Abstract
Dimethyl sulfate (DMS) is an effective and widely used probe for sequence-specific protein-DNA interactions. It is the only probe routinely used both for in vitro (methylation protection, methylation interference) and in vivo (DMS genomic footprinting) applications since it rapidly reacts with DNA at room temperature and readily penetrates intact cells (1). DMS predominantly methylates the 7-nitrogen of guanine and 3-nitrogen of adenine. Thus, reactivity with G residues occurs in the major groove and with A residues in the minor groove. In standard Maxam and Gilbert protocols (2), the methylated bases are subsequently converted to strand breaks and displayed on sequencing gels.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Church, G. M. and Gilbert, W. (1984) Genomic sequencing. Proc. Natl. Acad Sci. USA 81,1991–1995.
Maxam, A. and Gilbert, W. (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Meth. Enzymol. 65, 499–560.
Fried, A. and Crothers, D. M. (1981) Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res 9,6505–6525.
Garner, M. M. and Revzin, A. (1981) A gel electrophoresis method for quantifying the binding of protein to specific DNA regions: application to components of the E. coli lactose operon regulatory system. Nucleic Acids Res. 9, 3047–3059
Gilbert, W., Maxam, A., and Mirzabekov, A (1976) Contacts between the LAC repressor and DNA revealed by methylation, in Control of Ribosome Biosynthesis, Alfred Benzon Symposium IX (Kjelgaard, N. 0. and Maaloe, O., eds.), Academic, New York, pp 139–148.
Johnsrud, L. (1978) Contacts between Escherichia coli RNA polymerase and a lac operon promoter. Proc. Natl. Acad. Sci. USA 75, 5314–5318.
Herrera, R. E., Shaw, P. E., and Nordheim, A. (1989) Occupation of the c-fos serum response element in vivo by a multi-protein complex is unaltered by growth factor induction. Nature 340,68–70.
Siebenlist, U. and Gilbert, W. (1980) Contacts between E. coli RNA polymerase and an early promoter of phage T7. Proc. Natl. Acad. Sci. USA 77, 122–126.
Shaw, P. E., Schriiter, H., and Nordheim, A. (1989) The ability of a ternary complex to form over the serum response element correlates with serum inducibility of the human c-fos promoter. Cell 56, 563–572.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1994 Humana Press Inc.
About this protocol
Cite this protocol
Shaw, P.E., Stewart, A.F. (1994). Identification of Protein-DNA Contacts with Dimethyl Sulfate. In: Geoff Kneale, G. (eds) DNA-Protein Interactions. Methods in Molecular Biology™, vol 30. Humana Press. https://doi.org/10.1385/0-89603-256-6:79
Download citation
DOI: https://doi.org/10.1385/0-89603-256-6:79
Publisher Name: Humana Press
Print ISBN: 978-0-89603-256-9
Online ISBN: 978-1-59259-517-4
eBook Packages: Springer Protocols