寡核苷酸探针中荧光共振能量转移和接触介导猝灭的效率
Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes.
作者信息
Marras Salvatore A E, Kramer Fred Russell, Tyagi Sanjay
机构信息
Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA.
出版信息
Nucleic Acids Res. 2002 Nov 1;30(21):e122. doi: 10.1093/nar/gnf121.
Abstract
An important consideration in the design of oligonucleotide probes for homogeneous hybridization assays is the efficiency of energy transfer between the fluorophore and quencher used to label the probes. We have determined the efficiency of energy transfer for a large number of combinations of commonly used fluorophores and quenchers. We have also measured the quenching effect of nucleotides on the fluorescence of each fluorophore. Quenching efficiencies were measured for both the resonance energy transfer and the static modes of quenching. We found that, in addition to their photochemical characteristics, the tendency of the fluorophore and the quencher to bind to each other has a strong influence on quenching efficiency. The availability of these measurements should facilitate the design of oligonucleotide probes that contain interactive fluorophores and quenchers, including competitive hybridization probes, adjacent probes, TaqMan probes and molecular beacons.
摘要
在设计用于均相杂交分析的寡核苷酸探针时，一个重要的考虑因素是用于标记探针的荧光团与猝灭剂之间的能量转移效率。我们已经确定了大量常用荧光团和猝灭剂组合的能量转移效率。我们还测量了核苷酸对每种荧光团荧光的猝灭作用。测量了共振能量转移和静态猝灭模式的猝灭效率。我们发现，除了它们的光化学特性外，荧光团与猝灭剂相互结合的倾向对猝灭效率有很大影响。这些测量结果的可用性应有助于设计包含相互作用荧光团和猝灭剂的寡核苷酸探针，包括竞争性杂交探针、相邻探针、TaqMan探针和分子信标。
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2
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3
A new class of homogeneous nucleic acid probes based on specific displacement hybridization.一类基于特异性置换杂交的新型均相核酸探针。
Nucleic Acids Res. 2002 Jan 15;30(2):E5. doi: 10.1093/nar/30.2.e5.
4
Aptamer beacons for the direct detection of proteins.用于直接检测蛋白质的适配体信标。
Anal Biochem. 2001 Jul 15;294(2):126-31. doi: 10.1006/abio.2001.5169.
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