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Journal articles on the topic 'DNA systems'

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Author: Grafiati
Published: 6 September 2023

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1

Chakarov, Stoyan, Rumena Petkova, and George Russev. "DNA repair systems." BioDiscovery, no. 13 (September 22, 2014): 2. http://dx.doi.org/10.7750/biodiscovery.2014.13.2.

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2

Teo, Yin Nah, and Eric T. Kool. "DNA-Multichromophore Systems." Chemical Reviews 112, no. 7 (March 16, 2012): 4221–45. http://dx.doi.org/10.1021/cr100351g.

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3

Kaina, Bernd. "DNA repair systems." Toxicology Letters 164 (September 2006): S320. http://dx.doi.org/10.1016/j.toxlet.2006.07.328.

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4

Rao, D. N., and Yedu Prasad. "DNA repair systems." Resonance 21, no. 10 (October 2016): 925–36. http://dx.doi.org/10.1007/s12045-016-0401-x.

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5

Walker, G. C. "Inducible DNA Repair Systems." Annual Review of Biochemistry 54, no. 1 (June 1985): 425–57. http://dx.doi.org/10.1146/annurev.bi.54.070185.002233.

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6

Aerts, Diederik, and Marek Czachor. "Abstract DNA-type systems." Nonlinearity 19, no. 3 (January 31, 2006): 575–89. http://dx.doi.org/10.1088/0951-7715/19/3/003.

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7

Luo, Dan, and W. Mark Saltzman. "Synthetic DNA delivery systems." Nature Biotechnology 18, no. 1 (January 2000): 33–37. http://dx.doi.org/10.1038/71889.

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8

Ma, Ke, Alexander W. Harris, and Jennifer N. Cha. "DNA assembled photoactive systems." Current Opinion in Colloid & Interface Science 38 (November 2018): 18–29. http://dx.doi.org/10.1016/j.cocis.2018.08.003.

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9

Handelsman, Jo. "Call for Papers: Unique Model Systems." DNA and Cell Biology 27, no. 6 (June 2008): 287. http://dx.doi.org/10.1089/dna.2008.1504.

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10

Jolly, Pawan, Pedro Estrela, and Michael Ladomery. "Oligonucleotide-based systems: DNA, microRNAs, DNA/RNA aptamers." Essays in Biochemistry 60, no. 1 (June 30, 2016): 27–35. http://dx.doi.org/10.1042/ebc20150004.

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There are an increasing number of applications that have been developed for oligonucleotide-based biosensing systems in genetics and biomedicine. Oligonucleotide-based biosensors are those where the probe to capture the analyte is a strand of deoxyribonucleic acid (DNA), ribonucleic acid (RNA) or a synthetic analogue of naturally occurring nucleic acids. This review will shed light on various types of nucleic acids such as DNA and RNA (particularly microRNAs), their role and their application in biosensing. It will also cover DNA/RNA aptamers, which can be used as bioreceptors for a wide range of targets such as proteins, small molecules, bacteria and even cells. It will also highlight how the invention of synthetic oligonucleotides such as peptide nucleic acid (PNA) or locked nucleic acid (LNA) has pushed the limits of molecular biology and biosensor development to new perspectives. These technologies are very promising albeit still in need of development in order to bridge the gap between the laboratory-based status and the reality of biomedical applications.
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11

Bonincontro, A., R. Caneva, and F. Pedone. "Hydration of aminoacid-DNA and protein-DNA systems." Biochemical Pharmacology 37, no. 9 (May 1988): 1839–40. http://dx.doi.org/10.1016/0006-2952(88)90472-8.

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12

Winogradoff, David, Pin‐Yi Li, Himanshu Joshi, Lauren Quednau, Christopher Maffeo, and Aleksei Aksimentiev. "Chiral Systems Made from DNA." Advanced Science 8, no. 5 (January 21, 2021): 2003113. http://dx.doi.org/10.1002/advs.202003113.

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13

Sáez, Guillermo. "DNA Injury and Repair Systems." International Journal of Molecular Sciences 19, no. 7 (June 28, 2018): 1902. http://dx.doi.org/10.3390/ijms19071902.

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14

Kozulin, R. A., V. E. Kurochkin, and V. M. Zolotarev. "Fluorescence-based DNA-monitoring systems." Journal of Optical Technology 72, no. 1 (January 1, 2005): 20. http://dx.doi.org/10.1364/jot.72.000020.

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15

Martin, F. L. "DNA Repair Protocols: Eukaryotic Systems." Mutagenesis 14, no. 6 (November 1, 1999): 657. http://dx.doi.org/10.1093/mutage/14.6.657.

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16

DOERFLER, WALTER, RAINER SCHUBBERT, HILDE HELLER, JENNIFER HERTZ, RALPH REMUS, JÖRG SCHRÖER, CHRISTINA KÄMMER, et al. "Foreign DNA in mammalian systems." APMIS 106, S84 (November 1998): 62–68. http://dx.doi.org/10.1111/j.1600-0463.1998.tb05650.x.

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17

Brzeski, Henry. "DNA cloning 2. Expression systems." Biochemical Systematics and Ecology 24, no. 1 (January 1996): 92. http://dx.doi.org/10.1016/s0305-1978(96)90010-1.

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18

Glazer, Peter M. "DNA Repair Protocols: Eukaryotic Systems." Radiation Research 153, no. 2 (February 2000): 241–42. http://dx.doi.org/10.1667/0033-7587(2000)153[0241:drpes]2.0.co;2.

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19

Mardian, Rizki, and Kosuke Sekiyama. "Ant Systems-Based DNA Circuits." BioNanoScience 5, no. 4 (November 11, 2015): 206–16. http://dx.doi.org/10.1007/s12668-015-0182-9.

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20

Mayran, Alexandre, and Christopher Chase Bolt. "Transgenic Model Systems Have Revolutionized the Study of Disease." DNA and Cell Biology 41, no. 1 (January 1, 2022): 49–52. http://dx.doi.org/10.1089/dna.2021.0514.

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21

TAVERNIER, JAN, RENE DEVOS, JOSE VAN DER HEYDEN, GUIDO HAUQUIER, RITA BAUDEN, INA FACHE, ERIC KAWASHIMA, JOEL VANDEKERCKHOVE, ROLAND CONTRERAS, and WALTER FIERS. "Expression of Human and Murine Interleukin-5 in Eukaryotic Systems." DNA 8, no. 7 (September 1989): 491–501. http://dx.doi.org/10.1089/dna.1.1989.8.491.

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22

Huckenbeck, W., H. G. Scheil, H. D. Schmidt, L. Efremovska, and N. Xirotiris. "Population genetic studies in the Balkans. II. DNA-STR-systems." Anthropologischer Anzeiger 59, no. 3 (September 12, 2001): 213–25. http://dx.doi.org/10.1127/anthranz/59/2001/213.

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23

Bhandari, Deepika. "Touch DNA: Revolutionizing Evidentiary DNA Forensics." International Journal of Forensic Sciences 8, no. 3 (2023): 1–8. http://dx.doi.org/10.23880/ijfsc-16000314.

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Touch DNA is an advanced technique widely employed in modern criminal justice systems in many developed countries. It aims to extract genetic information from biological substances, specifically the cells shed from the outermost layer of skin, that are left behind on touched objects. This method involves recovering trace amounts of DNA from the biological cells released during contact, even though the quantity is usually very low. The recovered DNA is further analyzed to generate a person's DNA profile. Since dead cells are not really visible to the naked eye, successfully locating and recovering them can be challenging. Performing DNA profiling from the samples that are just touched is quite difficult, hence, requires a highly sensitive approach to its proper recovery, extraction, and amplification of the segment. The methods which are used for the collection, sampling procedure, preservation, removal of contaminants, quantification of DNA, the amplifying of the genetic material, and the subsequent analysis and interpretation of the findings all play a role in how well touch DNA analysis works. Various techniques have been created over time to gather touch DNA. Reliable DNA profiles are produced thanks to the use of sophisticated kits, tools, and well-equipped forensic laboratories, which benefit the criminal justice system.
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24

Patil, Siddhesh D., David G. Rhodes, and Diane J. Burgess. "DNA-based therapeutics and DNA delivery systems: A comprehensive review." AAPS Journal 7, no. 1 (March 2005): E61—E77. http://dx.doi.org/10.1208/aapsj070109.

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25

Chiaramoni, N. S., L. C. Baccarini, M. C. Taira, and S. del V. Alonso. "Liposome/DNA Systems: Correlation Between Hydrophobicity and DNA Conformational Changes." Journal of Biological Physics 34, no. 1-2 (April 2008): 179–88. http://dx.doi.org/10.1007/s10867-008-9103-2.

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26

SEKIGUCHI, Mutsuo. "Genetic systems for stability of DNA." Seibutsu Butsuri 37, no. 3 (1997): 100–105. http://dx.doi.org/10.2142/biophys.37.100.

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27

Guan, Chaoyang, Xiaoli Zhu, and Chang Feng. "DNA Nanodevice-Based Drug Delivery Systems." Biomolecules 11, no. 12 (December 10, 2021): 1855. http://dx.doi.org/10.3390/biom11121855.

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DNA, a natural biological material, has become an ideal choice for biomedical applications, mainly owing to its good biocompatibility, ease of synthesis, modifiability, and especially programmability. In recent years, with the deepening of the understanding of the physical and chemical properties of DNA and the continuous advancement of DNA synthesis and modification technology, the biomedical applications based on DNA materials have been upgraded to version 2.0: through elaborate design and fabrication of smart-responsive DNA nanodevices, they can respond to external or internal physical or chemical stimuli so as to smartly perform certain specific functions. For tumor treatment, this advancement provides a new way to solve the problems of precise targeting, controllable release, and controllable elimination of drugs to a certain extent. Here, we review the progress of related fields over the past decade, and provide prospects for possible future development directions.
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28

Lu, Shasha, Jianlei Shen, Chunhai Fan, Qian Li, and Xiurong Yang. "DNA Assembly‐Based Stimuli‐Responsive Systems." Advanced Science 8, no. 13 (May 14, 2021): 2100328. http://dx.doi.org/10.1002/advs.202100328.

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29

Linko, Veikko, Sami Nummelin, Laura Aarnos, Kosti Tapio, J. Toppari, and Mauri Kostiainen. "DNA-Based Enzyme Reactors and Systems." Nanomaterials 6, no. 8 (July 27, 2016): 139. http://dx.doi.org/10.3390/nano6080139.

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30

Xue, Han, Xihui Gao, and Chuan Zhang. "DNA nanostructure-based siRNA delivery systems." Chinese Science Bulletin 64, no. 10 (January 25, 2019): 1053–66. http://dx.doi.org/10.1360/n972018-00893.

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31

RADMAN, M., F. TADDEI, and I. MATIC. "DNA Repair Systems and Bacterial Evolution." Cold Spring Harbor Symposia on Quantitative Biology 65 (January 1, 2000): 11–20. http://dx.doi.org/10.1101/sqb.2000.65.11.

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32

Pannier, Angela K., and Lonnie D. Shea. "Controlled release systems for DNA delivery." Molecular Therapy 10, no. 1 (July 2004): 19–26. http://dx.doi.org/10.1016/j.ymthe.2004.03.020.

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33

Mai, Danielle J., Christopher Brockman, and Charles M. Schroeder. "Microfluidic systems for single DNA dynamics." Soft Matter 8, no. 41 (2012): 10560. http://dx.doi.org/10.1039/c2sm26036k.

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34

Radman, Miroslav. "DNA repair systems and genetic toxicology." Toxicology Letters 164 (September 2006): S3. http://dx.doi.org/10.1016/j.toxlet.2006.06.009.

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35

Ibraheem, D., A. Elaissari, and H. Fessi. "Gene therapy and DNA delivery systems." International Journal of Pharmaceutics 459, no. 1-2 (January 2014): 70–83. http://dx.doi.org/10.1016/j.ijpharm.2013.11.041.

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36

Morling, Niels, and Hanna E. Hansen. "Paternity testing with VNTR DNA systems." International Journal of Legal Medicine 105, no. 4 (July 1993): 189–96. http://dx.doi.org/10.1007/bf01642792.

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37

Hansen, Hanna E., and Niels Morling. "Paternity testing with VNTR DNA systems." International Journal of Legal Medicine 105, no. 4 (July 1993): 197–202. http://dx.doi.org/10.1007/bf01642793.

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38

Kari, Lila, Gheorghe Păun, Grzegorz Rozenberg, Arto Salomaa, and Sheng Yu. "DNA computing, sticker systems, and universality." Acta Informatica 35, no. 5 (May 1, 1998): 401–20. http://dx.doi.org/10.1007/s002360050125.

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39

Lee, Lan-Ying, and Stanton B. Gelvin. "T-DNA Binary Vectors and Systems." Plant Physiology 146, no. 2 (February 2008): 325–32. http://dx.doi.org/10.1104/pp.107.113001.

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40

Toumpanakis, Dimitrios, and Stamatios E. Theocharis. "DNA repair systems in malignant mesothelioma." Cancer Letters 312, no. 2 (December 2011): 143–49. http://dx.doi.org/10.1016/j.canlet.2011.08.021.

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41

Furniss, Caroline S. M., A. Bryan Hanley, Alan R. Mackie, and James Mingins. "DNA manipulation in low water systems." Enzyme and Microbial Technology 13, no. 6 (June 1991): 525. http://dx.doi.org/10.1016/0141-0229(91)90043-a.

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42

Malinina, L. V., V. V. Makhaldiani, V. A. Tereshko, V. F. Zarytova, and E. M. Ivanova. "Phase Diagrams for DNA Crystallization Systems." Journal of Biomolecular Structure and Dynamics 5, no. 2 (October 1987): 405–33. http://dx.doi.org/10.1080/07391102.1987.10506402.

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43

Nakakuki, Takashi, Jun-ichi Imura, Ibuki Kawamata, and Satoshi Murata. "Robustness of DNA Strand Displacement Systems⋆." IFAC-PapersOnLine 51, no. 33 (2018): 32–37. http://dx.doi.org/10.1016/j.ifacol.2018.12.081.

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44

Feldkamp, Udo, and Christof M Niemeyer. "Rational Engineering of Dynamic DNA Systems." Angewandte Chemie International Edition 47, no. 21 (May 13, 2008): 3871–73. http://dx.doi.org/10.1002/anie.200800675.

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45

Yu, Zhe, Jian Chen, Barry N. Ford, Moyra E. Brackley, and Barry W. Glickman. "Human DNA repair systems: An overview." Environmental and Molecular Mutagenesis 33, no. 1 (1999): 3–20. http://dx.doi.org/10.1002/(sici)1098-2280(1999)33:1<3::aid-em2>3.0.co;2-l.

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46

Lo, Chen-Yu, and Yang Gao. "DNA Helicase–Polymerase Coupling in Bacteriophage DNA Replication." Viruses 13, no. 9 (August 31, 2021): 1739. http://dx.doi.org/10.3390/v13091739.

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Bacteriophages have long been model systems to study the molecular mechanisms of DNA replication. During DNA replication, a DNA helicase and a DNA polymerase cooperatively unwind the parental DNA. By surveying recent data from three bacteriophage replication systems, we summarized the mechanistic basis of DNA replication by helicases and polymerases. Kinetic data have suggested that a polymerase or a helicase alone is a passive motor that is sensitive to the base-pairing energy of the DNA. When coupled together, the helicase–polymerase complex is able to unwind DNA actively. In bacteriophage T7, helicase and polymerase reside right at the replication fork where the parental DNA is separated into two daughter strands. The two motors pull the two daughter strands to opposite directions, while the polymerase provides a separation pin to split the fork. Although independently evolved and containing different replisome components, bacteriophage T4 replisome shares mechanistic features of Hel–Pol coupling that are similar to T7. Interestingly, in bacteriophages with a limited size of genome like Φ29, DNA polymerase itself can form a tunnel-like structure, which encircles the DNA template strand and facilitates strand displacement synthesis in the absence of a helicase. Studies on bacteriophage replication provide implications for the more complicated replication systems in bacteria, archaeal, and eukaryotic systems, as well as the RNA genome replication in RNA viruses.
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47

Fiebig, Torsten, and Hans-Achim Wagenknecht. "DNA Photonics – Photoinduced Electron Transfer in Synthetic DNA-Donor–Acceptor Systems." CHIMIA International Journal for Chemistry 61, no. 4 (April 25, 2007): 133–39. http://dx.doi.org/10.2533/chimia.2007.133.

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48

George, Aby K., and Harpreet Singh. "DNA Implementation of Fuzzy Inference Engine: Towards DNA Decision-Making Systems." IEEE Transactions on NanoBioscience 16, no. 8 (December 2017): 773–82. http://dx.doi.org/10.1109/tnb.2017.2760821.

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49

Lu, Chun-Hua, Bilha Willner, and Itamar Willner. "DNA Nanotechnology: From Sensing and DNA Machines to Drug-Delivery Systems." ACS Nano 7, no. 10 (September 26, 2013): 8320–32. http://dx.doi.org/10.1021/nn404613v.

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50

Thompson, Marlo K., Robert W. Sobol, and Aishwarya Prakash. "Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair." Biology 10, no. 6 (June 14, 2021): 530. http://dx.doi.org/10.3390/biology10060530.

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The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples.
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