posted on 2016-08-31, 00:00authored byThéo Calais, Vincent Baijot, Mehdi Djafari Rouhani, David Gauchard, Yves J. Chabal, Carole Rossi, Alain Estève
The DNA-directed
assembly of nano-objects has been the subject
of many recent studies as a means to construct advanced nanomaterial
architectures. Although much experimental in silico work has been
presented and discussed, there has been no in-depth consideration
of the proper design of single-strand sticky termination of DNA sequences,
noted as ssST, which is important in avoiding self-folding within
one DNA strand, unwanted strand-to-strand interaction, and mismatching.
In this work, a new comprehensive and computationally efficient optimization
algorithm is presented for the construction of all possible DNA sequences
that specifically prevents these issues. This optimization procedure
is also effective when a spacer section is used, typically repeated
sequences of thymine or adenine placed between the ssST and the nano-object,
to address the most conventional experimental protocols. We systematically
discuss the fundamental statistics of DNA sequences considering complementarities
limited to two (or three) adjacent pairs to avoid self-folding and
hybridization of identical strands due to unwanted complements and
mismatching. The optimized DNA sequences can reach maximum lengths
of 9 to 34 bases depending on the level of applied constraints. The
thermodynamic properties of the allowed sequences are used to develop
a ranking for each design. For instance, we show that the maximum
melting temperature saturates with 14 bases under typical solvation
and concentration conditions. Thus, DNA ssST with optimized sequences
are developed for segments ranging from 4 to 40 bases, providing a
very useful guide for all technological protocols. An experimental
test is presented and discussed using the aggregation of Al and CuO
nanoparticles and is shown to validate and illustrate the importance
of the proposed DNA coding sequence optimization.