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Nucleic Acids Research, 2000, Vol. 28, No. 21 e93
© 2000 Oxford University Press

Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX

Timur Shtatland1, Stanley C. Gill3, Brenda E. Javornik3, Hans E. Johansson2, Britta S. Singer1, Olke C. Uhlenbeck2, Dominic A. Zichi3 and Larry Gold1,3,*

1Department of Molecular, Cellular and Developmental Biology and 2Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0347, USA and 3NeXstar Pharmaceuticals, Inc., 2860 Wilderness Place, Boulder, CO 80301, USA

Genomic SELEX is a method for studying the network of nucleic acid–protein interactions within any organism. Here we report the discovery of several interesting and potentially biologically important interactions using genomic SELEX. We have found that bacteriophage MS2 coat protein binds several Escherichia coli mRNA fragments more tightly than it binds the natural, well-studied, phage mRNA site. MS2 coat protein binds mRNA fragments from rffG (involved in formation of lipopolysaccharide in the bacterial outer membrane), ebgR (lactose utilization repressor), as well as from several other genes. Genomic SELEX may yield experimentally induced artifacts, such as molecules in which the fixed sequences participate in binding. We describe several methods (annealing of oligonucleotides complementary to fixed sequences or switching fixed sequences) to eliminate some, or almost all, of these artifacts. Such methods may be useful tools for both randomized sequence SELEX and genomic SELEX.

* To whom correspondence should be addressed at Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA. Tel: +1 303 492 7864; Fax: +1 303 492 7744; Email: lgold@somalogic.com Present addresses: Timur Shtatland, LION Bioscience Research Inc., 141 Portland Street, 10th Floor, Cambridge, MA 02139, USA Stanley C. Gill, Gilead Sciences, Inc., 2860 Wilderness Place, Boulder, CO 80301, USA Brenda E. Javornik, SomaLogic, Inc., 1775 38th Street, Boulder, CO 80301, USA Hans E. Johansson, Department of Genetics and Pathology, Division of Medical Genetics, Uppsala University Biomedical Center, Box 589, S-75123 Uppsala, Sweden Dominic A. Zichi, SomaLogic, Inc., 1775 38th Street, Boulder, CO 80301, USA


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