EGNAS: an exhaustive DNA sequence design algorithm

• Published in: BMC bioinformatics Vol. 13; no. 1; p. 138
• Main Authors: Kick, Alfred, Bönsch, Martin, Mertig, Michael
• Format: Journal Article
• Language: English
• Published: London BioMed Central 20.06.2012; BioMed Central Ltd; Springer Nature B.V; BMC
• Subjects: Algorithms; Base Pairing; Base Sequence; Bioinformatics; Biomedical and Life Sciences; Chromosomes; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Deoxyribonucleic acid; Design; DNA; DNA - chemistry; DNA - genetics; DNA computing; DNA origami; DNA sequence design algorithm; DNA sequencers; DNA sequencing; Electric generators; Genetics; Genotype; Hairpin; Life Sciences; Microarrays; Nanotechnology; Nucleic Acid Conformation; Nucleic acids; Nucleotide sequence; Nucleotide sequencing; Operating systems; Physiological aspects; Polymerase Chain Reaction; Polymerase chain reaction (PCR); Polymorphism, Single Nucleotide; Purines; Pyrimidines; Risk reduction; Sequence analysis (methods); Sequence Analysis, DNA - methods; Single nucleotide polymorphism (SNP); Single nucleotide polymorphisms; Single-base extension (SBE); Software; stem-and-loop structure; Studies; Germany; Hairpin; Single-base extension (SBE); Polymerase chain reaction (PCR); DNA sequence design algorithm; stem-and-loop structure; DNA origami; Single nucleotide polymorphism (SNP); DNA computing
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-13-138

Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA) is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences) offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS .