Abstract
The interaction of several synthetic analogues of d-ApA with Poly U and Poly dT was examined to explore the effects of substituents at phosphorus on binding properties of oligonucleotides. These analogues contained a bulky, lipophilic group (2,2,2-trichloroethoxy or 2,2,2-trichloro-1,1-dimethylethoxy) a small, uncharged hydrogen-bonding group (amido), or a cationic phosphoramidate (2-aminoethylamido, protonated in neutral aqueous media) in place of the anionic oxygen of the internucleotide phosphate. As determined by "melting curves" each formed a complex with Poly U more stable than the Poly U.d-ApA complex. Binding to Poly dT was comparable or in some cases stronger. Checks on composition (mixing curves) revealed the expected stoichiometry of ldA:2U (or 2dT). Stereochemistry at phosphorus influenced stability of the complexes, but the effect was not a major one. These results suggest that oligonucleotides containing large, lipophilic groups, as well as small non-ionic groups (e.g., the methyl phosphonates) or polar groups, could be useful as probes in hybridization experiments.
Full text
PDF
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Adamiak R. W., Biala E., Grześkowiak, Kierzek R., Kraszewski A., Markiewicz W. T., Stawiński J., Wiewiórowski Nucleoside 3'-phosphotriesters as key intermediates for the oligoribonucleotide synthesis. IV. New method for removal of 2,2,2-trichloroethyl group and 31P NMR as a new tool for analysis of deblocking of internucleotide phosphate protecting groups. Nucleic Acids Res. 1977 Jul;4(7):2321–2329. doi: 10.1093/nar/4.7.2321. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Blake K. R., Murakami A., Spitz S. A., Glave S. A., Reddy M. P., Ts'o P. O., Miller P. S. Hybridization arrest of globin synthesis in rabbit reticulocyte lysates and cells by oligodeoxyribonucleoside methylphosphonates. Biochemistry. 1985 Oct 22;24(22):6139–6145. doi: 10.1021/bi00343a016. [DOI] [PubMed] [Google Scholar]
- Eckstein F. Nucleoside phosphorothioates. Annu Rev Biochem. 1985;54:367–402. doi: 10.1146/annurev.bi.54.070185.002055. [DOI] [PubMed] [Google Scholar]
- Gabbay E. J. Topography of nucleic acid helices in solutions. I. The nonidentity of polyadenylic-polyuridylic and polyinosinic-polycytidylic acid helices. Biochemistry. 1966 Sep;5(9):3036–3043. doi: 10.1021/bi00873a037. [DOI] [PubMed] [Google Scholar]
- Kondo N. S., Holmes H. M., Stempel L. M., Ts'o O. P. Influence of the phosphodiester linkage (3'-5', 2'-5', and 5'-5') on the conformation of dinucleoside monophosphate. Biochemistry. 1970 Sep 1;9(18):3479–3498. doi: 10.1021/bi00820a002. [DOI] [PubMed] [Google Scholar]
- Letsinger F. L., Wilkes J. S. Incorporation of 5'-amino-5'-deoxythymidine5'-phosphate in polynucleotides by use of DNA polymerase I and a phiX174 DNA template. Biochemistry. 1976 Jun 29;15(13):2810–2816. doi: 10.1021/bi00658a017. [DOI] [PubMed] [Google Scholar]
- Miller P. S., Fang K. N., Kondo N. S., Ts'o P. O. Syntheses and properties of adenine and thymine nucleoside alkyl phosphotriesters, the neutral analogs of dinucleoside monophosphates. J Am Chem Soc. 1971 Dec;93(24):6657–6665. doi: 10.1021/ja00753a054. [DOI] [PubMed] [Google Scholar]
- Miller P. S., Yano J., Yano E., Carroll C., Jayaraman K., Ts'o P. O. Nonionic nucleic acid analogues. Synthesis and characterization of dideoxyribonucleoside methylphosphonates. Biochemistry. 1979 Nov 13;18(23):5134–5143. doi: 10.1021/bi00590a017. [DOI] [PubMed] [Google Scholar]
- Ogilvie K. K., Theriault N., Sadana K. L. Synthesis of oligoribonucleotides. J Am Chem Soc. 1977 Nov 9;99(23):7741–7743. doi: 10.1021/ja00465a073. [DOI] [PubMed] [Google Scholar]
- RAZZELL W. E., KHORANA H. G. Studies on polynucleotides. IV. Enzymic degradation; the stepwise action of venom phosphodiesterase on deoxyribo-oligonucleotides. J Biol Chem. 1959 Aug;234(8):2114–2117. [PubMed] [Google Scholar]