G-四聯體：修订间差异

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2015年6月19日 (五) 00:11的版本

G-四聯體（英語：G-quadruplex、G-tetrads或G₄-DNA）是一種由富含鳥嘌呤的核酸序列所構成的四股型態。含有經由Hoogsteen（英语：Hoogsteen base pair）氫鍵維持穩定，並由鳥嘌呤以正方形方式排列而成的結構。在方形中央有一個單價陽離子（通常是鉀）^[1]。這種結構可見於DNA、RNA、LNA（鎖核酸）與PNA（肽核酸）；根據形成四聯體的各股的方向，可能有分子內（英语：intramolecular）（intramolecular）、雙分子（bimolecular）或四分子（tetramolecular）等不同類型^[2]。

在四聯體的結構中，我們可以根據四股的方向，將結構分為平行和反平行（英语：Antiparallel (biochemistry)）。

Structure of a G-quadruplex. Left: a G-tetrad. Right: an intramolecular G-quadruplex

3D Structure of the intramolecular human telomeric G-quadruplex in potassium solution (PDB ID 2HY9). The backbone is represented by a tube. The center of this structure contains three layers of G-tetrads. The hydrogen bonds in these layers are represented by blue dashed lines.

註釋

^ Campbell, Nancy H.; Neidle, Stephen. Chapter 4. G-Quadruplexes and Metal Ions. Astrid Sigel, Helmut Sigel and Roland K. O. Sigel (编). Interplay between Metal Ions and Nucleic Acids. Metal Ions in Life Sciences 10. Springer. 2012: 119–1134. doi:10.1007/978-94-007-2172-2_4.
^ Bochman, Matthew L.; Paeschke, Katrin; Zakian, Virginia A. DNA secondary structures: stability and function of G-quadruplex structures. Nature Reviews Genetics 13. Nature Publishing Group. 2012: 770–780. doi:10.1038/nrg3296.

參考文獻

Jiangtao Ren, Jiahai Wang* , Lei Han, Erkang Wang*, Jin Wang*. Kinetically grafting G-qaudruplex onto DNA nanostructure as structure and function encoding via DNA machine. Chem. Commun. 2011, 47: 10563–10565.
Johnson JE, Smith JS, Kozak ML, Johnson FB. In vivo veritas: using yeast to probe the biological functions of G-quadruplexes. Biochimie. 2008, 90 (8): 1250–1263. PMC 2585026 . PMID 18331848. doi:10.1016/j.biochi.2008.02.013.
Huppert JL and Balasubramanian S. Prevalence of quadruplexes in the human genome. NAR. 2005, 33 (9): 2908–2916. PMC 1140081 . PMID 15914667. doi:10.1093/nar/gki609.
Todd AK, Johnston M, Neidle S. Highly prevalent putative quadruplex sequence motifs in human DNA. NAR. 2005, 33 (9): 2901–2907. PMC 1140077 . PMID 15914666. doi:10.1093/nar/gki553.
Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S. Quadruplex DNA: sequence, topology and structure. NAR. 2006, 34 (19): 5402–5415. PMC 1636468 . PMID 17012276. doi:10.1093/nar/gkl655.
Siddiqui-Jain A, Grand CL, Bearss DJ, Hurley LH. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. PNAS. 2002, 99 (18): 11593–8. PMC 129314 . PMID 12195017. doi:10.1073/pnas.182256799.
Rawal P, Kummarasetti VB, Ravindran J, Kumar N, Halder K, Sharma R, Mukerji M, Das SK, Chowdhury S. Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation. Genome Res. 2006, 16 (5): 644–55. PMC 1457047 . PMID 16651665. doi:10.1101/gr.4508806.
Xu Hou, Wei Guo, Fan Xia, Fu-Qiang Nie, Hua Dong, Ye Tian, Liping Wen, Lin Wang, Liuxuan Cao, Yang Yang, Jianming Xue, Yanlin Song, Yugang Wang, Dongsheng Liu, and Lei Jiang. A biomimetic potassium responsive nanochannel: G-quadruplex DNA conformational switching in a synthetic nanopore. J. Am. Chem. Soc. 2009, 131 (22): 7800–7805. PMID 19435350. doi:10.1021/ja901574c.
Neidle & Balasubramanian (编). Quadruplex Nucleic Acids. 2006. ISBN 0-85404-374-8.

外部連結

Nanopore and Aptamer Biosensor group{NAB group}

四聯體網站

COST MP0802 Quadruplex Network – the European network of G-quadruplex community: From first principles to applications
Quadruplex.org – a website to serve the quadruplex community
G-Quadruplex World – a website to discuss publications and other information of interest to those working in the field of G-quadruplexes
Quadbase – downloadable data on predicted G-quadruplexes
Greglist – a database listing potential G-quadruplex regulated genes
Database on Quadruplex information: QuadBase from IGIB
GRSDB- a database of G-quadruplexes near RNA processing sites.
GRS_UTRdb- a database of G-quadruplexes in the UTRs.
G-quadruplex Resource Site
non-B Motif Search Tool at non-B DB- a web server to predict G-quadruplex forming motifs and other non-B DNA forming motifs from users' DNA sequences.

預測G-四聯體的工具

[1] Campbell, Nancy H.; Neidle, Stephen. Chapter 4. G-Quadruplexes and Metal Ions. Astrid Sigel, Helmut Sigel and Roland K. O. Sigel (编). Interplay between Metal Ions and Nucleic Acids. Metal Ions in Life Sciences 10. Springer. 2012: 119–1134. doi:10.1007/978-94-007-2172-2_4.

[2] Bochman, Matthew L.; Paeschke, Katrin; Zakian, Virginia A. DNA secondary structures: stability and function of G-quadruplex structures. Nature Reviews Genetics 13. Nature Publishing Group. 2012: 770–780. doi:10.1038/nrg3296.

[1]

[2]

@@ 第1行： / 第1行： @@
-'''G-四聯體'''（英語：'''G-quadruplex'''、'''G-tetrads'''或'''G<sub>4</sub>-DNA'''）是一種由富含[[鳥嘌呤]]的核酸序列所構成的四股型態。含有經由[[Hoogsteen base pair|Hoogsteen]][[氫鍵]]維持穩定，並由鳥嘌呤以正方形方式排列而成的結構。在方形中央有一個[[單價]][[陽離子]]（通常是[[鉀]]）。這種結構可見於[[DNA]]、[[RNA]]、[[鎖核酸|LNA]]（鎖核酸）與[[PNA]]（肽核酸）；根據形成四聯體的各股的方向，可能有[[分子內]]（intramolecular）、[[雙分子]]（bimolecular）或[[四分子]]（tetramolecular）等不同類型。
+'''G-四聯體'''（英語：'''G-quadruplex'''、'''G-tetrads'''或'''G<sub>4</sub>-DNA'''）是一種由富含[[鳥嘌呤]]的核酸序列所構成的四股型態。含有經由{{le|Hoogsteen base pair|Hoogsteen base pair|Hoogsteen}}[[氫鍵]]維持穩定，並由鳥嘌呤以正方形方式排列而成的結構。在方形中央有一個[[單價]][[陽離子]]（通常是[[鉀]]）<ref>{{cite book
+|last1=Campbell
+|first1=Nancy H.
+|last2=Neidle
+|first2=Stephen
+|editor=Astrid Sigel, Helmut Sigel and Roland K. O. Sigel
+|title=Interplay between Metal Ions and Nucleic Acids
+|series=Metal Ions in Life Sciences
+|volume=10
+|year=2012
+|publisher=Springer
+|doi=10.1007/978-94-007-2172-2_4
+|pages=119–1134
+|chapter=Chapter 4. G-Quadruplexes and Metal Ions
+}}</ref>。這種結構可見於[[DNA]]、[[RNA]]、[[鎖核酸|LNA]]（鎖核酸）與[[PNA]]（肽核酸）；根據形成四聯體的各股的方向，可能有{{le|分子內|intramolecular}}（intramolecular）、{{le|雙分子|bimolecular}}（bimolecular）或{{le|四分子|tetramolecular}}（tetramolecular）等不同類型<ref>{{cite book
+|last1=Bochman
+|first1=Matthew L.
+|last2=Paeschke
+|first2=Katrin
+|last3=Zakian
+|first3=Virginia A.
+|title=DNA secondary structures: stability and function of G-quadruplex structures
+|series=Nature Reviews Genetics
+|volume=13
+|year=2012
+|publisher=Nature Publishing Group
+|doi= 10.1038/nrg3296
+|pages=770–780
+}}</ref>。
+在四聯體的結構中，我們可以根據四股的方向，將結構分為{{le|平行 (幾何)|Parallel (geometry)|平行}}和{{le|反平行 (生化)|Antiparallel (biochemistry)|反平行}}。
-<!-- [[File:G-quadruplex.svg|thumb | 400px |Structure of a G-quadruplex. Left: a G-tetrad. Right: an intramolecular G-quadruplex]]
-[[File:Telomer-structure.gif|frame|3D Structure of the intramolecular human telomeric G-quadruplex in potassium solution (PDB ID 2HY9). The backbone is represented by a tube. The center of this structure contains three layers of G-tetrads. The hydrogen bonds in these layers are represented by blue dashed lines.]] -->
+[[File:G-quadruplex.svg|thumb | 400px |Structure of a G-quadruplex. Left: a G-tetrad. Right: an intramolecular G-quadruplex]]
-[[Category:核酸]]
+[[File:Telomer-structure.gif|frame|3D Structure of the intramolecular human telomeric G-quadruplex in potassium solution (PDB ID 2HY9). The backbone is represented by a tube. The center of this structure contains three layers of G-tetrads. The hydrogen bonds in these layers are represented by blue dashed lines.]]
+== 註釋 ==
+{{Reflist|30em}}
+== 參考文獻 ==
+* {{cite journal |title=Kinetically grafting G-qaudruplex onto DNA nanostructure as structure and function encoding via DNA machine |author=Jiangtao Ren, Jiahai Wang* , Lei Han, Erkang Wang*, Jin Wang* |journal=Chem. Commun |year=2011 |volume=47 |pages=10563–10565 |url=http://nanopore.weebly.com/publication-list.html}}
+* {{cite journal |title=In vivo veritas: using yeast to probe the biological functions of G-quadruplexes |author=Johnson JE, Smith JS, Kozak ML, Johnson FB |journal=Biochimie |year=2008 |volume=90 |issue=8 |pages=1250–1263 |url=http://linkinghub.elsevier.com/retrieve/pii/S0300-9084(08)00047-3 |doi=10.1016/j.biochi.2008.02.013 |pmid=18331848 |pmc=2585026}}
+* {{cite journal |title=Prevalence of quadruplexes in the human genome |author=Huppert JL and Balasubramanian S |journal=NAR |year=2005 |volume=33 |issue=9 |pages=2908–2916 |url=http://nar.oxfordjournals.org/cgi/content/abstract/33/9/2908 |pmid=15914667 |pmc=1140081 |doi=10.1093/nar/gki609 }}
+* {{cite journal |title=Highly prevalent putative quadruplex sequence motifs in human DNA |author=Todd AK, Johnston M, Neidle S |journal=NAR |year=2005 |volume=33 |issue=9 |pages=2901–2907 |url=http://nar.oxfordjournals.org/cgi/content/abstract/33/9/2901 |pmid=15914666 |pmc=1140077 |doi=10.1093/nar/gki553 }}
+* {{cite journal |title=Quadruplex DNA: sequence, topology and structure |author=Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S |journal=NAR |year=2006 |volume=34 |issue=19 |pages=5402–5415 |url=http://nar.oxfordjournals.org/cgi/content/abstract/34/19/5402 |pmid=17012276 |pmc=1636468 |doi=10.1093/nar/gkl655 }}
+* {{cite journal |title=Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription |author=Siddiqui-Jain A, Grand CL, Bearss DJ, Hurley LH |journal=PNAS |year=2002 |volume=99 |issue=18 |pages=11593–8 |url=http://www.pnas.org/cgi/content/abstract/99/18/11593 |pmid=12195017 |pmc=129314 |doi=10.1073/pnas.182256799 }}
+* {{cite journal |title=Genome-wide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation |author=Rawal P, Kummarasetti VB, Ravindran J, Kumar N, Halder K, Sharma R, Mukerji M, Das SK, Chowdhury S |journal=Genome Res. |year=2006 |volume=16 |issue=5 |pages=644–55 |url=http://www.genome.org/cgi/content/short/16/5/644 |pmid=16651665 |pmc=1457047 |doi=10.1101/gr.4508806 }}
+* {{cite journal |title=A biomimetic potassium responsive nanochannel: G-quadruplex DNA conformational switching in a synthetic nanopore |author=Xu Hou, Wei Guo, Fan Xia, Fu-Qiang Nie, Hua Dong, Ye Tian, Liping Wen, Lin Wang, Liuxuan Cao, Yang Yang, Jianming Xue, Yanlin Song, Yugang Wang, Dongsheng Liu, and Lei Jiang |journal=J. Am. Chem. Soc. |year=2009 |volume=131 |issue=22 |pages=7800–7805 |url=http://pubs.acs.org/doi/abs/10.1021/ja901574c |doi=10.1021/ja901574c |pmid=19435350}}
+* {{cite book |title=Quadruplex Nucleic Acids |editor=Neidle & Balasubramanian |year=2006 |url=http://chemistry.rsc.org/Publishing/Books/0854043748.asp |isbn=0-85404-374-8}}
+== 外部連結 ==
+* [http://nanopore.weebly.com/ Nanopore and Aptamer Biosensor group]{NAB group}
+=== 四聯體網站 ===
+* [http://www.g4net.org/ COST MP0802 Quadruplex Network] – the European network of G-quadruplex community: From first principles to applications
+* [http://www.quadruplex.org/ Quadruplex.org] – a website to serve the quadruplex community
+* [http://gquadruplex.wordpress.com/ G-Quadruplex World] – a website to discuss publications and other information of interest to those working in the field of G-quadruplexes
+* [http://www.quadruplex.org/?view=quadbase Quadbase] – downloadable data on predicted G-quadruplexes
+* [http://tubic.tju.edu.cn/greglist/ Greglist] – a database listing potential G-quadruplex regulated genes
+* [http://quadbase.igib.res.in: Database on Quadruplex information: QuadBase from IGIB]
+* [http://bioinformatics.ramapo.edu/GRSDB2/ GRSDB]- a database of G-quadruplexes near RNA processing sites.
+* [http://bioinformatics.ramapo.edu/GRS_UTRDB/ GRS_UTRdb]- a database of G-quadruplexes in the UTRs.
+* [http://bioinformatics.ramapo.edu/GQRS/ G-quadruplex Resource Site]
+* [http://nonb.abcc.ncifcrf.gov/apps/nBMST/default non-B Motif Search Tool at non-B DB]- a web server to predict G-quadruplex forming motifs and other non-B DNA forming motifs from users' DNA sequences.
+=== 預測G-四聯體的工具 ===
+* [http://www.quadruplex.org/?view=quadparser_web Quadparser: Downloadable program for finding putative quadruplex-forming sequences] from Balasubramanian's group.
+* [http://bioinformatics.ramapo.edu/QGRS/ QGRS Mapper: a web-based application for predicting G-quadruplexes in nucleotide sequences and NCBI genes] from Bagga's group.
+* [http://202.54.26.221/quadfinder/ Quadfinder: Tool for Prediction and Analysis of G Quadruplex Motifs in DNA/RNA Sequences from Maiti's group, IGIB, Delhi, India]
+[[Category:DNA]]