Real-Time Primer Design for DNA Chips

H. Simmler and H. Singpiel
Acconovis GmbH
Lindenhofstr. 42-44
68163 Mannheim, Germany
eMail: simmler@acconovis.com

R. M¨anner
Universit¨at Mannheim
B6, 23-29
68131 Mannheim, Germany
maenner@ti.uni-mannheim.de

Abstract
The design of PCR or DNA Chip experiments is a time consuming process where bioinformatics is extensively used. The selection of the primers, which are immobilized on the DNA chip, requires a complex algorithm. Based on several parameters an optimized set of primers is automatically detected for a given gene sequence.This paper describes a parallel architecture which performs the optimization of the primer selection on a hardware accelerator. In contrast to the pure software approach,the parallel architecture gains a speedup of factor 500 using a PCI based hardware accelerator. This approach allows an optimization of a specified primer set in real-time.

1 Introduction
Both, the amplification of DNA sequences using polymerase chain reaction (PCR) and the massive parallel analysis
of genes in biological cells using DNA chips (or DNA arrays) have a great impact on modern biological research. PCR is used to amplify a particular DNA fragment called target sequence. In general, a forward and a reverse primer is generated. The target sequence, located between the two primers, is duplicated using a complex process protocol [1].
DNA chips are used to analyse a large number of genes in parallel. This provides an insight view into cells or can improve the search for gene defects in a particular genome.The DNA chips perform up to 500.000 experiments in parallel and enable the researcher to monitor the whole genome on a single chip at the same time [2, 3].Although these two applications have different aims –amplification and analysis – both techniques make use of primers. Formally, primers are considered as strings that represent a DNA sequence. This DNA sequence consists of four bases represented by the letters {A; G; T;C}. The start of the DNA sequence is denoted by 5’ end and the termination is denoted 3’ end [4].

Prior to the biological experiments, either PCR or DNA chips, primers have to be designed and synthesized. In general,
primer design is based on several criteria that extend beyond string matching. Typical criteria used for the design are the exact string match, the primer length, the melting temperature, the salt concentration for the experiment and the hybridization effects that have to be taken into account for the selected primers. PCR experiments need only a few different primers whereas several thousand different primers are needed for a DNA chip. The complete processing time for an optimal primer set can take hours taking the various criteria into account.Preparing a DNA experiment can be described as a workflow consisting of three steps.

1. Define the genes that have to be analysed.
2. Design the optimum primer for the gene.
3. Verify the primer in a macroscopic experiment.
Furthermore, the second design step is separated into the computation of the primer sets and a database comparison
with each primer. The database check compares the selected primers against the genome database to avoid a “false positive”signal that is not generated by the specified gene. This paper concentrates on the design of the primers.In section two the basics of DNA chips are described.Section three specify various parameters that are used to select
the optimal primers. The computation steps performed to select these optimal primers are described in section four.
The fifth section shows the idea of the parallel architecture whereas its implementation is described in section six. The
results achieved with the parallel architecture are listed in section seven. The final section provides some conclusions
and further applications of the parallel architecture.

2.2 DNA Chip Design
A DNA chip is separated into a matrix of spots. The amount of spots can vary from low density chips with 96 spots up to high density chips with 500.000 spots on one chip. Each spot on a DNA chip contains primers with a unique coding. The primers are immobilized on the spots.As shown in Figure 1 the interesting gene sequence1 binds to the primer. Each primer base binds the corresponding position on the gene sequence. This prevents the gene sequence