charges that endows it with the ability to mimic ∼24 base pair stretches o...

Structural DNA Nanotechnology: From Design to Applications

The exploitation of DNA for the production of nanoscale architectures presents a young yet paradigm breaking approach, which addresses many of the barriers to the self-assembly of small molecules into highly-ordered nanostructures via construct addressability. There are two major methods to construct DNA nanostructures, and in the current review we will discuss the principles and some examples ...

Search Strategies for DNA Sequence Design Software

Designing oligonucleotide sequences that are suitable for applications in nanobiotechnology or DNA Computing is not feasable without the help of computers. Such molecules have to hybridize specifically and with high and homogeneous efficiency to their respective complement. A computer program called dsc (DNA Sequence Compiler) translates specifications of physical, chemical and logical properti...

Improving Sequence Design for DNA Computing