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Designing universal oligonucleotides for DNA/nanoparticle conjugates

G. Ivan, V. Grolmusz
Eotvos Lorand University, HU

Keywords: DNA/nanoparticle conjugates, oligonucleotide design, DNA sequence detection


As DNA sequences originating from different species are highly specific, it is a challenge to design “universal” DNA/nanoparticle conjugates that are able to hybridize to each member of a set of nucleotide sequences. Possible applications include the detection of highly different nucleotide sequences using only a few types of DNA/nanoparticle conjugates. Given a set ‘N’ of several nucleotide sequences, we would like to find a small set of oligonucleotides that ‘cover’ all the sequences in ‘N’. An oligonucleotide ‘covers’ a nucleotide sequence, if it occurs in it with at most ‘k’ mismatches (‘k’ is a small, pre-defined integer). In the nontrivial case, testing every possible oligonucleotide with a length of up to e.g. 50 is infeasible, as the size of the search space is an exponential function of the oligonucleotide length. Moreover, we are not after one single oligonucleotide, but the smallest possible set of them. We present a computational method that is suitable to design oligonucleotide probes that cover a given input set ‘N’ of nucleotide sequences. Correctness and efficiency of the method is validated by comparing the results to optimal solutions obtained by exhaustive search. Being able to optimize the oligonucleotide sequences attached to a nanoparticle, we believe our proposed method will prove to be useful in several areas of biotechnology where DNA/nanoparticle conjugates are involved.
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