Loop permutation affects the topology and stability of G-quadruplexes

doi:10.1093/nar/gky757

	Loop permutation affects the topology and stability of G-quadruplexes
	Cheng, Mingpan 2,3; Cheng, Yu 2,3; Hao, Jingya 2,3; Jia, Guoqing 2; Zhou, Jun 4; Mergny, Jean-Louis 1,4,5; Li, Can 2
刊名	NUCLEIC ACIDS RESEARCH
	2018-10-12
卷号	46 期号:18 页码:9264-9275
ISSN号	0305-1048
DOI	10.1093/nar/gky757
通讯作者	Mergny, Jean-Louis(jean-louis.mergny@inserm.fr) ; Li, Can(canli@dicp.ac.cn)
英文摘要	G-quadruplexes are unusual DNA and RNA secondary structures ubiquitous in a variety of organisms including vertebrates, plants, viruses and bacteria. The folding topology and stability of intramolecular G-quadruplexes are determined to a large extent by their loops. Loop permutation is defined as swapping two or three of these regions so that intramolecular G-quadruplexes only differ in the sequential order of their loops. Over the past two decades, both length and base composition of loops have been studied extensively, but a systematic study on the effect of loop permutation has been missing. In the present work, 99 sequences from 21 groups with different loop permutations were tested. To our surprise, both conformation and thermal stability are greatly dependent on loop permutation. Loop permutation actually matters as much as loop length and base composition on G-quadruplex folding, with effects on T-m as high as 17 degrees C. Sequences containing a longer central loop have a high propensity to adopt a stable non-parallel topology. Conversely, sequences containing a short central loop tend to form a parallel topology of lower stability. In addition, over half of interrogated sequences were found in the genomes of diverse organisms, implicating their potential regulatory roles in the genome or as therapeutic targets. This study illustrates the structural roles of loops in G-quadruplex folding and should help to establish rules to predict the folding pattern and stability of G-quadruplexes.
资助项目	National Natural Science Foundation of China[21227801] ; National Natural Science Foundation of China[21503229] ; Natural Science Foundation of Liaoning Province[2015020700] ; Fundamental Research Funds for the Central Universities[020514380144] ; SYM-BIT Project, European Regional Development Fund[CZ.02.1.01/0.0/0.0/15 003/0000477] ; Recruitment Program for Foreign Experts (1000plan) of China[WQ20163200397] ; Nanjing University[020514912216]
WOS关键词	TELOMERIC G-QUADRUPLEX ; DNA G-QUADRUPLEX ; SINGLE-BASE LOOPS ; K+ SOLUTION ; ANTI-HIV ; SEQUENCE ; LENGTH ; PROMOTER ; INSTABILITY ; INSIGHTS
WOS研究方向	Biochemistry & Molecular Biology
语种	英语
出版者	OXFORD UNIV PRESS
WOS记录号	WOS:000450953200008
资助机构	National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Liaoning Province ; Natural Science Foundation of Liaoning Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; SYM-BIT Project, European Regional Development Fund ; SYM-BIT Project, European Regional Development Fund ; Recruitment Program for Foreign Experts (1000plan) of China ; Recruitment Program for Foreign Experts (1000plan) of China ; Nanjing University ; Nanjing University ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Liaoning Province ; Natural Science Foundation of Liaoning Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; SYM-BIT Project, European Regional Development Fund ; SYM-BIT Project, European Regional Development Fund ; Recruitment Program for Foreign Experts (1000plan) of China ; Recruitment Program for Foreign Experts (1000plan) of China ; Nanjing University ; Nanjing University ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Liaoning Province ; Natural Science Foundation of Liaoning Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; SYM-BIT Project, European Regional Development Fund ; SYM-BIT Project, European Regional Development Fund ; Recruitment Program for Foreign Experts (1000plan) of China ; Recruitment Program for Foreign Experts (1000plan) of China ; Nanjing University ; Nanjing University ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Natural Science Foundation of Liaoning Province ; Natural Science Foundation of Liaoning Province ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; SYM-BIT Project, European Regional Development Fund ; SYM-BIT Project, European Regional Development Fund ; Recruitment Program for Foreign Experts (1000plan) of China ; Recruitment Program for Foreign Experts (1000plan) of China ; Nanjing University ; Nanjing University
内容类型	期刊论文
源URL	[http://cas-ir.dicp.ac.cn/handle/321008/166594]
专题	大连化学物理研究所_中国科学院大连化学物理研究所
通讯作者	Mergny, Jean-Louis; Li, Can
作者单位	1.Univ Bordeaux, CNRS, INSERM, ARNA Lab,IECB,U1212,UMR5320, F-33607 Pessac, France 2.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Catalysis, Dalian 116023, Peoples R China 3.Univ Chinese Acad Sci, 19A Yuquan Rd, Beijing 100049, Peoples R China 4.Nanjing Univ, Sch Chem & Chem Engn, State Key Lab Analyt Chem Life Sci, Nanjing 210023, Jiangsu, Peoples R China 5.CAS, Vvi, Inst Biophys, Kralovopolska 135, Brno 61265, Czech Republic
推荐引用方式 GB/T 7714	Cheng, Mingpan,Cheng, Yu,Hao, Jingya,et al. Loop permutation affects the topology and stability of G-quadruplexes[J]. NUCLEIC ACIDS RESEARCH,2018,46(18):9264-9275.
APA	Cheng, Mingpan.,Cheng, Yu.,Hao, Jingya.,Jia, Guoqing.,Zhou, Jun.,...&Li, Can.(2018).Loop permutation affects the topology and stability of G-quadruplexes.NUCLEIC ACIDS RESEARCH,46(18),9264-9275.
MLA	Cheng, Mingpan,et al."Loop permutation affects the topology and stability of G-quadruplexes".NUCLEIC ACIDS RESEARCH 46.18(2018):9264-9275.