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Статті в журналах з теми "DNA Synthesis"

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Автор: Grafiati

Опубліковано: 4 червня 2021

Оновлено: 6 вересня 2023

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1

Burke, Cassandra R., and Andrej Lupták. "DNA synthesis from diphosphate substrates by DNA polymerases." Proceedings of the National Academy of Sciences 115, no. 5 (January 16, 2018): 980–85. http://dx.doi.org/10.1073/pnas.1712193115.

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The activity of DNA polymerase underlies numerous biotechnologies, cell division, and therapeutics, yet the enzyme remains incompletely understood. We demonstrate that both thermostable and mesophilic DNA polymerases readily utilize deoxyribonucleoside diphosphates (dNDPs) for DNA synthesis and inorganic phosphate for the reverse reaction, that is, phosphorolysis of DNA. For Taq DNA polymerase, the KMs of the dNDP and phosphate substrates are ∼20 and 200 times higher than for dNTP and pyrophosphate, respectively. DNA synthesis from dNDPs is about 17 times slower than from dNTPs, and DNA phosphorolysis about 200 times less efficient than pyrophosphorolysis. Such parameters allow DNA replication without requiring coupled metabolism to sequester the phosphate products, which consequently do not pose a threat to genome stability. This mechanism contrasts with DNA synthesis from dNTPs, which yield high-energy pyrophosphates that have to be hydrolyzed to phosphates to prevent the reverse reaction. Because the last common ancestor was likely a thermophile, dNDPs are plausible substrates for genome replication on early Earth and may represent metabolic intermediates later replaced by the higher-energy triphosphates.

2

Shilkin, E. S., E. O. Boldinova, A. D. Stolyarenko, R. I. Goncharova, R. N. Chuprov-Netochin, M. P. Smal, and A. V. Makarova. "Translesion DNA Synthesis and Reinitiation of DNA Synthesis in Chemotherapy Resistance." Biochemistry (Moscow) 85, no. 8 (August 2020): 869–82. http://dx.doi.org/10.1134/s0006297920080039.

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3

Caruthers, Marvin H. "Chemical synthesis of DNA and DNA analogs." Accounts of Chemical Research 24, no. 9 (September 1991): 278–84. http://dx.doi.org/10.1021/ar00009a005.

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4

Church, Geoffrey A., Anindya Dasgupta, and Duncan W. Wilson. "Herpes Simplex Virus DNA Packaging without Measurable DNA Synthesis." Journal of Virology 72, no. 4 (April 1, 1998): 2745–51. http://dx.doi.org/10.1128/jvi.72.4.2745-2751.1998.

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ABSTRACT Herpes simplex virus (HSV) type 1 DNA synthesis and packaging occur within the nuclei of infected cells; however, the extent to which the two processes are coupled remains unclear. Correct packaging is thought to be dependent upon DNA debranching or other repair processes, and such events commonly involve new DNA synthesis. Furthermore, the HSV UL15 gene product, essential for packaging, nevertheless localizes to sites of active DNA replication and may link the two events. It has previously been difficult to determine whether packaging requires concomitant DNA synthesis due to the complexity of these processes and of the viral life cycle; however, we have recently described a model system which simplifies the study of HSV assembly. Cells infected with HSV strain tsProt.A accumulate unpackaged capsids at the nonpermissive temperature of 39°C. Following release of the temperature block, these capsids proceed to package viral DNA in a single, synchronous wave. Here we report that, when DNA replication was inhibited prior to release of the temperature block, DNA packaging and later events in viral assembly nevertheless occurred at near-normal levels. We conclude that, under our conditions, HSV DNA packaging does not require detectable levels of DNA synthesis.

5

Turgay Tun, Turgay Tun, Nadir Demirel Nadir Demirel, Mahmut Emir Mahmut Emir, Asl han G. nel Asl han G nel, R. fk Kad o. lu R fk Kad o lu, and Nurcan Karacan Nurcan Karacan. "Three New Copper (II) Complexes with CHIRAL SCHIFF BASES: Synthesis, Characterization, DNA Binding and DNA-Cleavage Studies." Journal of the chemical society of pakistan 41, no. 2 (2019): 334. http://dx.doi.org/10.52568/000730/jcsp/41.02.2019.

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New mononuclear copper (II) complexes (1, 2 and 3) were synthesized from Schiff bases (H2L) of chiral amino alcohols. The structures of the copper complexes were proposed by a combination of elemental analyses, FTIR, LCMS, magnetic susceptibility and molar conductance measurement methods. Spectroscopic and analytical data of the complexes suggest four-coordinated structures. Geometry optimization carried out with DFT/6-31G (d,p) were proposed to be distorted square planar geometry for the complexes. The similarity between experimental and theoretical IR spectra confirms the proposed structures. The interaction of copper (II) complexes with calf thymus (CT-DNA) was investigated using absorption titration method. The results suggest that the complex 1 and 2 can bind to DNA by intercalation. Binding constants Kb were found to be 2.46and#215;105 for 1, 5.41and#215;105 for 2 and 7.00and#215;104 for 3. Moreover, agarose gel electrophoresis assay demonstrates that all complexes were found to cleavage of plasmid pentry/d-topo plasmid DNA. Complex 2 shows the best cleavage activity (5 and#181;M).

6

Leslie, Mitch. "Double-checking DNA synthesis." Journal of Cell Biology 204, no. 2 (January 13, 2014): 148. http://dx.doi.org/10.1083/jcb.2042iti1.

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7

Doerr, Allison. "DNA synthesis lights up." Nature Methods 5, no. 4 (April 2008): 286. http://dx.doi.org/10.1038/nmeth0408-286.

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8

Uppenbrink, J. "ORGANIC SYNTHESIS: Sugarcoated DNA." Science 290, no. 5492 (October 27, 2000): 675b—675. http://dx.doi.org/10.1126/science.290.5492.675b.

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9

LeBrasseur, Nicole. "Geminin halts DNA synthesis." Journal of Cell Biology 165, no. 4 (May 24, 2004): 455. http://dx.doi.org/10.1083/jcb1654iti3.

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10

MILLS, W. RONALD, MICHELE REEVES, DIANA L. FOWLER, and STEPHEN F. CAPO. "DNA Synthesis in Chloroplasts." Journal of Experimental Botany 40, no. 4 (1989): 425–29. http://dx.doi.org/10.1093/jxb/40.4.425.

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11

Caruthers, Marvin H. "Chemical synthesis of DNA." Journal of Chemical Education 66, no. 7 (July 1989): 577. http://dx.doi.org/10.1021/ed066p577.

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12

HENRY, CELIA M. "DNA-PROGRAMMED ORGANIC SYNTHESIS." Chemical & Engineering News Archive 83, no. 5 (January 31, 2005): 35–36. http://dx.doi.org/10.1021/cen-v083n005.p035.

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13

Leake, Devin. "DNA Synthesis Steps Up." Genetic Engineering & Biotechnology News 36, no. 8 (April 15, 2016): 14–15. http://dx.doi.org/10.1089/gen.36.08.09.

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14

Wright, N. A. "DNA Synthesis and Genotoxicity." Digestion 47, no. 1 (1990): 24–30. http://dx.doi.org/10.1159/000200511.

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15

Hansen, Bjarke N., Kim S. Larsen, Daniel Merkle, and Alexei Mihalchuk. "DNA-templated synthesis optimization." Natural Computing 17, no. 4 (July 31, 2018): 693–707. http://dx.doi.org/10.1007/s11047-018-9697-7.

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16

LUCK, DENNIS N., JOHNNY K. NGSEE, FRITZ M. ROTTMAN, and MICHAEL SMITH. "Synthesis of Bovine Prolactin inEscherichia coli." DNA 5, no. 1 (February 1986): 21–28. http://dx.doi.org/10.1089/dna.1986.5.21.

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17

Hogg, Matthew, A. Elisabeth Sauer-Eriksson та Erik Johansson. "Promiscuous DNA synthesis by human DNA polymerase θ". Nucleic Acids Research 40, № 6 (30 листопада 2011): 2611–22. http://dx.doi.org/10.1093/nar/gkr1102.

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18

Bridges, Bryn A. "Error-prone DNA repair and translesion DNA synthesis." DNA Repair 4, no. 6 (June 2005): 725–39. http://dx.doi.org/10.1016/j.dnarep.2004.12.009.

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19

Ebara, Y., T. Sugiyama, K. Kaihatsu, and S. i. Ueji. "Synthesis of non-natural DNA using DNA polymerase." Nucleic Acids Symposium Series 44, no. 1 (October 1, 2000): 143–44. http://dx.doi.org/10.1093/nass/44.1.143.

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20

Chary, Parvathi, William A. Beard, Samuel H. Wilson та R. Stephen Lloyd. "DNA Polymerase β Gap-Filling Translesion DNA Synthesis". Chemical Research in Toxicology 25, № 12 (15 листопада 2012): 2744–54. http://dx.doi.org/10.1021/tx300368f.

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21

Zhang, Yanbin, Xiaohua Wu, Fenghua Yuan, Zhongwen Xie та Zhigang Wang. "Highly Frequent Frameshift DNA Synthesis by Human DNA Polymerase μ". Molecular and Cellular Biology 21, № 23 (1 грудня 2001): 7995–8006. http://dx.doi.org/10.1128/mcb.21.23.7995-8006.2001.

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ABSTRACT DNA polymerase μ (Polμ) is a newly identified member of the polymerase X family. The biological function of Polμ is not known, although it has been speculated that human Polμ may be a somatic hypermutation polymerase. To help understand the in vivo function of human Polμ, we have performed in vitro biochemical analyses of the purified polymerase. Unlike any other DNA polymerases studied thus far, human Polμ catalyzed frameshift DNA synthesis with an unprecedentedly high frequency. In the sequence contexts examined, −1 deletion occurred as the predominant DNA synthesis mechanism opposite the single-nucleotide repeat sequences AA, GG, TT, and CC in the template. Thus, the fidelity of DNA synthesis by human Polμ was largely dictated by the sequence context. Human Polμ was able to efficiently extend mismatched bases mainly by a frameshift synthesis mechanism. With the primer ends, containing up to four mismatches, examined, human Polμ effectively realigned the primer to achieve annealing with a microhomology region in the template several nucleotides downstream. As a result, human Polμ promoted microhomology search and microhomology pairing between the primer and the template strands of DNA. These results show that human Polμ is much more prone to cause frameshift mutations than base substitutions. The biochemical properties of human Polμ suggest a function in nonhomologous end joining and V(D)J recombination through its microhomology searching and pairing activities but do not support a function in somatic hypermutation.

22

HAYDEN, MARK A., and WLODEK MANDECKI. "Gene Synthesis by Serial Cloning of Oligonucleotides." DNA 7, no. 8 (October 1988): 571–77. http://dx.doi.org/10.1089/dna.1.1988.7.571.

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23

EBE, KAZUYU, MONICA SCHÖLD, JOHN J. ROSSI, and R. BRUCE WALLACE. "Enzymatic Synthesis of Oligoribonucleotides of Defined Sequence." DNA 6, no. 5 (October 1987): 497–504. http://dx.doi.org/10.1089/dna.1987.6.497.

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24

Sariban, E., R. S. Wu, L. C. Erickson, and W. M. Bonner. "Interrelationships of protein and DNA syntheses during replication of mammalian cells." Molecular and Cellular Biology 5, no. 6 (June 1985): 1279–86. http://dx.doi.org/10.1128/mcb.5.6.1279-1286.1985.

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During the replication of chromatin, the syntheses of the histone protein and DNA components are closely coordinated but not totally linked. The interrelationships of total protein synthesis, histone protein synthesis, DNA synthesis, and mRNA levels have been investigated in Chinese hamster ovary cells subjected to several different types of inhibitors in several different temporal combinations. The results from these studies and results reported elsewhere can be brought together into a consistent framework which combines the idea of autoregulation of histone biosynthesis as originally proposed by W. B. Butler and G. C. Mueller (Biochim. Biophys. Acta 294:481-496, 1973] with the presence of basal histone synthesis and the effects of protein synthesis on DNA synthesis. The proposed framework obviates the difficulties of Butler and Mueller's model and may have wider application in understanding the control of cell growth.

25

Sariban, E., R. S. Wu, L. C. Erickson, and W. M. Bonner. "Interrelationships of protein and DNA syntheses during replication of mammalian cells." Molecular and Cellular Biology 5, no. 6 (June 1985): 1279–86. http://dx.doi.org/10.1128/mcb.5.6.1279.

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During the replication of chromatin, the syntheses of the histone protein and DNA components are closely coordinated but not totally linked. The interrelationships of total protein synthesis, histone protein synthesis, DNA synthesis, and mRNA levels have been investigated in Chinese hamster ovary cells subjected to several different types of inhibitors in several different temporal combinations. The results from these studies and results reported elsewhere can be brought together into a consistent framework which combines the idea of autoregulation of histone biosynthesis as originally proposed by W. B. Butler and G. C. Mueller (Biochim. Biophys. Acta 294:481-496, 1973] with the presence of basal histone synthesis and the effects of protein synthesis on DNA synthesis. The proposed framework obviates the difficulties of Butler and Mueller's model and may have wider application in understanding the control of cell growth.

26

SHIMKUS, MARY L., PERRY GUAGLIANONE, and TIMOTHY M. HERMAN. "Synthesis and Characterization of Biotin-Labeled Nucleotide Analogs." DNA 5, no. 3 (June 1986): 247–55. http://dx.doi.org/10.1089/dna.1986.5.247.

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27

BODESCOT, MYRIAM, and OLIVIER BRISON. "Efficient Second-Strand cDNA Synthesis Using T7 DNA Polymerase." DNA and Cell Biology 13, no. 9 (September 1994): 977–85. http://dx.doi.org/10.1089/dna.1994.13.977.

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28

Xiong, X., J. L. Smith, and M. S. Chen. "Effect of incorporation of cidofovir into DNA by human cytomegalovirus DNA polymerase on DNA elongation." Antimicrobial Agents and Chemotherapy 41, no. 3 (March 1997): 594–99. http://dx.doi.org/10.1128/aac.41.3.594.

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Cidofovir (CDV) (HPMPC) has potent in vitro and in vivo activity against human cytomegalovirus (HCMV), CDV diphosphate (CDVpp), the putative antiviral metabolite of CDV, is an inhibitor and an alternate substrate of HCMV DNA polymerase. CDV is incorporated with the correct complementation to dGMP in the template, and the incorporated CDV at the primer end is not excised by the 3'-to-5' exonuclease activity of HCMV DNA polymerase. The incorporation of a CDV molecule causes a decrease in the rate of DNA elongation for the addition of the second natural nucleotide from the singly incorporated CDV molecule. The reduction in the rate of DNA (36-mer) synthesis from an 18-mer by one incorporated CDV is 31% that of the control. However, the fidelity of HCMV DNA polymerase is maintained for the addition of the nucleotides following a single incorporated CDV molecule. The rate of DNA synthesis by HCMV DNA polymerase is drastically decreased after the incorporation of two consecutive CDV molecules; the incorporation of a third consecutive CDV molecule is not detectable. Incorporation of two CDV molecules separated by either one or two deoxynucleoside monophosphates (dAMP, dGMP, or dTMP) also drastically decreases the rate of DNA chain elongation by HCMV DNA polymerase. The rate of DNA synthesis decreases by 90% when a template which contains one internally incorporated CDV molecule is used. The inhibition by CDVpp of DNA synthesis by HCMV DNA polymerase and the inability of HCMV DNA polymerase to excise incorporated CDV from DNA may account for the potent and long-lasting anti-CMV activity of CDV.

29

MacCulloch, Tara, Alexandra Novacek, and Nicholas Stephanopoulos. "Proximity-enhanced synthesis of DNA–peptide–DNA triblock molecules." Chemical Communications 58, no. 25 (2022): 4044–47. http://dx.doi.org/10.1039/d1cc04970d.

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30

Chaput, John C., Justin K. Ichida, and Jack W. Szostak. "DNA Polymerase-Mediated DNA Synthesis on a TNA Template." Journal of the American Chemical Society 125, no. 4 (January 2003): 856–57. http://dx.doi.org/10.1021/ja028589k.

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31

Arana, M. E., M. Seki, R. D. Wood, I. B. Rogozin, and T. A. Kunkel. "Low-fidelity DNA synthesis by human DNA polymerase theta." Nucleic Acids Research 36, no. 11 (May 28, 2008): 3847–56. http://dx.doi.org/10.1093/nar/gkn310.

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32

Gomez Godinez, Veronica, Sami Kabbara, Adria Sherman, Tao Wu, Shirli Cohen, Xiangduo Kong, Jose Luis Maravillas-Montero, et al. "DNA damage induced during mitosis undergoes DNA repair synthesis." PLOS ONE 15, no. 4 (April 28, 2020): e0227849. http://dx.doi.org/10.1371/journal.pone.0227849.

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33

Paz-Elizur, Tamar, Masaru Takeshita, Myron Goodman, Michael O'Donnell, and Zvi Livneh. "Mechanism of Translesion DNA Synthesis by DNA Polymerase II." Journal of Biological Chemistry 271, no. 40 (October 4, 1996): 24662–69. http://dx.doi.org/10.1074/jbc.271.40.24662.

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34

Lee, S. H., Z. Q. Pan, A. D. Kwong, P. M. Burgers, and J. Hurwitz. "Synthesis of DNA by DNA polymerase epsilon in vitro." Journal of Biological Chemistry 266, no. 33 (November 1991): 22707–17. http://dx.doi.org/10.1016/s0021-9258(18)54626-3.

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35

Tomiyasu, Shinjiro, Kazuhiko Kuwahara, Nobuo Sakaguchi, and Michio Ogawa. "GANP DNA primase associated with MCM3 and DNA synthesis." International Congress Series 1255 (August 2003): 283–88. http://dx.doi.org/10.1016/s0531-5131(03)00917-8.

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36

Liang, X., T. Kato, and H. Asanuma. "Mechanism of DNA elongation during de novo DNA synthesis." Nucleic Acids Symposium Series 52, no. 1 (September 1, 2008): 411–12. http://dx.doi.org/10.1093/nass/nrn209.

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37

Barone, G., L. De Napoli, G. Di Fabio, E. Erra, C. Giancola, A. Messere, D. Montesarchio, L. Petraccone, and G. Piccialli. "Synthesis and DNA Binding Properties of DNA-PNA Chimeras." Nucleosides, Nucleotides and Nucleic Acids 22, no. 5-8 (October 2003): 1089–91. http://dx.doi.org/10.1081/ncn-120022743.

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38

Matsuda, Toshiro, Katarzyna Bebenek, Chikahide Masutani, Fumio Hanaoka та Thomas A. Kunkel. "Low fidelity DNA synthesis by human DNA polymerase-η". Nature 404, № 6781 (квітень 2000): 1011–13. http://dx.doi.org/10.1038/35010014.

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39

CARUTHERS, M. H. "ChemInform Abstract: Chemical Synthesis of DNA and DNA Analogues." ChemInform 23, no. 4 (August 22, 2010): no. http://dx.doi.org/10.1002/chin.199204308.

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40

Zhang, Hui Yong. "Solid-Phase Synthesis of DNA Chemical Sensor." Advanced Materials Research 815 (October 2013): 305–11. http://dx.doi.org/10.4028/www.scientific.net/amr.815.305.

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Oligonucleotides are essential components of many applications in molecular biology. The synthesis chemistry is robust and commercial oligonucleotide synthesizers have taken advantage of the chemistry to provide oligonucleotides of high quality and purity. This paper established nucleic acid synthesis platform to carry out the synthesis of the labeled nucleic acid probes based on the DNA synthesizer and solid-phase synthesis technology. We chose to study the automated synthesis starting from DMT protected FAM labeled amidite attached to controlled pore glass (CPG) support and the standard trityl-off oligonucleotide synthesis cycle was performed, yielding the solid-supported oligonucleotide. The reported automated solid-phase oligonucleotide synthesis procedure successfully employs the common iterative synthesis, deblocking, activation, coupling, capping, oxidation, and isolation steps in standard oligonucleotide synthesis. The automated synthetic approach can also be applied to oligonucleotides of different length, composition of nucleotide, demonstrating the universality of the method. Moreover, the synthesis involved the use of commercially available, safe, stable, and inexpensive reagents, particularly advantageous and attractive for their use in automated solid-phase synthesis. The synthesis allows custom tailoring of their structure to the requirements of biological assays within hours, as opposed to traditional approaches that require weeks or months of work in the laboratory. Therefore it will become much easier to investigate biological interactions and optimize for objectives such as the receptor mediated targeting of oligonucleotides.

41

Bügl, Hans, John P. Danner, Robert J. Molinari, John T. Mulligan, Han-Oh Park, Bas Reichert, David A. Roth, et al. "DNA synthesis and biological security." Nature Biotechnology 25, no. 6 (June 2007): 627–29. http://dx.doi.org/10.1038/nbt0607-627.

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42

Shivalingam, Arun, and Tom Brown. "Synthesis of chemically modified DNA." Biochemical Society Transactions 44, no. 3 (June 9, 2016): 709–15. http://dx.doi.org/10.1042/bst20160051.

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Naturally occurring DNA is encoded by the four nucleobases adenine, cytosine, guanine and thymine. Yet minor chemical modifications to these bases, such as methylation, can significantly alter DNA function, and more drastic changes, such as replacement with unnatural base pairs, could expand its function. In order to realize the full potential of DNA in therapeutic and synthetic biology applications, our ability to ‘write’ long modified DNA in a controlled manner must be improved. This review highlights methods currently used for the synthesis of moderately long chemically modified nucleic acids (up to 1000 bp), their limitations and areas for future expansion.

43

Yamashita, Takayuki, Tsukasa Oda, and Takayuki Sekimoto. "Translesion DNA Synthesis and Hsp90." Genes and Environment 34, no. 2 (2012): 89–93. http://dx.doi.org/10.3123/jemsge.34.89.

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44

Pincus, SH, KS Ramesh, and DJ Wyler. "Eosinophils stimulate fibroblast DNA synthesis." Blood 70, no. 2 (August 1, 1987): 572–74. http://dx.doi.org/10.1182/blood.v70.2.572.572.

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Abstract Fibrosis complicates a number of chronic inflammatory diseases and occurs in some conditions following chronic hypereosinophilic syndromes. We assessed whether eosinophils might be a source of fibrogenic factors. Extracts of human and guinea pig cell populations enriched for eosinophils contained substances that stimulated tritiated thymidine incorporation by human fibroblasts. Supernatants derived from resting eosinophils and extracts prepared from eosinophil granules also contained fibrogenic factors. Our findings demonstrate a new potential role for eosinophils and suggest a causal relationship between tissue eosinophilia and scar formation in certain parasitic condition.

45

Pincus, SH, KS Ramesh, and DJ Wyler. "Eosinophils stimulate fibroblast DNA synthesis." Blood 70, no. 2 (August 1, 1987): 572–74. http://dx.doi.org/10.1182/blood.v70.2.572.bloodjournal702572.

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Fibrosis complicates a number of chronic inflammatory diseases and occurs in some conditions following chronic hypereosinophilic syndromes. We assessed whether eosinophils might be a source of fibrogenic factors. Extracts of human and guinea pig cell populations enriched for eosinophils contained substances that stimulated tritiated thymidine incorporation by human fibroblasts. Supernatants derived from resting eosinophils and extracts prepared from eosinophil granules also contained fibrogenic factors. Our findings demonstrate a new potential role for eosinophils and suggest a causal relationship between tissue eosinophilia and scar formation in certain parasitic condition.

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HANNIGAN, B. H., K. L. O'NEILL, R. H. PEARCE, P. G. McKENNA, and W. P. ABRAM. "Lymphocyte DNA synthesis in malignancy." Biochemical Society Transactions 14, no. 1 (February 1, 1986): 81–82. http://dx.doi.org/10.1042/bst0140081.

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Bong, Dennis, and Jie Mao. "Synthesis of DNA-Binding Peptoids." Synlett 26, no. 11 (May 11, 2015): 1581–85. http://dx.doi.org/10.1055/s-0034-1380698.

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Chow, B. Y., C. J. Emig, and J. M. Jacobson. "Photoelectrochemical synthesis of DNA microarrays." Proceedings of the National Academy of Sciences 106, no. 36 (August 21, 2009): 15219–24. http://dx.doi.org/10.1073/pnas.0813011106.

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Nicolaou, K. C., Brian Smith, Joaquin Pastor, Yoshihiko Watanabe, and David Weinstein. "Synthesis of DNA-Binding Oligosaccharides." Synlett 1997, Sup. I (June 1997): 401–10. http://dx.doi.org/10.1055/s-1997-6114.

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Mandala, S. K., and P. Dutta. "Synthesis of DNA-Polypyrrole Nanocapsule." Journal of Nanoscience and Nanotechnology 4, no. 8 (November 1, 2004): 972–75. http://dx.doi.org/10.1166/jnn.2004.127.

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