851
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Roychoudhury R, Wu R. Novel properties of Escherichia coli exonuclease III. J Biol Chem 1977; 252:4786-9. [PMID: 326780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The specificity of hydrolysis of polynucleotide termini by Escherichia coli exonuclease III was studied with the use of oligothymidylate annealed to polydeoxyadenylate. The size of the products after 3' leads to 5'-hydrolysis of 5'-labeled substrate is temperature-dependent. At 25 degrees the enzyme can hydrolyze a polynucleotide chain up to the last 5'-terminal dinucleotide. A gradation of higher 5'-terminal oligonucleotides of defined chain lengths is produced after limit digestion by the enzyme when the temperature is raised between 25 degrees to 60 degrees. When the oligothymidylate was labeled at the 3'-ends with ribonucleotides, it was observed that exonuclease III can cleave a single or two consecutive ribonucleotides regardless of whether the ribonucleotides are base-paired or mismatched.
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852
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Ruben G, Spielman P, Tu CD, Jay E, Siegel B, Wu R. Relaxed circular SV40 DNA as cleavage intermediate of two restriction endonucleases. Nucleic Acids Res 1977; 4:1803-13. [PMID: 197493 PMCID: PMC342523 DOI: 10.1093/nar/4.6.1803] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have determined the mode of cleavage of superhelical SV40 DNA (Form I) by restriction endonucleases EcoRI and HpaII at 37 degrees C. By analysis with agarose gel electrophoresis and direct examination with dark field electron microscopy, we found that a large amount of the single-nicked circular DNA (Form II) was produced before the linear SV40 DNA (Form III) appeared. Thus, both restriction enzymes cleave only one strand of the superhelical DNA first. The second cleavage on the complementary strand occurred after a lag period. The first order rate constant for the second cleavage by EcoRI endonuclease was determined and a kinetic reaction scheme for both enzymes is proposed.
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853
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Bahl CP, Wu R, Stawinsky J, Narang SA. Minimal length of the lactose operator sequence for the specific recognition by the lactose repressor. Proc Natl Acad Sci U S A 1977; 74:966-70. [PMID: 265588 PMCID: PMC430549 DOI: 10.1073/pnas.74.3.966] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A number of specific duplex DNA sequences which correspond to varying lengths of the lactose operator region have been synthesized by a combination of chemical and enzymatic methods. Repressor binding studies on these synthetic duplex operator molecules show that all the nucleotides essential for full lactose operator-repressor interactions are included in a 17-nucleotide-long duplex DNA that constitutes the minimal recognition sequence for this DNA-protein interaction.
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854
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Stawinski J, Hozumi T, Narang SA, Bahl CP, Wu R. Arylsulfonyltetrazoles, new coupling reagents and further improvements in the triester method for the synthesis of deoxyribooligonucleotides. Nucleic Acids Res 1977; 4:353-71. [PMID: 190591 PMCID: PMC342437 DOI: 10.1093/nar/4.2.353] [Citation(s) in RCA: 219] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The modified triester approach has been further improved and refined to the synthesis of defined sequences of deoxyribo-oligonucleotides. Improvements include arylsulfonyltetrazoles as faster and milder condensing agents, benzenesulfonic acid to avoid depurination during deblocking of trityl protecting groups and improved chromatographic procedures for purification of triester intermediates and purification of the final product containing 3'-5' phosphodiester linkages.
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855
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Szostak JW, Stiles JI, Bahl CP, Wu R. Specific binding of a synthetic oligodeoxyribonucleotide to yeast cytochrome c mRNA. Nature 1977; 265:61-3. [PMID: 189200 DOI: 10.1038/265061a0] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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856
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Marians KJ, Wu R, Stawinski J, Hozumi T, Narang SA. Cloned synthetic lac operator DNA is biologically active. Nature 1976; 263:744-8. [PMID: 792711 DOI: 10.1038/263744a0] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A chemically synthesised duplex DNA fragment containing the sequence of the lac operator was cloned in E. coli using the vehicle pMB9. Clones containing lac-pMB9 hybrid DNA produced beta-galactosidase constitutively and the hybrid DNA bound the lac repressor specifically.
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857
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Petrie RH, Wu R, Miller FC, Sacks DA, Sugarman R, Paul RH, Hon EH. The effect of drugs on uterine activity. Obstet Gynecol 1976; 48:431-5. [PMID: 967381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Uterine activity was measured for a 30-minute preinjection period and a 30-minute postinjection period for six drugs commonly used in labor. Uterine activity was quantitated by measuring the area below the uterine pressure curve with an on-line technic utilizing a voltage control oscillator. Uterine activity readings were obtained every 2.5 minutes and reported in uterine activity units (UAU). Unmedicated labor demonstrated a relatively static increase in UAU per unit of time in labor. On comparing total UAU before and after injection, only magnesium sulfate was noted to cause a decrease in total UAU. Utilizing 10-minute summations of UAU, the pre- and postinjection periods were compared to the calculated expected UAU for the 30 minutes following the preinjection period (assuming no drug had been used). For each of the other drugs, the positive slope of the calculated expected UAU shifted to a negative slope of the actual observed UAU following drug administration.
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858
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Tu CD, Roychoudhury R, Wu R. Nucleotide recognition sequence at the cleavage site of Haemophilus aegyptius II (Hae II) restriction endonuclease. Biochem Biophys Res Commun 1976; 72:355-62. [PMID: 985479 DOI: 10.1016/0006-291x(76)91001-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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859
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Jay E, Wu R. Arthrobacter luteus restriction endonuclease recognition sequence and its cleavage map of SV40 DNA. Biochemistry 1976; 15:3612-20. [PMID: 182213 DOI: 10.1021/bi00661a032] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The nucleotide sequence at the cleavage site of the restriction endonuclease isolated from Arthrobacter luteus (Alu) has been determined. The endonuclease cleaves at the center of a palindromic tetranucleotide sequence to give even-ended duplex DNA fragments phosphorylated at the 5'-end. The endonuclease cleaves SV40 form I DNA into 32 fragments. The order and sizes of these fragments have been determined to provide an Alu cleavage map of the SV40 genome.
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860
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Tu CP, Jay E, Bahl CP, Wu R. A reliable mapping method for sequence determination of oligodeoxyribonucleotides by mobility shift analysis. Anal Biochem 1976; 74:73-93. [PMID: 962085 DOI: 10.1016/0003-2697(76)90311-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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861
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Jay E, Roychoudhury R, Wu R. Nucleotide sequence with elements of an unusual two-fold rotational symmetry in the region of origin of replication of SV40 DNA+. Biochem Biophys Res Commun 1976; 69:678-86. [PMID: 178315 DOI: 10.1016/0006-291x(76)90929-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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862
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Roychoudhury R, Jay E, Wu R. Terminal labeling and addition of homopolymer tracts to duplex DNA fragments by terminal deoxynucleotidyl transferase. Nucleic Acids Res 1976; 3:863-77. [PMID: 775445 PMCID: PMC342951 DOI: 10.1093/nar/3.4.863] [Citation(s) in RCA: 215] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Terminal deoxynucleotidyl transferase, which requires a single-stranded DNA primer under the usual assay conditions, can be made to accept double-stranded DNA as primer for the addition of either rNMP or dNMP, if Mg+2 ion is replaced by Co+2 ion. The priming efficiency in the presence of Co+2 ion with respect to initial rate tested with 2 single-stranded primer, is 5-6 fold higher than that observed with Mg+2 ion. In the presence of Co+2 ion, the primer specificity is altered so that all forms of duplex DNA molecules can be labeled at their unique 3'-ends regardless of whether such ends are staggered or even. Thus, using ribonucleotide incorporation, we have for the first time employed this reaction for sequence analysis of duplex DNA fragments generated by restriction endonuclease cleavages. Furthermore, by using Co+2 ion, it is possible to add a long homopolymer tract of deoxyribonucleotides to the 3'-terminus of double-stranded DNA. Therefore, without prior treatment with lambda exonuclease to expose the 3' terminus as single-stranded primer, this reaction now permits insertion of homopolymer tails at the 3'-ends of all types of DNA molecules for the purpose of in vitro construction of recombinant DNA.
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863
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Wu R, Ruben G, Siegel B, Jay E, Spielman P, Tu CP. Synchronous digestion of SV40 DNA by exonuclease III. Biochemistry 1976; 15:734-40. [PMID: 174717 DOI: 10.1021/bi00649a003] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have established an optimal condition for the synchronous digestion of SV40 DNA with Escherichia coli exonuclease III. Electron microscopy and polyacrylamide gel electrophoresis were used to obtain accurate measurements on the lengths of DNA before and after exonuclease III digestion. Based on this finding, a new method for determining the sequence of long duplex DNA can be realized. It involves (a) the synchronous digestion of the DNA from the 3' ends with exonuclease III, followed by (b) repair synthesis with labeled nucleotides and DNA polymerase, and (c) sequence analysis of the repaired DNA.
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864
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Zakin JL, Wu R, Luh H, Mayhan KG. Generalized correlations for molecular weight and concentration dependence of zero-shear viscosity of high polymer solutions. ACTA ACUST UNITED AC 1976. [DOI: 10.1002/pol.1976.180140209] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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865
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Abermann R, Bahl CP, Marians KJ, Salpeter MM, Wu R. Studies on the lactose operon. III. Visualization and physical mapping of the lactose repressor-operator complex. J Mol Biol 1976; 100:109-14. [PMID: 765470 DOI: 10.1016/s0022-2836(76)80038-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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866
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Abstract
A general method has been developed to introduce any double-stranded DNA molecule into cloning vehicles at different restriction endonuclease sites. In this method a chemically synthesized decadeoxyribonucleotide duplex, containing a specific restriction endonuclease sequence, is joinlex DNA is cut by the same restriction endonuclease to generate the cohesive ends. It is then inserted into the restriction endonuclease cleavage site of the cloning vehicle. To demonstrate the feasibility of this new method, we have inserted separately the synthetic lac operator DNA at the Bam I and HindIII cleavage sites of the plasmid pMB9 DNA.
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867
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Roychoudhury R, Jay E, Wu R. Terminal labeling and addition of homopolymer tracts to duplex DNA fragments by terminal deoxynucleotidyl transferase. Nucleic Acids Res 1976; 3:101-16. [PMID: 765970 PMCID: PMC342881 DOI: 10.1093/nar/3.1.101] [Citation(s) in RCA: 268] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Terminal deoxynucleotidyl transferase, which requires a single-stranded DNA primer under the usual assay conditions, can be made to accept double-stranded DNA as primer for the addition of either rNMP or dNMP, if Mg+2 ion is replaced by Co+2 ion. The priming efficiency in the presence of (C leads to) CO+2 ion with respect to initial rate tested with 2 single-stranded primer, is 5-6 fols higher than that observed with Mg+2 ion. In the presence of Co+2 ion, the primer specificity is altered so that all forms of duplex DNA molecules can be labeled at their unique 3' -ends regardless of whether such ends are staggered or even. Thus, using ribonucleotide incorporation, we have for the first time employed this reaction for sequence analysis of duplex DNA fragments generated by restriction endonuclease cleavages. Furthermore, by using Co+2 ion, it is possible to add a long homopolymer tract of deoxyribonucleotides to the 3'-terminus of double-stranded DNA. Therefore, without prior treatment with lambda exonuclease to expose the 3' terminus as single-stranded primer, this reaction now permits insertion of homopolymer tails at the 3'-ends of all types of DNA molecules for the purpose of in vitro construction of recombinant DNA.
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868
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Bahl CP, Wu R, Itakura K, Katagiri N, Narang SA. Chemical and enzymatic synthesis of lactose operator of Escherichia coli and its binding to lactose repressor. Proc Natl Acad Sci U S A 1976; 73:91-4. [PMID: 1108022 PMCID: PMC335845 DOI: 10.1073/pnas.73.1.91] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The 21-nucleotide-long duplex DNA constituting the lactose operator sequence of E. coli has been synthesized by both chemical and enzymatic methods. The synthetic duplex has the essential feature of the lactose operator as seen by its binding to the lactose repressor. The binding of the synthetic operator fragment to the lactose repressor is specific because it is inhibited by the inducing ligand isopropyl-beta-D-thiogalactoside. Thus, it is now possible to show that a chemically synthesized oligodeoxynucleotide can be specifically recognized by its natural regulatory protein.
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869
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Wu R, Geiduschek EP. The role of replication proteins in the regulation of bacteriophage T4 transcription. I. Gene 45 and hydroxymethyl-C-containing DNA. J Mol Biol 1975; 96:513-38. [PMID: 1104860 DOI: 10.1016/0022-2836(75)90137-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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870
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Wu R, Geiduschek EP. The role of replication proteins in the regulation of bacteriophage T4 transcription. II. Gene 45 and late transcription uncoupled from replication. J Mol Biol 1975; 96:539-62. [PMID: 1195366 DOI: 10.1016/0022-2836(75)90138-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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871
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Wu R, Wu JL, Yeh YC. Role of gene 59 of bacteriophage T4 in repair of UV-irradiated and alkylated DNA in vivo. J Virol 1975; 16:5-16. [PMID: 166207 PMCID: PMC354626 DOI: 10.1128/jvi.16.1.5-16.1975] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nonsense mutants in gene 59 (amC5, amHL628) were used to study the role of this gene in the repair of UV-damaged and alkylated DNA of bacteriophage T4 in vivo. The higher sensitivity to UV irradiation and alkylation of gene 59 mutants after exposure to these agents was established by a comparison of the survival fractions with wild type. Zonal centrifugal analysis of both parental and nascent mutant intracellular DNA molecules after UV irradiation showed that immediately after exposure the size of single-stranded DNA fragments was the same as the wild-type intracellular DNA. However, the capability of rejoining fragmented intracellular DNA was greatly reduced in the mutant. In contrast, the wild-type-infected cells under the same condition resumed DNA replication and repaired its DNA to normal size. Methyl methanesulfonate induced more randomly fragmented intracellular DNA, when compared to UV irradiation. The rate of rejoining under these conditions as judged from their sedimentation profiles was also greatly reduced in mutant-infected cells. Further evidence is presented that UV repair is not a simple consequence of arrested DNA replication, which is a phenotype of the mutant when infected in a nonpermissive host, Escherichia coli B (su minus), but rather that the DNA repair function of gene 59 is independent of the replication function. These and other data presented indicate that a product(s) of gene 59 is essential for both repair of UV lesions and repair of alkylation damage of DNA in vivo. It is suggested that gene 59 may have two functions during viral development: DNA replication and replication repair of DNA molecules.
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872
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Marians KJ, Padmanabhan R, Wu R. Ribo-substitution at the ends of duplex DNA: complete nucleotide sequence of the right-hand cohesive end of coliphage 186 DNA. Arch Biochem Biophys 1975; 169:108-15. [PMID: 169737 DOI: 10.1016/0003-9861(75)90322-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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873
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Ghangas GS, Wu R. Specific hydrolysis of the cohesive ends of bacteriophage lambda DNA by three single strand-specific nucleases. J Biol Chem 1975; 250:4601-6. [PMID: 1141222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Procedures have been worked out for Aspergillus nuclease S1 and mung been nuclease to quantitatively cleave off both of the 12-nucleotide long, single-stranded cohesive ends of lambdaDNA. This cleavage is indicated by the almost complete elimination of the repair incorporation of radioactive nucleotides by DNA polymerase into the digested DNA. With S1 nuclease, cleavage was complete at 10 degrees as well as at 30 degrees. Under the conditions for quantitative cleavage of the single-stranded regions there was no digestion of the double-stranded lambdaDNA. The mung bean nuclease cleaved off the cohesive ends completely at 30 degrees but at 5 degrees, the cleavage was not complete even at high enzyme concentration. The nearest neighbor analysis of the repaired DNA indicates that at 5 degrees about four nucleotides remained undigested. The mung bean nuclease also introduced, under the conditions used, some nicks into double-stranded DNA as determined by the repair incorporation. The Escherichia coli exonuclease VII cleaved off part of the cohesive ends of lambdaDNA, leaving two nucleotides on each end as single-stranded tails.
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874
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Itakura K, Katagiri N, Narang SA, Bahl CP, Marians KJ, Wu R. Chemical synthesis and sequence studies of deoxyribooligonucleotides which constitute the duplex sequence of the lactose operator of Escherichia coli. J Biol Chem 1975; 250:4592-600. [PMID: 166998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have synthesized the deoxyribooligonucleotide fragments, constituting the sequence of the lac operator of Escherichia coli. Two of these fragments, d(pApApTpTpGpTpTpApT) (nonamer) and d(pApApTpTpGpTpGpApG) (nonamer), corresponding to the 5' termini of lac operator have been synthesized by the phosphodiester method. The remaining four fragments, d(ApCpApApTpT) (hexamer), d(ApTpApApCpApApTpT) (nonamer), d(ApApTpTpGpTpGpApGpCpGpG) (dodecamer), and d(ApApTpTpGpTpTpApTpCpCpGpCpTpC) (pentadecamer), have been synthesized by an improved phosphotriester method. All of the compounds were first characterized by venom and spleen phosphodiesterase digestion to obtain their base composition. The sequence of these oligonucleotides was fully confirmed by the characteristic mobility shifts of their partial venom phosphodiesterase digestion products on two-dimensional homochromatography. A comparative study of the two methods for the synthesis of oligonucleotides has revealed that the phosphotriester method is more convenient than the phosphodiester method because of higher yields and ease of handling large scale preparations.
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875
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Bambara R, Wu R. DNA sequence analysis. Terminal sequences of bacteriophage phi80. J Biol Chem 1975; 250:4607-18. [PMID: 166999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sequences of the cohesive ends and the 3'-terminal regions of phi80 DNA have been determined. Sequences of the cohesive ends were obtained through the use of two standard methods. The first method involved the incorporation of all four labeled deoxyribonucleotides into the phi80 cohesive ends using DNA polymerase I. The DNA was then partially digested with micrococcal nuclease or pancreatic DNase. The products were separated by two-dimensional electrophoresis and characterized by composition, 3'-terminal, and nearest neighbor analyses. The second method involved partial incorporation using one, two, or three labeled deoxyribonucleotides followed by similar analyses. Sequences of the double-stranded regions adjacent to the cohesive ends were determined by three new methods. These methods were: (a) the DNA was specifically labeled at the 3' terminus and then partially degraded. Labeled oligonucleotide products were sequenced by their mobilities on various separation systems. (b) The cohesive ends were enlarged by limited degradation with exonuclease III. After this treatment, the DNA was partially repaired with labeled nucleotides, digested, and the products were analyzed. (c) A synthetic ologonucleotide primer was bound to phi80 DNA which had been repaired with DNA polymerase I, and then partially digested with lambda-exonuclease. The primer was extended into the region of interest by partial repair with labeled nucleotides. The extended primer was isolated and analyzed.
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876
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877
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Ghangas GS, Wu R. Specific hydrolysis of the cohesive ends of bacteriophage lambda DNA by three single strand-specific nucleases. J Biol Chem 1975. [DOI: 10.1016/s0021-9258(19)41344-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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878
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Dykes G, Bambara R, Marians K, Wu R. On the statistical significance of primary structural features found in DNA-protein interaction sites. Nucleic Acids Res 1975; 2:327-45. [PMID: 1093137 PMCID: PMC342839 DOI: 10.1093/nar/2.3.327] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Probabilities of occurrence for a number of the symmetries and other sequence regularities found in DNA-protein interaction site sequences have been calculated for segments of random DNA sequence. Results show that many of the symmetrical and repetitive features seen in these interaction sites are likely to have occured by chance. Other features are so unlikely to have occurred by chance that they are probably involved in the DNA-protein interaction processes.
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879
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Wu R, Bambara R, Jay E. Recent advances in DNA sequence analysis. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1975; 2:455-512. [PMID: 164328 DOI: 10.3109/10409237509102550] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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880
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Ghangas GS, Wu R. Specific hydrolysis of the cohesive ends of bacteriophage lambda-deoxyribonucleic acid by Micrococcus luteus ultraviolet exonuclease. J Biol Chem 1974; 249:7550-4. [PMID: 4612037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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881
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Bambara R, Jay E, Wu R. DNA sequence analysis: a formula to predict electrophoretic mobilities of oligonucleotides on cellulose acetate. Nucleic Acids Res 1974; 1:1503-20. [PMID: 10793706 PMCID: PMC343427 DOI: 10.1093/nar/1.11.1503] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A simple method has recently become available for sequence analysis of large oligonucleotide fragments. Sequences are derived from the characteristic mobility shifts of the sequential partial degradation products of the oligonucleotide on two dimensional homochromatography. We have now developed an empirical formula for predicting the relative mobilities of each of the partial products in the first dimension (electrophoresis on cellulose acetate gel). The formula allows a more precise interpretation of the sequence of the oligonucleotide. It eliminates the ambiguities present in the method previously reported for sequence analysis by simple inspection of the mobility shifts. In order to amplify the mobility shifts so that they may be more easily and accurately measured, methods have been developed for preparing and fractionating the oligonucleotides on 40 x 40 cm DEAE-cellulose plates. Both improvements have proven valuable for direct sequence analysis by mapping.
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882
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Padmanabhan R, Wu R, Calendar R. Complete nucleotide sequence of the cohesive ends of bacteriophage P2 deoxyribonucleic acid. J Biol Chem 1974; 249:6197-207. [PMID: 4371195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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883
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Padmanabhan R, Jay E, Wu R. Chemical synthesis of a primer and its use in the sequence analysis of the lysozyme gene of bacteriophage T4. Proc Natl Acad Sci U S A 1974; 71:2510-4. [PMID: 4526223 PMCID: PMC388489 DOI: 10.1073/pnas.71.6.2510] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We have developed a general approach for determining the nucleotide sequence of a gene, with the aid of a deoxyribonucleotide primer of defined sequence. The selection of the primer sequence was based on a short segment of mRNA sequence of T4 phage lysozyme. A tetradecadeoxyribonucleotide primer was chemically synthesized and its sequence verified by sequence analysis. This primer was found to bind to the single-stranded region of the exonuclease III-treated T4 DNA, and specific nucleotides were incorporated to its 3' end. The result indicated that this primer was bound to the expected location on the T4 DNA. Therefore, long sequences of the T4 lysozyme gene can now be determined from this specific starting point.
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884
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885
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Hamilton RT, Wu R. Nucleotide sequence analysis of deoxyribonucleic acid. XIV. Conditions for the incorporation of ribonucleotides and deoxyribonucleotides into single-stranded areas of long double-stranded deoxyribonucleic acids. J Biol Chem 1974; 249:2466-72. [PMID: 4595652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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886
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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; 1:331-53. [PMID: 10793670 PMCID: PMC344020 DOI: 10.1093/nar/1.3.331] [Citation(s) in RCA: 362] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Several electrophoretic and chromatographic systems have been investigated and compared for sequence analysis of oligodeoxyribonucleotides. Three systems were found to be useful for the separation of a series of sequential degradation products resulting from a labeled oligonucleotide: (I) 2-D electrophoresisdagger; (II) 2-D PEI-cellulose; and (III) 2-D homochromatography. System (III) proved generally most informative regardless of base composition and sequence. Furthermore, only in this system will the omission of an oligonucleotide in a series of oligonucleotides be self-evident from the two-dimensional map. The sequence of up to fifteen nucleotides can be determined solely by the characteristic mobility shifts of its sequential degradation products distributed on the two-dimensional map. With this method, ten nucleotides from the double-stranded region adjacent to the left-hand 3'-terminus and seven from the right-hand 3'-terminus of bacteriophage lambda DNA have been sequenced. Similarly, nine nucleotides from the double-stranded region adjacent to the left-hand 3'-terminus and five nucleotides from the right-hand terminus of bacteriophage phi80 DNA have also been sequenced. The advantages and disadvantages of each separation system with respect to sequence analysis are discussed.
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887
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888
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Wu R, Tu CD, Padmanabhan R. Nucleotide sequence analysis of DNA. XII. The chemical synthesis and sequence analysis of a dodecadeoxynucleotide which binds to the endolysin gene of bacteriophage lambda. Biochem Biophys Res Commun 1973; 55:1092-9. [PMID: 4358929 DOI: 10.1016/s0006-291x(73)80007-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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889
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Ghangas GS, Jay E, Bambara R, Wu R. Nucleotide sequence analysis of DNA. XI. The 3' terminal sequences of bacteriophage lambda and phi 80 DNA. Biochem Biophys Res Commun 1973; 54:998-1007. [PMID: 4753202 DOI: 10.1016/0006-291x(73)90793-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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890
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Bambara R, Padmanabhan R, Wu R. Nucleotide sequence analysis of DNA. X. Complete nucleotide sequence of the cohesive ends of bacteriophage phi80 DNA. J Mol Biol 1973; 75:741-4. [PMID: 4732072 DOI: 10.1016/0022-2836(73)90305-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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891
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Padmanabhan R, Wu R. Nucleotide sequence analysis of DNA. IX. Use of oligonucleotides of defined sequence as primers in DNA sequence analysis. Biochem Biophys Res Commun 1972; 48:1295-302. [PMID: 4560009 DOI: 10.1016/0006-291x(72)90852-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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892
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Padmanabhan R, Wu R, Bode VC. Arrangement of DNA in lambda bacteriophage heads. 3. Location and number of nucleotides cleaved from lambda-DNA by micrococcal nuclease attack on heads. J Mol Biol 1972; 69:201-7. [PMID: 4560947 DOI: 10.1016/0022-2836(72)90225-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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893
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Donelson JE, Wu R. Nucleotide sequence analysis of deoxyribonucleic acid. VI. Determination of 3'-terminal dnucleotide sequences of several species of duplex deoxyribonucleic acid using Escherichia coli deoxyribonucleic acid polymerase I. J Biol Chem 1972; 247:4654-60. [PMID: 4557849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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894
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Donelson JE, Wu R. Nucleotide sequence analysis of deoxyribonucleic acid. VII. Characterization of Escherichia coli exonuclease 3 activity for possible use in terminal nucleotide sequence analysis of duplex deoxyribonucleic acid. J Biol Chem 1972; 247:4661-8. [PMID: 4557850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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895
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896
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Padmanabhan R, Wu R. Nucleotide sequence analysis of DNA. IV. Complete nucleotide sequence of the left-hand cohesive end of coliphage 186 DNA. J Mol Biol 1972; 65:447-67. [PMID: 4554112 DOI: 10.1016/0022-2836(72)90201-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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897
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Wu R, Ma FJ, Yeh YC. Suppression of DNA-arrested synthesis in mutants defective in gene 59 of bacteriophage T4. Virology 1972; 47:147-56. [PMID: 4550789 DOI: 10.1016/0042-6822(72)90248-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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898
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Wu R. Inhibition of polynucleotide kinase by agar, dextran sulfate and other polysaccharide sulfates. Biochem Biophys Res Commun 1971; 43:927-34. [PMID: 4935295 DOI: 10.1016/0006-291x(71)90706-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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899
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Wu R, Taylor E. Nucleotide sequence analysis of DNA. II. Complete nucleotide sequence of the cohesive ends of bacteriophage lambda DNA. J Mol Biol 1971; 57:491-511. [PMID: 4931680 DOI: 10.1016/0022-2836(71)90105-7] [Citation(s) in RCA: 179] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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900
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Wu R. Nucleotide sequence analysis of DNA. I. Partial sequence of the cohesive ends of bacteriophage lambda and 186 DNA. J Mol Biol 1970; 51:501-21. [PMID: 4321727 DOI: 10.1016/0022-2836(70)90004-5] [Citation(s) in RCA: 128] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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