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Journal articles on the topic 'DNA. RNA'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Arnott, Struther, R. Chandrasekaran, R. P. Millane, and H. S. Park. "RNA-RNA, DNA-DNA, and DNA-RNA Polymorphism." Biophysical Journal 49, no. 1 (January 1986): 3–5. http://dx.doi.org/10.1016/s0006-3495(86)83568-8.

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2

Urata, Hidehito, Hana Shimizu, and Masao Akagi. "Structural Studies of Heterochiral DNA/DNA, RNA/RNA, AND DNA/RNA Duplexes." Nucleosides, Nucleotides and Nucleic Acids 25, no. 4-6 (June 2006): 359–67. http://dx.doi.org/10.1080/15257770600683920.

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3

Afonin, Kirill A., Mathias Viard, Ioannis Kagiampakis, Christopher L. Case, Marina A. Dobrovolskaia, Jen Hofmann, Ashlee Vrzak, et al. "Triggering of RNA Interference with RNA–RNA, RNA–DNA, and DNA–RNA Nanoparticles." ACS Nano 9, no. 1 (December 18, 2014): 251–59. http://dx.doi.org/10.1021/nn504508s.

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4

Banfalvi, Gaspar. "Origin of Coding RNA from Random-Sequence RNA." DNA and Cell Biology 38, no. 3 (March 2019): 223–28. http://dx.doi.org/10.1089/dna.2018.4389.

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5

Fugmann, Sebastian D., and David G. Schatz. "RNA AIDs DNA." Nature Immunology 4, no. 5 (May 2003): 429–30. http://dx.doi.org/10.1038/ni0503-429.

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6

Steitz, Thomas A. "DNA- and RNA-dependent DNA polymerases." Current Opinion in Structural Biology 3, no. 1 (February 1993): 31–38. http://dx.doi.org/10.1016/0959-440x(93)90198-t.

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7

Malonga, Herman, Jean-Francois Neault, and Heidar-Ali Tajmir-Riahi. "Transfer RNA Binding to Human Serum Albumin: A Model for Protein–RNA Interaction." DNA and Cell Biology 25, no. 7 (July 2006): 393–98. http://dx.doi.org/10.1089/dna.2006.25.393.

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8

Melkonyan, Lena, Mathilde Bercy, Thierry Bizebard, and Ulrich Bockelmann. "Overstretching Double-Stranded RNA, Double-Stranded DNA, and RNA-DNA Duplexes." Biophysical Journal 117, no. 3 (August 2019): 509–19. http://dx.doi.org/10.1016/j.bpj.2019.07.003.

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9

Nafisi, Shohreh, Maryam Adelzadeh, Zeinab Norouzi, and Mohammad Nabi Sarbolouki. "Curcumin Binding to DNA and RNA." DNA and Cell Biology 28, no. 4 (April 2009): 201–8. http://dx.doi.org/10.1089/dna.2008.0840.

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10

Huang, Yuegao, and Irina M. Russu. "Dynamic and Energetic Signatures of Adenine Tracts in a rA-dT RNA-DNA Hybrid and in Homologous RNA-DNA, RNA-RNA, and DNA-DNA Double Helices." Biochemistry 56, no. 19 (May 2017): 2446–54. http://dx.doi.org/10.1021/acs.biochem.6b01122.

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11

Krasnorutskii, Michael A., Valentina N. Buneva, and Georgy A. Nevinsky. "Antibodies against RNA hydrolyze RNA and DNA." Journal of Molecular Recognition 21, no. 5 (September 2008): 338–47. http://dx.doi.org/10.1002/jmr.906.

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12

Dalakouras, Athanasios, and Michael Wassenegger. "Revisiting RNA-directed DNA methylation." RNA Biology 10, no. 3 (March 2013): 453–55. http://dx.doi.org/10.4161/rna.23542.

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13

Mahfouz, Magdy M. "RNA-directed DNA methylation." Plant Signaling & Behavior 5, no. 7 (July 2010): 806–16. http://dx.doi.org/10.4161/psb.5.7.11695.

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14

Angeleska, Angela, Nataša Jonoska, Masahico Saito, and Laura F. Landweber. "RNA-guided DNA assembly." Journal of Theoretical Biology 248, no. 4 (October 2007): 706–20. http://dx.doi.org/10.1016/j.jtbi.2007.06.007.

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15

Piper, Peter. "Of DNA and RNA." Nature 326, no. 6109 (March 1987): 223. http://dx.doi.org/10.1038/326223c0.

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16

Erdmann, Robert M., and Colette L. Picard. "RNA-directed DNA Methylation." PLOS Genetics 16, no. 10 (October 8, 2020): e1009034. http://dx.doi.org/10.1371/journal.pgen.1009034.

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17

Mathieu, O. "RNA-directed DNA methylation." Journal of Cell Science 117, no. 21 (October 1, 2004): 4881–88. http://dx.doi.org/10.1242/jcs.01479.

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18

LIU, Tao. "DNA and RNA sensor." Science in China Series B 48, no. 1 (2005): 1. http://dx.doi.org/10.1360/03yb0151.

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19

Zhang, Huiming, and Jian-Kang Zhu. "RNA-directed DNA methylation." Current Opinion in Plant Biology 14, no. 2 (April 2011): 142–47. http://dx.doi.org/10.1016/j.pbi.2011.02.003.

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20

Storici, Francesca, Katarzyna Bebenek, Thomas A. Kunkel, Dmitry A. Gordenin, and Michael A. Resnick. "RNA-templated DNA repair." Nature 447, no. 7142 (April 11, 2007): 338–41. http://dx.doi.org/10.1038/nature05720.

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21

Weiss, R. A. "How RNA Makes DNA." Science 264, no. 5167 (June 24, 1994): 1954–55. http://dx.doi.org/10.1126/science.264.5167.1954-a.

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22

Weintraub, Harold M. "Antisense RNA and DNA." Scientific American 262, no. 1 (January 1990): 40–46. http://dx.doi.org/10.1038/scientificamerican0190-40.

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23

Brown, Robert V., and Laurence H. Hurley. "DNA acting like RNA." Biochemical Society Transactions 39, no. 2 (March 22, 2011): 635–40. http://dx.doi.org/10.1042/bst0390635.

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Over the last decade or so, secondary non-B-DNA structures such as G-quadruplexes and i-motifs have come into focus as biologically functioning moieties that are potentially involved in telomeric interactions and the control of gene expression. In the present short review, we first describe the structural and dynamic parallels with complex RNA structures, including the importance of sequence and ions in folding, and then we describe the biological consequences of the folded structures. We conclude that there are considerable parallels between secondary and tertiary structures in RNA and DNA from both the folding and the biological perspectives.

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24

Liu, Tao, Lin Lin, Hong Zhao, and Long Jiang. "DNA and RNA sensor." Science in China Series B: Chemistry 48, no. 1 (January 2005): 1–10. http://dx.doi.org/10.1007/bf02990906.

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25

Vågbø, Cathrine Broberg, and Geir Slupphaug. "RNA in DNA repair." DNA Repair 95 (November 2020): 102927. http://dx.doi.org/10.1016/j.dnarep.2020.102927.

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26

Zheng, Xiaojuan, Lianlian Hong, Yifei Li, Junqing Guo, Gaiping Zhang, and Jiyong Zhou. "In VitroExpression and Monoclonal Antibody of RNA-Dependent RNA Polymerase for Infectious Bursal Disease Virus." DNA and Cell Biology 25, no. 11 (November 2006): 646–53. http://dx.doi.org/10.1089/dna.2006.25.646.

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27

Urata, H., H. Shimizu, H. Hiroaki, D. Kohda, and M. Akagi. "Characterization of DNA, RNA and DNA/RNA duplexes containing an L-nucleotide." Nucleic Acids Symposium Series 1, no. 1 (November 1, 2001): 243–44. http://dx.doi.org/10.1093/nass/1.1.243.

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28

Krasnorutskii, M. A., V. N. Buneva, and G. A. Nevinsky. "Antibodies against DNA hydrolyze DNA and RNA." Biochemistry (Moscow) 73, no. 11 (November 2008): 1242–53. http://dx.doi.org/10.1134/s0006297908110114.

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29

Gavette, Jesse V., Matthias Stoop, Nicholas V. Hud, and Ramanarayanan Krishnamurthy. "RNA-DNA Chimeras in the Context of an RNA World Transition to an RNA/DNA World." Angewandte Chemie 128, no. 42 (October 6, 2016): 13398–403. http://dx.doi.org/10.1002/ange.201607919.

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30

Gavette, Jesse V., Matthias Stoop, Nicholas V. Hud, and Ramanarayanan Krishnamurthy. "RNA-DNA Chimeras in the Context of an RNA World Transition to an RNA/DNA World." Angewandte Chemie International Edition 55, no. 42 (October 6, 2016): 13204–9. http://dx.doi.org/10.1002/anie.201607919.

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31

Ahmed Ouameur, Amin, Regis Marty, Jean-François Neault, and Heidar-Ali Tajmir-Riahi. "AZT Binds RNA at Multiple Sites." DNA and Cell Biology 23, no. 11 (November 2004): 783–88. http://dx.doi.org/10.1089/dna.2004.23.783.

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32

Lawson, Jonathan N., and Stephen Albert Johnston. "Amplification of Sense-Stranded Prokaryotic RNA." DNA and Cell Biology 25, no. 11 (November 2006): 627–34. http://dx.doi.org/10.1089/dna.2006.25.627.

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33

Huang, Chao-Feng, and Jian-Kang Zhu. "RNA Splicing Factors and RNA-Directed DNA Methylation." Biology 3, no. 2 (March 26, 2014): 243–54. http://dx.doi.org/10.3390/biology3020243.

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34

Bae, Sangsu, Yuyoung Kim, Doyoun Kim, Kyeong Kyu Kim, Yang-Gyun Kim, and Sungchul Hohng. "Energetics of Z-DNA Binding Protein-Mediated Helicity Reversals in DNA, RNA, and DNA–RNA Duplexes." Journal of Physical Chemistry B 117, no. 44 (October 28, 2013): 13866–71. http://dx.doi.org/10.1021/jp409862j.

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35

Tsybulskyi, Volodymyr, Mohamed Mounir, and Irmtraud M. Meyer. "R-chie: a web server and R package for visualizing cis and trans RNA–RNA, RNA–DNA and DNA–DNA interactions." Nucleic Acids Research 48, no. 18 (September 25, 2020): e105-e105. http://dx.doi.org/10.1093/nar/gkaa708.

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Abstract Interactions between biological entities are key to understanding their potential functional roles. Three fields of research have recently made particular progress: the investigation of transRNA–RNA and RNA–DNA transcriptome interactions and of trans DNA–DNA genome interactions. We now have both experimental and computational methods for examining these interactions in vivo and on a transcriptome- and genome-wide scale, respectively. Often, key insights can be gained by visually inspecting figures that manage to combine different sources of evidence and quantitative information. We here present R-chie, a web server and R package for visualizing cis and transRNA–RNA, RNA–DNA and DNA–DNA interactions. For this, we have completely revised and significantly extended an earlier version of R-chie (1) which was initially introduced for visualizing RNA secondary structure features. The new R-chie offers a range of unique features for visualizing cis and transRNA–RNA, RNA–DNA and DNA–DNA interactions. Particularly note-worthy features include the ability to incorporate evolutionary information, e.g. multiple-sequence alignments, to compare two alternative sets of information and to incorporate detailed, quantitative information. R-chie is readily available via a web server as well as a corresponding R package called R4RNA which can be used to run the software locally.

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36

Hannan, Katherine M., Lawrence I. Rothblum, and Leonard S. Jefferson. "Regulation of ribosomal DNA transcription by insulin." American Journal of Physiology-Cell Physiology 275, no. 1 (July 1, 1998): C130—C138. http://dx.doi.org/10.1152/ajpcell.1998.275.1.c130.

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The experiments reported here used 3T6-Swiss albino mouse fibroblasts and H4-II-E-C3 rat hepatoma cells as model systems to examine the mechanism(s) through which insulin regulates rDNA transcription. Serum starvation of 3T6 cells for 72 h resulted in a marked reduction in rDNA transcription. Treatment of serum-deprived cells with insulin was sufficient to restore rDNA transcription to control values. In addition, treatment of exponentially growing H4-II-E-C3 with insulin stimulated rDNA transcription. However, for both cell types, the stimulation of rDNA transcription in response to insulin was not associated with a change in the cellular content of RNA polymerase I. Thus we conclude that insulin must cause alterations in formation of the active RNA polymerase I initiation complex and/or the activities of auxiliary rDNA transcription factors. In support of this conclusion, insulin treatment of both cell types was found to increase the nuclear content of upstream binding factor (UBF) and RNA polymerase I-associated factor 53. Both of these factors are thought to be involved in recruitment of RNA polymerase I to the rDNA promoter. Nuclear run-on experiments demonstrated that the increase in cellular content of UBF was due to elevated transcription of the UBF gene. In addition, overexpression of UBF was sufficient to directly stimulate rDNA transcription from a reporter construct. The results demonstrate that insulin is capable of stimulating rDNA transcription in both 3T6 and H4-II-E-C3 cells, at least in part by increasing the cellular content of components required for assembly of RNA polymerase I into an active complex.

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37

Zhang, Heng, Xinjian He, and Jian-Kang Zhu. "RNA-directed DNA methylation in plants." RNA Biology 10, no. 10 (October 2013): 1593–96. http://dx.doi.org/10.4161/rna.26312.

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38

Szymanski, Michal R., Maria J. Jezewska, Paul J. Bujalowski, Cecile Bussetta, Mengyi Ye, Kyung H. Choi, and Wlodzimierz Bujalowski. "Full-length Dengue Virus RNA-dependent RNA Polymerase-RNA/DNA Complexes." Journal of Biological Chemistry 286, no. 38 (July 2, 2011): 33095–108. http://dx.doi.org/10.1074/jbc.m111.255034.

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39

Nafisi, Shohreh, Zahra Mokhtari Malekabady, and Mohammad Ali Khalilzadeh. "Interaction of β-Carboline Alkaloids with RNA." DNA and Cell Biology 29, no. 12 (December 2010): 753–61. http://dx.doi.org/10.1089/dna.2010.1087.

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40

Goldberg, Lior, Mor Abutbul-Amitai, Gideon Paret, and Yael Nevo-Caspi. "Alternative Splicing ofSTAT3Is Affected by RNA Editing." DNA and Cell Biology 36, no. 5 (May 2017): 367–76. http://dx.doi.org/10.1089/dna.2016.3575.

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41

KÖHRER, KARL, TONI M. KUTCHAN, and HORST DOMDEY. "Specific Oligodeoxynucleotide Probes Obtained through RNA Sequencing." DNA 8, no. 2 (March 1989): 143–47. http://dx.doi.org/10.1089/dna.1.1989.8.143.

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42

LOGAN, KELLEY, JIMIN ZHANG, ELIZABETH A. DAVIS, and STEVEN ACKERMAN. "Drug Inhibitors of RNA Polymerase II Transcription." DNA 8, no. 8 (October 1989): 595–604. http://dx.doi.org/10.1089/dna.1989.8.595.

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43

Ren, Huiwen, and Qiuyue Wang. "Non-Coding RNA and Diabetic Kidney Disease." DNA and Cell Biology 40, no. 4 (April 1, 2021): 553–67. http://dx.doi.org/10.1089/dna.2020.5973.

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44

Zhou, Yu-Jie, Gui-Qi Zhu, Qing-Wei Zhang, Kenneth I. Zheng, Jin-Nan Chen, Xin-Tian Zhang, Qi-Wen Wang, and Xiao-Bo Li. "Survival-Associated Alternative Messenger RNA Splicing Signatures in Pancreatic Ductal Adenocarcinoma: A Study Based on RNA-Sequencing Data." DNA and Cell Biology 38, no. 11 (November 1, 2019): 1207–22. http://dx.doi.org/10.1089/dna.2019.4862.

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45

Zheng, Qiuxian, Junjun Jia, Ziyuan Zhou, Qingfei Chu, Wenwen Lian, and Zhi Chen. "The Emerging Role of Thymopoietin-Antisense RNA 1 as Long Noncoding RNA in the Pathogenesis of Human Cancers." DNA and Cell Biology 40, no. 7 (July 1, 2021): 848–57. http://dx.doi.org/10.1089/dna.2021.0024.

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46

Nafisi, Shohreh, Amir Sobhanmanesh, Kamran Alimoghaddam, Ardeshir Ghavamzadeh, and Heidar-Ali Tajmir- Riahi. "Interaction of Arsenic Trioxide As2O3with DNA and RNA." DNA and Cell Biology 24, no. 10 (October 2005): 634–40. http://dx.doi.org/10.1089/dna.2005.24.634.

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47

Parenrengi, Andi, Syarifuddin Tonnek, and Andi Tenriulo. "ANALISIS RASIO RNA/DNA UDANG WINDU Penaeus monodon HASIL SELEKSI TUMBUH CEPAT Andi." Jurnal Riset Akuakultur 8, no. 1 (February 26, 2016): 1. http://dx.doi.org/10.15578/jra.8.1.2013.1-12.

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<p>Seleksi udang windu Penaeus monodon tumbuh cepat menggunakan marker DNA telah berhasil dilakukan dalam upaya perakitan strain unggul udang windu. Udang windu hasil seleksi menunjukkan adanya peningkatan pertumbuhan dibandingkan dengan tanpa seleksi (kontrol). Rasio RNA/DNA merupakan salah satu parameter yang telah banyak digunakan dalam menentukan kualitas ikan/udang di antaranya adalah pertumbuhan. Penelitian ini bertujuan untuk mengetahui rasio RNA/DNA pada udang windu hasil seleksi tumbuh cepat dan kontrol (tanpa seleksi). Sampel udang windu tumbuh cepat yang digunakan berukuran bobot 50,66±16,51 g dan panjang 17,55±1,93 cm; sedangkan udang kontrol berukuran bobot 29,64±11,93 g dan panjang 14,78±2,53 cm. Metode isolasi total RNA dilakukan dengan menggunakan kit isogen, sedangkan genom DNA menggunakan metode konvensional fenol kloroform. Konsentrasi RNA dan DNA hasil isolasi diukur menggunakan GeneQuant. T-test dari Statistix Versi 3,0 digunakan untuk membedakan rasio RNA/DNA antara kedua perlakuan yang dianalisis. Hasil penelitian menunjukkan bahwa genom DNA dan total RNA mempunyai tingkat kemurnian yang tinggi. Hasil analisis t-test menunjukkan<br />bahwa rasio RNA/DNA udang windu tumbuh cepat (4,51) berbeda secara nyata (P<0,05) dengan udang windu kontrol (3,19). Kecenderungan rasio RNA/DNA semakin tinggi dengan semakin beratnya bobot badan, di mana rasio RNA/DNA udang betina (4,96) lebih tinggi (P<0,05) dari udang jantan (2,93). Analisis regresi menunjukkan bahwa rasio RNA/DNA udang windu memiliki hubungan erat dengan panjang (R=0,5628) dan bobot (R=0,6539). Hasil penelitian ini berimplikasi bahwa parameter rasio RNA/DNA dapat dijadikan sebagai indikator pertumbuhan udang windu.</p>

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48

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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49

Chen, Ji-Ren, Xingyao Xiong, Tian-Xiang Wang, Jing-Jing Lü, Shou-Yi Chen, and Hua-Fang Wang. "Rapid Construction of a Plant RNA Interference Expression Vector for Hairpin RNA–Mediated Targeting Using a PCR-Based Method." DNA and Cell Biology 28, no. 12 (December 2009): 605–13. http://dx.doi.org/10.1089/dna.2009.0897.

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50

O’Donoghue and Heinemann. "Synthetic DNA and RNA Programming." Genes 10, no. 7 (July 11, 2019): 523. http://dx.doi.org/10.3390/genes10070523.

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Synthetic biology is a broad and emerging discipline that capitalizes on recent advances in molecular biology, genetics, protein and RNA engineering as well as omics technologies. Together these technologies have transformed our ability to reveal the biology of the cell and the molecular basis of disease. This Special Issue on “Synthetic RNA and DNA Programming” features original research articles and reviews, highlighting novel aspects of basic molecular biology and the molecular mechanisms of disease that were uncovered by the application and development of novel synthetic biology-driven approaches.

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