A Mammalian High Mobility Group Protein Recognizes Any Stretch of Six A.T Base Pairs in Duplex DNA

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1986 Mar 1

PMID 3456586

Citations 127

Authors

M J Solomon

F Strauss

A Varshavsky

Affiliations

Soon will be listed here.

Abstract

alpha-Protein is a high mobility group protein originally purified from African green monkey cells based on its affinity for the 172-base-pair repeat of monkey alpha-satellite DNA. We have used DNase I footprinting to identify 50 alpha-protein binding sites on simian virus 40 DNA and thereby to determine the DNA binding specificity of this mammalian nuclear protein. alpha-Protein binds with approximately equal affinity to any run of six or more A X T base pairs in duplex DNA, to many, if not all, runs of five A X T base pairs, and to a small number of other sequences within otherwise (A + T)-rich regions. Unlike well characterized sequence-specific DNA binding proteins such as bacterial repressors, alpha-protein makes extensive contacts within the minor groove of B-DNA. These and related findings indicate that, rather than binding to a few specific DNA sequences, alpha-protein recognizes a configuration of the minor groove characteristic of short runs of A X T base pairs. We discuss possible functions of alpha-protein and the similarities in DNA recognition by alpha-protein and the antibiotic netropsin.

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References

Wartell R, Larson J, Wells R . Netropsin. A specific probe for A-T regions of duplex deoxyribonucleic acid. J Biol Chem. 1974; 249(21):6719-31. View

Hendrickson W, Schleif R . A dimer of AraC protein contacts three adjacent major groove regions of the araI DNA site. Proc Natl Acad Sci U S A. 1985; 82(10):3129-33. PMC: 397728. DOI: 10.1073/pnas.82.10.3129. View

Camerini-Otero R, Simon R, Williamson P, Zasloff M, Felsenfeld G . Nucleosome structure, DNA folding, and gene activity. Cold Spring Harb Symp Quant Biol. 1978; 42 Pt 1:57-75. DOI: 10.1101/sqb.1978.042.01.008. View

McCutchan T, Singer M, Rosenberg M . Structure of simian virus 40 recombinants that contain both host and viral DNA sequences. II. The structure of variant 1103 and its comparison to variant CVPS/1P2 (EcoRI res). J Biol Chem. 1979; 254(9):3592-7. View

Siebenlist U, Gilbert W . Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. Proc Natl Acad Sci U S A. 1980; 77(1):122-6. PMC: 348220. DOI: 10.1073/pnas.77.1.122. View

Maxam A, Gilbert W . Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980; 65(1):499-560. DOI: 10.1016/s0076-6879(80)65059-9. View

Rodriguez Alfageme C, RUDKIN G, Cohen L . Isolation, properties and cellular distribution of D1, a chromosomal protein of Drosophila. Chromosoma. 1980; 78(1):1-31. DOI: 10.1007/BF00291907. View

McGhee J, Felsenfeld G . Nucleosome structure. Annu Rev Biochem. 1980; 49:1115-56. DOI: 10.1146/annurev.bi.49.070180.005343. View

Weisbrod S, Weintraub H . Isolation of actively transcribed nucleosomes using immobilized HMG 14 and 17 and an analysis of alpha-globin chromatin. Cell. 1981; 23(2):391-400. DOI: 10.1016/0092-8674(81)90134-3. View

10.

Levinger L, Varshavsky A . Selective arrangement of ubiquitinated and D1 protein-containing nucleosomes within the Drosophila genome. Cell. 1982; 28(2):375-85. DOI: 10.1016/0092-8674(82)90355-5. View

11.

Cartwright I, Abmayr S, Fleischmann G, Lowenhaupt K, Elgin S, Keene M . Chromatin structure and gene activity: the role of nonhistone chromosomal proteins. CRC Crit Rev Biochem. 1982; 13(1):1-86. DOI: 10.3109/10409238209108709. View

12.

Van Dyke M, Hertzberg R, Dervan P . Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA.Fe(II). Proc Natl Acad Sci U S A. 1982; 79(18):5470-4. PMC: 346925. DOI: 10.1073/pnas.79.18.5470. View

13.

Levinger L, Varshavsky A . Protein D1 preferentially binds A + T-rich DNA in vitro and is a component of Drosophila melanogaster nucleosomes containing A + T-rich satellite DNA. Proc Natl Acad Sci U S A. 1982; 79(23):7152-6. PMC: 347296. DOI: 10.1073/pnas.79.23.7152. View

14.

Sakonju S, Brown D . Contact points between a positive transcription factor and the Xenopus 5S RNA gene. Cell. 1982; 31(2 Pt 1):395-405. DOI: 10.1016/0092-8674(82)90133-7. View

15.

Rosenberg J, Greene P . Eco RI* specificity and hydrogen bonding. DNA. 1982; 1(2):117-24. DOI: 10.1089/dna.1.1982.1.117. View

16.

Zhang X, FITTLER F, Horz W . Eight different highly specific nucleosome phases on alpha-satellite DNA in the African green monkey. Nucleic Acids Res. 1983; 11(13):4287-306. PMC: 326047. DOI: 10.1093/nar/11.13.4287. View

17.

Wu K, Strauss F, Varshavsky A . Nucleosome arrangement in green monkey alpha-satellite chromatin. Superimposition of non-random and apparently random patterns. J Mol Biol. 1983; 170(1):93-117. DOI: 10.1016/s0022-2836(83)80228-9. View

18.

Sheflin L, Celeste A . Recombination in simian virus 40-infected cells. Structure of naturally arising variants ev-2114, ev-2102, and ev-1110. J Biol Chem. 1983; 258(23):14315-21. View

19.

Fried M, Crothers D . Equilibrium studies of the cyclic AMP receptor protein-DNA interaction. J Mol Biol. 1984; 172(3):241-62. DOI: 10.1016/s0022-2836(84)80025-x. View

20.

Garreau H, G Williams J . Two nuclear DNA binding proteins of Dictyostelium discoideum with a high affinity for poly(dA)-poly(dT). Nucleic Acids Res. 1983; 11(23):8473-84. PMC: 326596. DOI: 10.1093/nar/11.23.8473. View