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

✍ Scribed by Masato Mitsuhashi

• Publisher: John Wiley and Sons
• Year: 1996
• Tongue: English
• Weight: 695 KB
• Volume: 10
• Category: Article
• ISSN: 0887-8013
• DOI: 10.1002/(sici)1098-2825(1996)10:5<277::aid-jcla8>3.0.co;2-5

✦ Synopsis

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 analy-ses. 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.