Technical report: Part 1. Basic requirements for designing optimal oligonucleotide probe sequences.

Although oligonucleotides can be easily synthesized and used in a variety of scientific fields, a major problem exists for each application: the difficulty of obtaining optimal oligonucleotide sequences. Oligonucleotide sequences have been described in each publication; however, little is disclosed on how to design such sequences and how specific each sequence is. This report introduces a new concept of computer hybridization simulation based on "thermodynamic hybridizability", which can overcome the problems of conventional homology analyses. Then, all the necessary components and factors for designing optimal probe sequences, such as hybridization strength, specificity, secondary structure, length of probes, probe-to-probe interaction, are discussed in detail. Also included are procedures for manipulating various types of data for selection of optimal oligonucleotides. This report provides a general guideline for optimal probe design and encourages basic and clinical scientists to enhance their research activities by using optimal oligonucleotides.