Abstract
The kinetics for imino hydrogen exchange, at individual base pairs in the DNA sequence corresponding to the lactose operon operator of Escherichia coli, has been examined by NMR saturation recovery measurements as a function of temperature. Three 17-base-pair subsections of the lac operator DNA were chemically synthesized for these studies. The results support our previous observations in the 36-base-pair complete lac operator DNA fragment that has been used in our previous NMR studies. The results indicate faster opening kinetics at a GTG/CAC that is also the site of operator mutations leading to the highest level of constitutive beta-galactosidase synthesis. The GTG/CAC sequence occurs frequently and often symmetrically in prokaryotic and eukaryotic DNA sites where one anticipates specific protein interaction for gene regulation or recombination.
Full text
PDF




Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Arnott S., Hukins D. W. Optimised parameters for A-DNA and B-DNA. Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504–1509. doi: 10.1016/0006-291X(72)90243-4. [DOI] [PubMed] [Google Scholar]
- Bahl C. P., Wu R., Stawinsky J., Narang S. A. Minimal length of the lactose operator sequence for the specific recognition by the lactose repressor. Proc Natl Acad Sci U S A. 1977 Mar;74(3):966–970. doi: 10.1073/pnas.74.3.966. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chan H. W., Dodgson J. B., Wells R. D. Influence of DNA structure on the lactose operator-repressor interaction. Biochemistry. 1977 May 31;16(11):2356–2366. doi: 10.1021/bi00630a008. [DOI] [PubMed] [Google Scholar]
- Chou S. H., Hare D. R., Wemmer D. E., Reid B. R. Sequence-specific recognition of deoxyribonucleic acid. Chemical synthesis and nuclear magnetic resonance assignment of the imino protons of lambda OR3 operator deoxyribonucleic acid. Biochemistry. 1983 Jun 21;22(13):3037–3041. doi: 10.1021/bi00282a002. [DOI] [PubMed] [Google Scholar]
- Dickerson R. E. Base sequence and helix structure variation in B and A DNA. J Mol Biol. 1983 May 25;166(3):419–441. doi: 10.1016/s0022-2836(83)80093-x. [DOI] [PubMed] [Google Scholar]
- Dickerson R. E., Drew H. R., Conner B. N., Wing R. M., Fratini A. V., Kopka M. L. The anatomy of A-, B-, and Z-DNA. Science. 1982 Apr 30;216(4545):475–485. doi: 10.1126/science.7071593. [DOI] [PubMed] [Google Scholar]
- Donahue T. F., Daves R. S., Lucchini G., Fink G. R. A short nucleotide sequence required for regulation of HIS4 by the general control system of yeast. Cell. 1983 Jan;32(1):89–98. doi: 10.1016/0092-8674(83)90499-3. [DOI] [PubMed] [Google Scholar]
- Early T. A., Kearns D. R., Hillen W., Wells R. D. A 300- and 600-MHz proton nuclear magnetic resonance investigation of a 12 base pair deoxyribonucleic acid restriction fragment: relaxation behavior of the low-field resonances in water. Biochemistry. 1981 Jun 23;20(13):3756–3764. doi: 10.1021/bi00516a014. [DOI] [PubMed] [Google Scholar]
- Early T. A., Kearns D. R., Hillen W., Wells R. D. A 300-MHz proton nuclear magnetic resonance investigation of deoxyribonucleic acid restriction fragments: dynamic properties. Biochemistry. 1981 Jun 23;20(13):3764–3769. doi: 10.1021/bi00516a015. [DOI] [PubMed] [Google Scholar]
- FRANKLIN R. E., GOSLING R. G. Molecular configuration in sodium thymonucleate. Nature. 1953 Apr 25;171(4356):740–741. doi: 10.1038/171740a0. [DOI] [PubMed] [Google Scholar]
- Feigon J., Denny W. A., Leupin W., Kearns D. R. Proton nuclear magnetic resonance investigation of the conformation and dynamics in the synthetic deoxyribonucleic acid decamers d(ATATCGATAT) and d(ATATGCATAT). Biochemistry. 1983 Dec 6;22(25):5930–5942. doi: 10.1021/bi00294a037. [DOI] [PubMed] [Google Scholar]
- Gilbert W., Maxam A. The nucleotide sequence of the lac operator. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3581–3584. doi: 10.1073/pnas.70.12.3581. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Haniford D. B., Pulleyblank D. E. Facile transition of poly[d(TG) x d(CA)] into a left-handed helix in physiological conditions. Nature. 1983 Apr 14;302(5909):632–634. doi: 10.1038/302632a0. [DOI] [PubMed] [Google Scholar]
- Hurd R. E., Reid B. R. Helix-coil dynamics in RNA: the amino acid acceptor helix of Escherichia coli phenylalanine transfer RNA. J Mol Biol. 1980 Sep 15;142(2):181–193. doi: 10.1016/0022-2836(80)90044-3. [DOI] [PubMed] [Google Scholar]
- Ito H., Ike Y., Ikuta S., Itakura K. Solid phase synthesis of polynucleotides. VI. Further studies on polystyrene copolymers for the solid support. Nucleic Acids Res. 1982 Mar 11;10(5):1755–1769. doi: 10.1093/nar/10.5.1755. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Johnson R. C., Reznikoff W. S. DNA sequences at the ends of transposon Tn5 required for transposition. Nature. 1983 Jul 21;304(5923):280–282. doi: 10.1038/304280a0. [DOI] [PubMed] [Google Scholar]
- Johnsrud L. Contacts between Escherichia coli RNA polymerase and a lac operon promoter. Proc Natl Acad Sci U S A. 1978 Nov;75(11):5314–5318. doi: 10.1073/pnas.75.11.5314. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Johnston P. D., Redfield A. G. An NMR study of the exchange rates for protons involved in the secondary and tertiary structure of yeast tRNA Phe. Nucleic Acids Res. 1977 Oct;4(10):3599–3615. doi: 10.1093/nar/4.10.3599. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Johnston P. D., Redfield A. G. Study of transfer ribonucleic acid unfolding by dynamic nuclear magnetic resonance. Biochemistry. 1981 Jul 7;20(14):3996–4006. doi: 10.1021/bi00517a008. [DOI] [PubMed] [Google Scholar]
- Kearns D. R., Patel D. J., Shulman R. G. High resolution nuclear magnetic resonance studies of hydrogen bonded protons of tRNA in water. Nature. 1971 Jan 29;229(5283):338–339. doi: 10.1038/229338a0. [DOI] [PubMed] [Google Scholar]
- Khoury G., Gruss P. Enhancer elements. Cell. 1983 Jun;33(2):313–314. doi: 10.1016/0092-8674(83)90410-5. [DOI] [PubMed] [Google Scholar]
- Lee S. J., Akutsu H., Kyogoku Y., Kitano K., Tozuka Z., Ohta A., Ohtsuka E., Ikehara M. Behavior of the imino protons of the lambda OR3 17mer studied by high resolution NMR. Nucleic Acids Symp Ser. 1983;(12):197–200. [PubMed] [Google Scholar]
- Lillis M., Nick H., Lu P., Sadler J., Caruthers M. H. Iac operon operator DNA: isolation and trimming for NMR spectroscopy. Anal Biochem. 1982 Feb;120(1):52–58. doi: 10.1016/0003-2697(82)90316-5. [DOI] [PubMed] [Google Scholar]
- Lu P., Cheung S., Arndt K. Possible molecular detent in the DNA structure at regulatory sequences. J Biomol Struct Dyn. 1983 Oct;1(2):509–521. doi: 10.1080/07391102.1983.10507458. [DOI] [PubMed] [Google Scholar]
- Maquat L. E., Thornton K., Reznikoff W. S. lac Promoter mutations located downstream from the transcription start site. J Mol Biol. 1980 May 25;139(3):537–549. doi: 10.1016/0022-2836(80)90145-x. [DOI] [PubMed] [Google Scholar]
- Marians K. J., Brooker J. D. Structure of the lactose operator. Nature. 1976 Mar 25;260(5549):360–363. doi: 10.1038/260360a0. [DOI] [PubMed] [Google Scholar]
- Neidle S. New twists to left-handed DNA. Nature. 1983 Apr 14;302(5909):574–574. doi: 10.1038/302574a0. [DOI] [PubMed] [Google Scholar]
- Nick H., Arndt K., Boschelli F., Jarema M. A., Lillis M., Sommer H., Lu P., Sadler J. Repressor--operator interaction in the lac operon. II. Observations at the tyrosines and tryptophans. J Mol Biol. 1982 Nov 5;161(3):417–438. doi: 10.1016/0022-2836(82)90247-9. [DOI] [PubMed] [Google Scholar]
- Nordheim A., Lafer E. M., Peck L. J., Wang J. C., Stollar B. D., Rich A. Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding. Cell. 1982 Dec;31(2 Pt 1):309–318. doi: 10.1016/0092-8674(82)90124-6. [DOI] [PubMed] [Google Scholar]
- Nordheim A., Pardue M. L., Lafer E. M., Möller A., Stollar B. D., Rich A. Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature. 1981 Dec 3;294(5840):417–422. doi: 10.1038/294417a0. [DOI] [PubMed] [Google Scholar]
- Nordheim A., Rich A. Negatively supercoiled simian virus 40 DNA contains Z-DNA segments within transcriptional enhancer sequences. Nature. 1983 Jun 23;303(5919):674–679. doi: 10.1038/303674a0. [DOI] [PubMed] [Google Scholar]
- Nordheim A., Tesser P., Azorin F., Kwon Y. H., Möller A., Rich A. Isolation of Drosophila proteins that bind selectively to left-handed Z-DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7729–7733. doi: 10.1073/pnas.79.24.7729. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Panganiban A. T., Temin H. M. The terminal nucleotides of retrovirus DNA are required for integration but not virus production. Nature. 1983 Nov 10;306(5939):155–160. doi: 10.1038/306155a0. [DOI] [PubMed] [Google Scholar]
- Pardi A., Morden K. M., Patel D. J., Tinoco I., Jr Kinetics for exchange of the imino protons of the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix in complexes with the antibiotics netropsin and/or actinomycin. Biochemistry. 1983 Mar 1;22(5):1107–1113. doi: 10.1021/bi00274a018. [DOI] [PubMed] [Google Scholar]
- Pardi A., Tinoco I., Jr Kinetics for exchange of imino protons in deoxyribonucleic acid, ribonucleic acid, and hybrid oligonucleotide helices. Biochemistry. 1982 Sep 14;21(19):4686–4693. doi: 10.1021/bi00262a026. [DOI] [PubMed] [Google Scholar]
- Pardi A., Tinoco I., Jr Kinetics for exchange of imino protons in deoxyribonucleic acid, ribonucleic acid, and hybrid oligonucleotide helices. Biochemistry. 1982 Sep 14;21(19):4686–4693. doi: 10.1021/bi00262a026. [DOI] [PubMed] [Google Scholar]
- Patel D. J., Hilbers C. W. Proton nuclear magnetic resonance investigations of fraying in double-stranded d-ApTpGpCpApT in H2O solution. Biochemistry. 1975 Jun 17;14(12):2651–2656. doi: 10.1021/bi00683a014. [DOI] [PubMed] [Google Scholar]
- Patel D. J., Ikuta S., Kozlowski S., Itakura K. Sequence dependence of hydrogen exchange kinetics in DNA duplexes at the individual base pair level in solution. Proc Natl Acad Sci U S A. 1983 Apr;80(8):2184–2188. doi: 10.1073/pnas.80.8.2184. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Patel D. J., Kozlowski S. A., Bhatt R. Sequence dependence of base-pair stacking in right-handed DNA in solution: proton nuclear Overhauser effect NMR measurements. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3908–3912. doi: 10.1073/pnas.80.13.3908. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Patel D. J., Pardi A., Itakura K. DNA conformation, dynamics, and interactions in solution. Science. 1982 May 7;216(4546):581–590. doi: 10.1126/science.6280281. [DOI] [PubMed] [Google Scholar]
- Peck L. J., Wang J. C. Sequence dependence of the helical repeat of DNA in solution. Nature. 1981 Jul 23;292(5821):375–378. doi: 10.1038/292375a0. [DOI] [PubMed] [Google Scholar]
- Rhodes D., Klug A. Sequence-dependent helical periodicity of DNA. Nature. 1981 Jul 23;292(5821):378–380. doi: 10.1038/292378a0. [DOI] [PubMed] [Google Scholar]
- Rogers J. Molecular biology. CACA sequences - the ends and the means? Nature. 1983 Sep 8;305(5930):101–102. doi: 10.1038/305101a0. [DOI] [PubMed] [Google Scholar]
- Roy S., Papastavros M. Z., Redfield A. G. Nuclear overhauser effect study of yeast aspartate transfer ribonucleic acid. Biochemistry. 1982 Nov 23;21(24):6081–6088. doi: 10.1021/bi00267a009. [DOI] [PubMed] [Google Scholar]
- Sadler J. R., Sasmor H., Betz J. L. A perfectly symmetric lac operator binds the lac repressor very tightly. Proc Natl Acad Sci U S A. 1983 Nov;80(22):6785–6789. doi: 10.1073/pnas.80.22.6785. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Scheek R. M., Zuiderweg E. R., Klappe K. J., van Boom J. H., Kaptein R., Rüterjans H., Beyreuther K. lac Repressor headpiece binds specifically to half of the lac operator: a proton nuclear magnetic resonance study. Biochemistry. 1983 Jan 4;22(1):228–235. doi: 10.1021/bi00270a033. [DOI] [PubMed] [Google Scholar]
- Smith G. R. Chi hotspots of generalized recombination. Cell. 1983 Oct;34(3):709–710. doi: 10.1016/0092-8674(83)90525-1. [DOI] [PubMed] [Google Scholar]
- Tonegawa S. Somatic generation of antibody diversity. Nature. 1983 Apr 14;302(5909):575–581. doi: 10.1038/302575a0. [DOI] [PubMed] [Google Scholar]
- Tran-Dinh S., Neumann J. M., Taboury J., Huynh-Dinh T., Renous S., Genissel B., Igolen J. DNA fragment conformations. 1H-NMR comparative studies of helix-coil transition and conformation of d(C-A-C-G-T-G) and d(G-T-G-C-A-C). Influence of helix formation on proton chemical shifts. Eur J Biochem. 1983 Jul 1;133(3):579–589. doi: 10.1111/j.1432-1033.1983.tb07502.x. [DOI] [PubMed] [Google Scholar]
- Treisman R., Orkin S. H., Maniatis T. Specific transcription and RNA splicing defects in five cloned beta-thalassaemia genes. Nature. 1983 Apr 14;302(5909):591–596. doi: 10.1038/302591a0. [DOI] [PubMed] [Google Scholar]
- Ulrich E. L., John E. M., Gough G. R., Brunden M. J., Gilham P. T., Westler W. M., Markley J. L. Imino proton assignments in the proton nuclear magnetic resonance spectrum of the lambda phage OR3 deoxyribonucleic acid fragment. Biochemistry. 1983 Sep 13;22(19):4362–4365. doi: 10.1021/bi00288a003. [DOI] [PubMed] [Google Scholar]
- Wang A. H., Fujii S., van Boom J. H., Rich A. Molecular structure of the octamer d(G-G-C-C-G-G-C-C): modified A-DNA. Proc Natl Acad Sci U S A. 1982 Jul;79(13):3968–3972. doi: 10.1073/pnas.79.13.3968. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang A. H., Quigley G. J., Kolpak F. J., Crawford J. L., van Boom J. H., van der Marel G., Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680–686. doi: 10.1038/282680a0. [DOI] [PubMed] [Google Scholar]
- Zimmerman S. B. The three-dimensional structure of DNA. Annu Rev Biochem. 1982;51:395–427. doi: 10.1146/annurev.bi.51.070182.002143. [DOI] [PubMed] [Google Scholar]