Nucleic acid design

sequences, where the bases are matched into only A-T or G-C pairs. The structure of nucleic acids consists of a sequence of nucleotides. There are four types of nucleotides distinguished by which of the four nucleobases they contain: in DNA these are adenine (A), cytosine (C), guanine (G), and thymine (T). Nucleic acids have the property that two molecules will bind to each other to form a double helix only if the two sequences are complementary, that is, they can form matching sequences of base pairs. Thus, in nucleic acids the sequence determines the pattern of binding and thus the overall structure. Nucleic acid design is the process by which, given a desired target structure or functionality, sequences are generated for nucleic acid strands which will self-assemble into that target structure. Nucleic acid design encompasses all levels of nucleic acid structure: • Primary structure—the raw sequence of nucleobases of each of the component nucleic acid strands; • Secondary structure—the set of interactions between bases, i.e., which parts of which strands are bound to each other; and • Tertiary structure—the locations of the atoms in three-dimensional space, taking into consideration geometrical and steric constraints. One of the greatest concerns in nucleic acid design is ensuring that the target structure has the lowest free energy (i.e. is the most thermodynamically favorable) whereas misformed structures have higher values of free energy and are thus unfavored. These goals can be achieved through the use of a number of approaches, including heuristic, thermodynamic, and geometrical ones. Almost all nucleic acid design tasks are aided by computers, and a number of software packages are available for many of these tasks. Two considerations in nucleic acid design are that desired hybridizations should have melting temperatures in a narrow range, and any spurious interactions should have very low melting temperatures (i.e. they should be very weak). There is also a contrast between affinity-optimizing "positive design", seeks to minimize the energy of the desired structure in an absolute sense, and specificity-optimizing "negative design", which considers the energy of the target structure relative to those of undesired structures. Algorithms which implement both kinds of design tend to perform better than those that consider only one type. == Approaches ==

Heuristic methods Heuristic methods use simple criteria which can be quickly evaluated to judge the suitability of different sequences for a given secondary structure. They have the advantage of being much less computationally expensive than the energy minimization algorithms needed for thermodynamic or geometrical modeling, and being easier to implement, but at the cost of being less rigorous than these models. Sequence symmetry minimization is the oldest approach to nucleic acid design and was first used to design immobile versions of branched DNA structures. Sequence symmetry minimization divides the nucleic acid sequence into overlapping subsequences of a fixed length, called the criterion length. Each of the 4N possible subsequences of length N is allowed to appear only once in the sequence. This ensures that no undesired hybridizations can occur which have a length greater than or equal to the criterion length. A related heuristic approach is to consider the "mismatch distance", meaning the number of positions in a certain frame where the bases are not complementary. A greater mismatch distance lessens the chance that a strong spurious interaction can happen. mfold/UNAFold, and Vienna. A related approach, inverse secondary structure prediction, uses stochastic local search which improves a nucleic acid sequence by running a structure prediction algorithm and the modifying the sequence to eliminate unwanted features. Models of this type are useful for ensuring that tertiary structure constraints do not cause excessive strain to the molecule. Geometrical models of nucleic acids are used to predict tertiary structure. This is important because designed nucleic acid complexes usually contain multiple junction points, which introduces geometric constraints to the system. These constraints stem from the basic structure of nucleic acids, mainly that the double helix formed by nucleic acid duplexes has a fixed helicity of about 10.4 base pairs per turn, and is relatively stiff. Because of these constraints, the nucleic acid complexes are sensitive to the relative orientation of the major and minor grooves at junction points. Geometrical modeling can detect strain stemming from misalignments in the structure, which can then be corrected by the designer. Software for geometrical modeling of nucleic acids includes GIDEON, Tiamat, Nanoengineer-1, and UNIQUIMER 3D. Geometrical concerns are especially of interest in the design of DNA origami, because the sequence is predetermined by the choice of scaffold strand. Software specifically for DNA origami design has been made, including caDNAno and SARSE. ==Applications==

Nucleic acid design is used in DNA nanotechnology to design strands which will self-assemble into a desired target structure. These include examples such as DNA machines, periodic two- and three-dimensional lattices, polyhedra, and DNA origami. It can also be used to create sets of nucleic acid strands which are "orthogonal", or non-interacting with each other, so as to minimize or eliminate spurious interactions. This is useful in DNA computing, as well as for molecular barcoding applications in chemical biology and biotechnology. ==See also==