Abstract
In vitro transcription of double-stranded DNA (dsDNA) induces a formation of two types of G-quadruplexes, intramolecular DNA G-quadruplexes or DNA:RNA hybrid G-quadruplexes, in clusters of guanine tracts. The formation of G-quadruplexes can be characterized by native PEG polyacrylamide gel electrophoresis, DMS footprinting, and ligand-induced photocleavage footprinting. The type of G-quadruplexes can be distinguished by transcription with 7-deaza-GTP (dzGTP) or 4-thio-uridine-5′-triphosphate (4SU) to detect the participation of RNA transcript.
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References
Parkinson GN, Lee MP, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417(6891):876–880. https://doi.org/10.1038/nature755
Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006) Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 34(19):5402–5415. https://doi.org/10.1093/nar/gkl655
Phillips K, Dauter Z, Murchie AI, Lilley DM, Luisi B (1997) The crystal structure of a parallel-stranded guanine tetraplex at 0.95 a resolution. J Mol Biol 273(1):171–182. https://doi.org/10.1006/jmbi.1997.1292
Schaffitzel C, Berger I, Postberg J, Hanes J, Lipps HJ, Pluckthun A (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc Natl Acad Sci U S A 98(15):8572–8577. https://doi.org/10.1073/pnas.141229498
Biffi G, Tannahill D, McCafferty J, Balasubramanian S (2013) Quantitative visualization of DNA G-quadruplex structures in human cells. Nat Chem 5(3):182–186. https://doi.org/10.1038/nchem.1548
Wu RY, Zheng KW, Zhang JY, Hao YH, Tan Z (2015) Formation of DNA:RNA hybrid G-quadruplex in bacterial cells and its dominance over the intramolecular DNA G-quadruplex in mediating transcription termination. Angew Chem Int Ed Engl 54(8):2447–2451. https://doi.org/10.1002/anie.201408719
Zhang C, Liu HH, Zheng KW, Hao YH, Tan Z (2013) DNA G-quadruplex formation in response to remote downstream transcription activity: long-range sensing and signal transducing in DNA double helix. Nucleic Acids Res 41(14):7144–7152. https://doi.org/10.1093/nar/gkt443
Zheng KW, Chen Z, Hao YH, Tan Z (2010) Molecular crowding creates an essential environment for the formation of stable G-quadruplexes in long double-stranded DNA. Nucleic Acids Res 38(1):327–338. https://doi.org/10.1093/nar/gkp898
Zheng KW, He YD, Liu HH, Li XM, Hao YH, Tan Z (2017) Superhelicity constrains a localized and R-loop-dependent formation of G-quadruplexes at the upstream region of transcription. ACS Chem Biol 12(10):2609–2618. https://doi.org/10.1021/acschembio.7b00435
Zheng KW, Wu RY, He YD, Xiao S, Zhang JY, Liu JQ, Hao YH, Tan Z (2014) A competitive formation of DNA:RNA hybrid G-quadruplex is responsible to the mitochondrial transcription termination at the DNA replication priming site. Nucleic Acids Res 42(16):10832–10844. https://doi.org/10.1093/nar/gku764
Zheng KW, Xiao S, Liu JQ, Zhang JY, Hao YH, Tan Z (2013) Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control. Nucleic Acids Res 41(10):5533–5541. https://doi.org/10.1093/nar/gkt264
Zhang JY, Zheng KW, Xiao S, Hao YH, Tan Z (2014) Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA. J Am Chem Soc 136(4):1381–1390. https://doi.org/10.1021/ja4085572
Sun D, Hurley LH (2010) Biochemical techniques for the characterization of G-quadruplex structures: EMSA, DMS footprinting, and DNA polymerase stop assay. Methods Mol Biol 608:65–79. https://doi.org/10.1007/978-1-59745-363-9_5
Green MR (2012) Isolation of high-molecular-weight DNA from mammalian cells using proteinase K and phenol. In: Molecular cloning: a laboratory manual (Fourth Edition), vol 1. Cold Spring Harbor Laboratory, Cold Spring Harbor, pp 47–53
Zhang AM, Huang J, Weng XC, Li JX, Ren LG, Song ZB, Xiong XQ, Zhou X, Cao XP, Zhou Y (2007) A water-soluble, octacationic zinc phthalocyanine as molecular probe for nucleic acid secondary structure. Chem Biodivers 4(2):215–223. https://doi.org/10.1002/cbdv.200790026
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Zheng, Kw., Zhang, Jy., Tan, Z. (2019). Characterization of Co-transcriptional Formation of G-Quadruplexes in Double-Stranded DNA. In: Yang, D., Lin, C. (eds) G-Quadruplex Nucleic Acids. Methods in Molecular Biology, vol 2035. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9666-7_14
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DOI: https://doi.org/10.1007/978-1-4939-9666-7_14
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