Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production
Authors: Rydzanicz, Roman; Zhao, X. Sharon; Johnson, Philip E.
Source: Nucleic Acids Research, Volume 33, Supplement 1, 1 July 2005 , pp. W521-W525(5)
Publisher: Oxford University Press
Abstract:We describe a computer program, Assembly PCR Oligo Maker, created to automate the design of oligodeoxynucleotides for the PCR-based construction of long DNA molecules. This program is freely available at http://publish.yorku.ca/~pjohnson/AssemblyPCRoligomaker.html and has been specifically designed to aid in the construction of DNA molecules that are to be used for the production of RNA molecules by in vitro synthesis with T7 RNA polymerase. The input for Assembly PCR Oligo Maker is either the desired DNA sequence to be made or an RNA sequence. If RNA is the input, the program first determines the DNA sequence necessary to produce the desired RNA molecule. The program then determines the sequences of all the oligodeoxynucleotides necessary for a two-step assembly PCR-based synthesis of the desired DNA molecule. The oligodeoxynucleotide sequences outputted are designed to have a uniform melt temperature and are checked for regions of overlap outside of the desired priming regions necessary for the PCR reaction. The validity of the program was verified experimentally by synthesizing a 191-nt long DNA molecule using the DNA sequences suggested by the program.
Document Type: Research Article
Publication date: 1 July 2005
- Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.