Abstract
We have isolated RNA ligands with low-nanomolar affinity and high specificity to basic fibroblast growth factor from a pool of 10(14) molecules containing 30 randomized positions by the systematic evolution of ligands by exponential enrichment (SELEX) procedure. High-affinity ligands could be classified into two families based on sequence and secondary structure similarities. Representative RNA ligands from the two families compete with one another as well as with heparin for binding to the protein. Furthermore, we show that these ligands inhibit the first step in the signaling pathway of basic fibroblast growth factor: binding of the growth factor to its cell-surface receptors. These findings emphasize the general usefulness of SELEX as a tool for discovering potent, specific oligonucleotide antagonists of target proteins.
Full text
PDF




Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Bartel D. P., Zapp M. L., Green M. R., Szostak J. W. HIV-1 Rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA. Cell. 1991 Nov 1;67(3):529–536. doi: 10.1016/0092-8674(91)90527-6. [DOI] [PubMed] [Google Scholar]
- Basilico C., Moscatelli D. The FGF family of growth factors and oncogenes. Adv Cancer Res. 1992;59:115–165. doi: 10.1016/s0065-230x(08)60305-x. [DOI] [PubMed] [Google Scholar]
- Bock L. C., Griffin L. C., Latham J. A., Vermaas E. H., Toole J. J. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature. 1992 Feb 6;355(6360):564–566. doi: 10.1038/355564a0. [DOI] [PubMed] [Google Scholar]
- Ellington A. D., Szostak J. W. In vitro selection of RNA molecules that bind specific ligands. Nature. 1990 Aug 30;346(6287):818–822. doi: 10.1038/346818a0. [DOI] [PubMed] [Google Scholar]
- Ellington A. D., Szostak J. W. Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature. 1992 Feb 27;355(6363):850–852. doi: 10.1038/355850a0. [DOI] [PubMed] [Google Scholar]
- Folkman J., Klagsbrun M. Angiogenic factors. Science. 1987 Jan 23;235(4787):442–447. doi: 10.1126/science.2432664. [DOI] [PubMed] [Google Scholar]
- Gill S. C., von Hippel P. H. Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem. 1989 Nov 1;182(2):319–326. doi: 10.1016/0003-2697(89)90602-7. [DOI] [PubMed] [Google Scholar]
- Gospodarowicz D., Cheng J. Heparin protects basic and acidic FGF from inactivation. J Cell Physiol. 1986 Sep;128(3):475–484. doi: 10.1002/jcp.1041280317. [DOI] [PubMed] [Google Scholar]
- Gospodarowicz D. Fibroblast growth factors: from genes to clinical applications. Cell Biol Rev. 1991;25(4):307-16, 337-9. [PubMed] [Google Scholar]
- Gutell R. R., Power A., Hertz G. Z., Putz E. J., Stormo G. D. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res. 1992 Nov 11;20(21):5785–5795. doi: 10.1093/nar/20.21.5785. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Heus H. A., Uhlenbeck O. C., Pardi A. Sequence-dependent structural variations of hammerhead RNA enzymes. Nucleic Acids Res. 1990 Mar 11;18(5):1103–1108. doi: 10.1093/nar/18.5.1103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Irvine D., Tuerk C., Gold L. SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. J Mol Biol. 1991 Dec 5;222(3):739–761. doi: 10.1016/0022-2836(91)90509-5. [DOI] [PubMed] [Google Scholar]
- James B. D., Olsen G. J., Pace N. R. Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol. 1989;180:227–239. doi: 10.1016/0076-6879(89)80104-1. [DOI] [PubMed] [Google Scholar]
- Middaugh C. R., Mach H., Burke C. J., Volkin D. B., Dabora J. M., Tsai P. K., Bruner M. W., Ryan J. A., Marfia K. E. Nature of the interaction of growth factors with suramin. Biochemistry. 1992 Sep 22;31(37):9016–9024. doi: 10.1021/bi00152a044. [DOI] [PubMed] [Google Scholar]
- Mignatti P., Tsuboi R., Robbins E., Rifkin D. B. In vitro angiogenesis on the human amniotic membrane: requirement for basic fibroblast growth factor-induced proteinases. J Cell Biol. 1989 Feb;108(2):671–682. doi: 10.1083/jcb.108.2.671. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Moscatelli D. High and low affinity binding sites for basic fibroblast growth factor on cultured cells: absence of a role for low affinity binding in the stimulation of plasminogen activator production by bovine capillary endothelial cells. J Cell Physiol. 1987 Apr;131(1):123–130. doi: 10.1002/jcp.1041310118. [DOI] [PubMed] [Google Scholar]
- Prestrelski S. J., Fox G. M., Arakawa T. Binding of heparin to basic fibroblast growth factor induces a conformational change. Arch Biochem Biophys. 1992 Mar;293(2):314–319. doi: 10.1016/0003-9861(92)90401-h. [DOI] [PubMed] [Google Scholar]
- Rapraeger A. C., Krufka A., Olwin B. B. Requirement of heparan sulfate for bFGF-mediated fibroblast growth and myoblast differentiation. Science. 1991 Jun 21;252(5013):1705–1708. doi: 10.1126/science.1646484. [DOI] [PubMed] [Google Scholar]
- Reidy M. A. Factors controlling smooth-muscle cell proliferation. Arch Pathol Lab Med. 1992 Dec;116(12):1276–1280. [PubMed] [Google Scholar]
- Rifkin D. B., Moscatelli D. Recent developments in the cell biology of basic fibroblast growth factor. J Cell Biol. 1989 Jul;109(1):1–6. doi: 10.1083/jcb.109.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schneider D., Tuerk C., Gold L. Selection of high affinity RNA ligands to the bacteriophage R17 coat protein. J Mol Biol. 1992 Dec 5;228(3):862–869. doi: 10.1016/0022-2836(92)90870-p. [DOI] [PubMed] [Google Scholar]
- Schneider T. D., Stormo G. D., Gold L., Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol. 1986 Apr 5;188(3):415–431. doi: 10.1016/0022-2836(86)90165-8. [DOI] [PubMed] [Google Scholar]
- Tuerk C., Eddy S., Parma D., Gold L. Autogenous translational operator recognized by bacteriophage T4 DNA polymerase. J Mol Biol. 1990 Jun 20;213(4):749–761. doi: 10.1016/S0022-2836(05)80261-X. [DOI] [PubMed] [Google Scholar]
- Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990 Aug 3;249(4968):505–510. doi: 10.1126/science.2200121. [DOI] [PubMed] [Google Scholar]
- Tuerk C., MacDougal S., Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):6988–6992. doi: 10.1073/pnas.89.15.6988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tyrrell D. J., Ishihara M., Rao N., Horne A., Kiefer M. C., Stauber G. B., Lam L. H., Stack R. J. Structure and biological activities of a heparin-derived hexasaccharide with high affinity for basic fibroblast growth factor. J Biol Chem. 1993 Mar 5;268(7):4684–4689. [PubMed] [Google Scholar]
- Yayon A., Klagsbrun M., Esko J. D., Leder P., Ornitz D. M. Cell surface, heparin-like molecules are required for binding of basic fibroblast growth factor to its high affinity receptor. Cell. 1991 Feb 22;64(4):841–848. doi: 10.1016/0092-8674(91)90512-w. [DOI] [PubMed] [Google Scholar]