Abstract
One of the main problems in constructing synthetic genes is the incorrect hybridisation between the oligonucleotides. The problem is resolved if the sequence uniquely defines the position of the oligonucleotide in the assembled gene. This can be accomplished through the wise partition of dsDNA sequence in the fragments. We describe a program for use in designing such gene assembly. For a given DNA sequence and the approximate location of oligonucleotide boundary it generates all sets of protruding ends that share the smallest homology.
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Selected References
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- Breslauer K. J., Frank R., Blöcker H., Marky L. A. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. doi: 10.1073/pnas.83.11.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Breslauer K. J., Frank R., Blöcker H., Marky L. A. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. doi: 10.1073/pnas.83.11.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Comay E., Nussinov R., Comay O. An accelerated algorithm for calculating the secondary structure of single stranded RNAs. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):53–66. doi: 10.1093/nar/12.1part1.53. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ferretti L., Karnik S. S., Khorana H. G., Nassal M., Oprian D. D. Total synthesis of a gene for bovine rhodopsin. Proc Natl Acad Sci U S A. 1986 Feb;83(3):599–603. doi: 10.1073/pnas.83.3.599. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fortkamp E., Rieger M., Heisterberg-Moutses G., Schweitzer S., Sommer R. Cloning and expression in Escherichia coli of a synthetic DNA for hirudin, the blood coagulation inhibitor in the leech. DNA. 1986 Dec;5(6):511–517. doi: 10.1089/dna.1.1986.5.511. [DOI] [PubMed] [Google Scholar]
- Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. doi: 10.1073/pnas.83.24.9373. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jacobson A. B., Good L., Simonetti J., Zuker M. Some simple computational methods to improve the folding of large RNAs. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):45–52. doi: 10.1093/nar/12.1part1.45. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kanehisa M. I., Goad W. B. Pattern recognition in nucleic acid sequences. II. An efficient method for finding locally stable secondary structures. Nucleic Acids Res. 1982 Jan 11;10(1):265–278. doi: 10.1093/nar/10.1.265. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Khorana H. G. Total synthesis of a gene. Science. 1979 Feb 16;203(4381):614–625. doi: 10.1126/science.366749. [DOI] [PubMed] [Google Scholar]
- Maizel J. V., Jr, Lenk R. P. Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7665–7669. doi: 10.1073/pnas.78.12.7665. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rossi J. J., Kierzek R., Huang T., Walker P. A., Itakura K. An alternate method for synthesis of double-stranded DNA segments. J Biol Chem. 1982 Aug 25;257(16):9226–9229. [PubMed] [Google Scholar]
- Sproat B. S., Gait M. J. Chemical synthesis of a gene for somatomedin C. Nucleic Acids Res. 1985 Apr 25;13(8):2959–2977. doi: 10.1093/nar/13.8.2959. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Turk V., Brzin J., Longer M., Ritonja A., Eropkin M., Borchart U., Machleidt W. Protein inhibitors of cysteine proteinases. III. Amino-acid sequence of cystatin from chicken egg white. Hoppe Seylers Z Physiol Chem. 1983 Nov;364(11):1487–1496. doi: 10.1515/bchm2.1983.364.2.1487. [DOI] [PubMed] [Google Scholar]