ICCAS OpenIR
Modulating Molecular Level Space Proximity: A Simple and Efficient Strategy to Design Structured DNA Probes
Zheng, Jing1; Li, Jishan1; Gao, Xiaoxia1; Jin, Jianyu1,2; Wang, Kemin1; Tan, Weihong1; Yang, Ronghua1
2010-05-01
Source PublicationANALYTICAL CHEMISTRY
ISSN0003-2700
Volume82Issue:9Pages:3914-3921
AbstractTo construct efficient oligonucleotide probes, specific nucleic acid is designed as a conformationally constrained form based on the formation of a Watson-Crick-based duplex. However, instability of Watson-Crick hydrogen bonds in a complex biological environment usually leads to high background signal from the probe itself and false positive signal caused by nonspecific binding. To solve this problem, we propose a way to restrict the labeled-dyes in a hydrophobic cavity of cyclodextrin. This bounding, which acts like extra base pairs to form the Watson-Crick duplex, achieves variation of level of space proximity of the two labels and thus the degree of conformational constraint. To demonstrate the feasibility of the design, a stem-containing oligonucleotide probe (P1) for DNA hybridization assay and a stemless one (P2) for protein detection were examined as models. Both oligonucleotides were doubly labeled with pyrene at the 5'- and 3'-ends, respectively. It is the cyclodextrin/pyrene inclusion interaction that allows modulating the degree of conformational constraints of P1 and P2 and thus their background signals and selectivity. Under the optimal conditions, the ratio of signal-to-background of P1/gamma-CD induced by 1.0 equiv target DNA is near 174, which is 4-fold higher than that in the absence of gamma-CD. In addition, the usage of gamma-CD shifts the melting temperature of P1 from 57 to 68 degrees C, which is reasonable for improving target-binding selectivity. This approach is simple in design, avoiding any variation of the stem's length and sequences. Furthermore, the strategy is generalizable which is suited for not only the stem-containing probe but also the linear probe with comparable sensitivity and selectivity to conventional structured DNA probes.
DOI10.1021/ac1004713
Indexed BySCI
Language英语
WOS IDWOS:000277213400075
PublisherAMER CHEMICAL SOC
Citation statistics
Cited Times:24[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.iccas.ac.cn/handle/121111/70950
Collection中国科学院化学研究所
Corresponding AuthorYang, Ronghua
Affiliation1.Hunan Univ, State Key Lab Chemo Biosensing & Chemometr, Coll Chem & Chem Engn, Changsha 410082, Hunan, Peoples R China
2.Peking Univ, Coll Chem & Mol Engn, Beijing Natl Lab Mol Sci, Beijing 100871, Peoples R China
Recommended Citation
GB/T 7714
Zheng, Jing,Li, Jishan,Gao, Xiaoxia,et al. Modulating Molecular Level Space Proximity: A Simple and Efficient Strategy to Design Structured DNA Probes[J]. ANALYTICAL CHEMISTRY,2010,82(9):3914-3921.
APA Zheng, Jing.,Li, Jishan.,Gao, Xiaoxia.,Jin, Jianyu.,Wang, Kemin.,...&Yang, Ronghua.(2010).Modulating Molecular Level Space Proximity: A Simple and Efficient Strategy to Design Structured DNA Probes.ANALYTICAL CHEMISTRY,82(9),3914-3921.
MLA Zheng, Jing,et al."Modulating Molecular Level Space Proximity: A Simple and Efficient Strategy to Design Structured DNA Probes".ANALYTICAL CHEMISTRY 82.9(2010):3914-3921.
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