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. 1984 Apr 11;12(7):3387–3404. doi: 10.1093/nar/12.7.3387

Methylphosphonates as probes of protein-nucleic acid interactions.

S A Noble, E F Fisher, M H Caruthers
PMCID: PMC318753  PMID: 6718253

Abstract

Deoxydinucleoside methylphosphonates were prepared by chemical synthesis and were introduced stereospecifically into the lac operator at two sites. These sites within d(ApApTpTpGpTpGpApGpCpGpGpApTpApApCpApApTpT), segment I, and d(ApApTpTpGpTpTpApTpCpCpGpCpTpCpApCpApApTpT), segment II, are indicated by p. Each segment containing a chiral methylphosphonate was annealed to the complementary unmodified segment. The interactions of these four modified lac operators with lac repressor were analyzed by the nitrocellulose filter binding assay. Introduction of either chiral phosphonate in segment II had little effect on the stability of the repressor-operator complex. When methylphosphonates were introduced into segment I, the affinity of lac repressor for the modified operators was shown to be dependent on the stereochemical configuration of the methylphosphonate.

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Selected References

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  1. Agarwal K. L., Riftina F. Synthesis and enzymatic properties of deoxyribooligonucleotides containing methyl and phenylphosphonate linkages. Nucleic Acids Res. 1979 Jul 11;6(9):3009–3024. doi: 10.1093/nar/6.9.3009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Caruthers M. H., Beaucage S. L., Efcavitch J. W., Fisher E. F., Goldman R. A., deHaseth P. L., Mandecki W., Matteucci M. D., Rosendahl M. S., Stabinsky Y. Chemical synthesis and biological studies on mutated gene-control regions. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):411–418. doi: 10.1101/sqb.1983.047.01.048. [DOI] [PubMed] [Google Scholar]
  3. Chacko K. K., Lindner K., Saenger W., Miller P. S. Molecular structure of deoxyadenylyl-3'-methylphosphonate-5'-thymidine dihydrate, (d-ApT x 2H2O), a dinucleoside monophosphate with neutral phosphodiester backbone. An X-ray crystal study. Nucleic Acids Res. 1983 May 11;11(9):2801–2814. doi: 10.1093/nar/11.9.2801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Goeddel D. V., Yansura D. G., Caruthers M. H. Binding of synthetic lactose operator DNAs to lactose represessors. Proc Natl Acad Sci U S A. 1977 Aug;74(8):3292–3296. doi: 10.1073/pnas.74.8.3292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Goeddel D. V., Yansura D. G., Caruthers M. H. How lac repressor recognizes lac operator. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3578–3582. doi: 10.1073/pnas.75.8.3578. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hassner A., Strand G., Rubenstein M., Patchornik A. Letter: Levulinic esters. An alcohol protecting group applicable to some nucleosides. J Am Chem Soc. 1975 Mar 19;97(6):1614–1615. doi: 10.1021/ja00839a077. [DOI] [PubMed] [Google Scholar]
  7. Jay E., Bambara R., Padmanabhan R., Wu R. DNA sequence analysis: a general, simple and rapid method for sequencing large oligodeoxyribonucleotide fragments by mapping. Nucleic Acids Res. 1974 Mar;1(3):331–353. doi: 10.1093/nar/1.3.331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Jessel D., Landau T., Hudson J., Lalor T., Tenen D., Livingston D. M. Identification of regions of the SV40 genome which contain preferred SV40 T antigen-binding sites. Cell. 1976 Aug;8(4):535–545. doi: 10.1016/0092-8674(76)90222-1. [DOI] [PubMed] [Google Scholar]
  9. Kan L. S., Cheng D. M., Miller P. S., Yano J., Ts'o P. O. Proton nuclear magnetic resonance studies on dideoxyribonucleoside methylphosphonates. Biochemistry. 1980 May 13;19(10):2122–2132. doi: 10.1021/bi00551a020. [DOI] [PubMed] [Google Scholar]
  10. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Miller P. S., Yano J., Yano E., Carroll C., Jayaraman K., Ts'o P. O. Nonionic nucleic acid analogues. Synthesis and characterization of dideoxyribonucleoside methylphosphonates. Biochemistry. 1979 Nov 13;18(23):5134–5143. doi: 10.1021/bi00590a017. [DOI] [PubMed] [Google Scholar]
  12. Narang S. A., Brousseau R., Hsiung H. M., Michniewicz J. J. Chemical synthesis of deoxyoligonucleotides by the modified triester method. Methods Enzymol. 1980;65(1):610–620. doi: 10.1016/s0076-6879(80)65063-0. [DOI] [PubMed] [Google Scholar]
  13. Ogata R. T., Gilbert W. DNA-binding site of lac repressor probed by dimethylsulfate methylation of lac operator. J Mol Biol. 1979 Aug 25;132(4):709–728. doi: 10.1016/0022-2836(79)90384-x. [DOI] [PubMed] [Google Scholar]
  14. Richter P. H., Eigen M. Diffusion controlled reaction rates in spheroidal geometry. Application to repressor--operator association and membrane bound enzymes. Biophys Chem. 1974 Oct;2(3):255–263. doi: 10.1016/0301-4622(74)80050-5. [DOI] [PubMed] [Google Scholar]
  15. Riggs A. D., Bourgeois S., Cohn M. The lac repressor-operator interaction. 3. Kinetic studies. J Mol Biol. 1970 Nov 14;53(3):401–417. doi: 10.1016/0022-2836(70)90074-4. [DOI] [PubMed] [Google Scholar]
  16. Rosenberg J. M., Khallai O. B., Kopka M. L., Dickerson R. E., Riggs A. D. Lac repressor purification without inactivation of DNA binding activity. Nucleic Acids Res. 1977 Mar;4(3):567–572. doi: 10.1093/nar/4.3.567. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Shenk T. E., Rhodes C., Rigby P. W., Berg P. Biochemical method for mapping mutational alterations in DNA with S1 nuclease: the location of deletions and temperature-sensitive mutations in simian virus 40. Proc Natl Acad Sci U S A. 1975 Mar;72(3):989–993. doi: 10.1073/pnas.72.3.989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  19. deHaseth P. L., Goldman R. A., Cech C. L., Caruthers M. H. Chemical synthesis and biochemical reactivity of bacteriophage lambda PR promoter. Nucleic Acids Res. 1983 Feb 11;11(3):773–787. doi: 10.1093/nar/11.3.773. [DOI] [PMC free article] [PubMed] [Google Scholar]

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