RNA-Cleaving Deoxyribozyme Sensor for Nucleic Acid Analysis: The Limit of Detection

    Authors

    Y. V. Gerasimova; E. Cornett;D. M. Kolpashchikov

    Comments

    Authors: contact us about adding a copy of your work at STARS@ucf.edu

    Abbreviated Journal Title

    ChemBioChem

    Keywords

    deoxyribozyme sensor; DNA enzyme; DNA; fluorescence; limit of detection; CATALYTIC MOLECULAR BEACONS; DNA ENZYME; LOGIC GATES; IN-VITRO; DNAZYME; HYBRIDIZATION; PROBES; SELECTIVITY; RIBOZYMES; IONS; Biochemistry & Molecular Biology; Chemistry, Medicinal

    Abstract

    Along with biocompatibility, chemical stability, and simplicity of structural prediction and modification, deoxyribozyme, based molecular sensors have the potential of an improved detection limit due to their ability to catalytically amplify signal. This study contributes to the understanding of the factors responsible for the limit of detection (LOD) of RNA-cleaving deoxyribozyme sensors. A new sensor that detects specific DNA/RNA sequences was designed from deoxyribozyme OA-II [Chiuman, W.; Li, Y. (2006) J. Mol. Biol. 357,748-754]. The sensor architecture allows for a unique combination of high selectivity, low LOD and the convenience of fluorescent signal monitoring, in homogeneous solution. The LOD of the sensor was found to. be similar to 1.6 x 10(-10) M after 3 h of incubation. An equation that allows estimation of the lowest theoretical LOD using characteristics of parent deoxyribozymes and their fluorogenic substrates was derived and experimentally verified. According to the equation, "catalytically perfect" enzymes can serve as scaffolds for the design of sensors with the LOD not lower than similar to 2 x 10(-15) M after 3 h of incubation. A new value termed the; detection efficiency (DE) is suggested as a time-independent characteristic of a sensor's sensitivity. The expressions for the. theoretical LOD and DE can be used to evaluate nucleic acid and protein enzymes for their application as biosensing platforms.

    Journal Title

    Chembiochem

    Volume

    11

    Issue/Number

    6

    Publication Date

    1-1-2010

    Document Type

    Article

    Language

    English

    First Page

    811

    Last Page

    817

    WOS Identifier

    WOS:000277299800014

    ISSN

    1439-4227

    Share

    COinS