Colorimetric aptasensor based on truncated aptamer and trivalent

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Food Safety and Toxicology

Colorimetric aptasensor based on truncated aptamer and trivalent DNAzyme for Vibrio parahemolyticus determination Yuhan Sun, Nuo Duan, Pengfei Ma, Yao Liang, Xiaoyin Zhu, and Zhouping Wang J. Agric. Food Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jafc.8b06893 • Publication Date (Web): 05 Feb 2019 Downloaded from http://pubs.acs.org on February 6, 2019

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Journal of Agricultural and Food Chemistry

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Colorimetric aptasensor based on truncated aptamer and trivalent

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DNAzyme for Vibrio parahemolyticus determination

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Yuhan Suna,b, Nuo Duana,b, Pengfei Maa,b, Yao Lianga,b, Xiaoyin Zhua,b, Zhouping

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Wanga,b,c,d,e*

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a

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China

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b

School of Food Science and Technology, Jiangnan University, Wuxi 214122, China

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c

National Engineering Research Center of Seafood, School of Food Science and Technology,

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Dalian Polytechnic University, Dalian 116034, China

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d

International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China

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e

Collaborative Innovation Center of Food safety and Quality Control of Jiangsu Province,

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Jiangnan University, Wuxi 214122, China

State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122,

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*

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Zhouping Wang

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Tel. / Fax: +86 510 8532 6195 20

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E-mail address: [email protected]

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Postal address: Jiangnan University, No. 1800 Lihu Avenue, Wuxi, Jiangsu, 214122, P.R.C.

Corresponding author:

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ACS Paragon Plus Environment


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Abstract

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In this work, after optimizing the original aptamer sequence by truncation and site-directed

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mutagenesis, a simple and sensitive colorimetric aptasensor was established for detecting the

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widespread food-borne pathogen Vibrio parahemolyticus (V. parahemolyticus). The detection

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strategy was based on the competition for an V. parahemolyticus specific aptamer between its

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complementary DNA (cDNA) and V. parahemolyticus. The aptamer-conjugated magnetic

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nanoparticles (MNPs) were used as capture probes, and the G-quadruplex (G4) DNAzyme

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was employed as signal amplifying element. Under optimal conditions, a wide linear

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detection range (from 102 to 107 cfu/mL) was available, and the detection limit could be as

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low as 10 cfu/mL. This method was also used to detect V. parahemolyticus in contaminated

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salmon samples, and the results showed good consistency with those obtained from standard

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plate counting method. Therefore, this novel aptasensor could be a good candidate for

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sensitive and selective detection of V. parahemolyticus without complicated operations.

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Keywords: Vibrio parahemolyticus; Aptamer; Post-SELEX optimization; Magnetic

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nanoparticles; DNAzyme

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Introduction

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V. parahemolyticus is a Gram-negative, halophilic and mesophilic bacterium which

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naturally thrives in warm marine or estuarine environments, and has been isolated from the

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intestines and gills of freshwater farmed fish. It is a wildly concerned food-borne pathogen

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that could be acquired through consuming raw or undercooked aquatic products, especially

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shellfish.1-2 With global warming, rising ocean temperatures directly lead to the further

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proliferation and spread of Vibrio bacteria which are the source of acute gastroenteritis and

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primary septicemia, and V. parahemolyticus has become the main cause of food poisoning

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derived from seafood worldwide.3 Routine detection of V. parahemolyticus in food is

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typically conducted under a series of culture-based morphological and biochemical

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characterization methods which are time-consuming, making it difficult to satisfy the demand

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for rapid identification. Based on this situation, various detection methods have been reported,

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such as electrochemiluminescence (ECL) immunosensor,4 surface-enhanced Raman scattering

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(SERS) immunosensor,5 multiplex real-time PCR,6-7 and loop-mediated isothermal

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amplification (LAMP),8 etc. These strategies have attractive features such as fast detection

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and excellent sensitivity, however, they also have unsatisfactory shortcomings, including

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laborious sample pretreatment, expensive instruments and reagents, and the need for

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sufficient expertise. Therefore, it is necessary to establish rapid and simple methods for

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detecting V. parahemolyticus to control food safety and supervise entry-exit inspection and

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quarantine efficiently.

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Aptamers indicate functional single-stranded non-coding RNA, DNA, and their derivatives,

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which could specifically bind to targets with high affinity.9-10 They are obtained by the

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SELEX (Systematic Evolution of Ligands by Exponential Enrichment) method in vitro and

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could identify sundry target molecules by the formation of various secondary structures

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including stem, loop, hairpin, bulge, pseudoknot, and G-quadruplex.11-15 In comparison with

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traditional identification component antibodies, aptamers have such unique advantages as

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small size, excellent affinity and specificity, high stability, non-immunogenicity, and

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controllable modification.16-17 Because of these excellent biochemical features, in the past two

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decades, aptamer researches in the fields of biosensing,18-19 diagnostics and therapeutics,20-21

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and bioimaging22-23 have yielded extraordinary achievements.

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However, original aptamers obtained by SELEX, which contain 60–100 nucleotides, are

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not appropriate for directly applying to clinical or laboratory.24 They might contain some

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extra bases, which could self-stack to form steric hindrance and even hybridize to key

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functional bases of the aptamer, thereby reducing the binding affinity of the aptamer to the

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target.25-26 At the same time, considering the later applications of aptamers, it is undoubted

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that longer sequences lead to reduced synthesis yield and increased cost. Hence, in practical

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application, obtaining truncated aptamer sequences with better affinity characteristics than the

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original ones would be beneficial.25 Furthermore, PCR amplification bias and reduced library

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diversity due to experimental operation could also affect the binding properties of aptamers.

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Thus, apart from truncation, several other post-SELEX optimization methods have also been

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adopted, such as multivalent aptamers,27 chemical modification,28-29 and random or

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site-directed mutagenesis.30 The application of these post-SELEX optimization methods

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significantly improved the binding affinity of the aptamers, indicating that post-SELEX

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optimization could make up for the drawbacks of SELEX.

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Colorimetric aptasensors, especially those utilizing G-quadruplex DNAzymes with

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peroxidase activity as signal-amplifying elements, have been used for detecting various

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targets, due to its simplicity in design, robustness under different conditions, and economical

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efficiency.31-32 G-quadruplex DNAzyme is peroxidase-like complex formed by G-quadruplex

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DNA and hemin. The G4-DNA is similar to an apoenzyme to some extent, and hemin

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(Fe(III)-protoporphyrin IX) is the cofactor for catalyzing H2O2.33 Long G-rich DNA

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sequences could fold into multimeric G-quadruplex with multiple G-quadruplex units, and

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each G-quadruplex unit had the potential to form an active G-quadruplex DNAzyme, which

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was beneficial for amplifying signal in colorimetric assays.34 Trivalent DNAzymes stood out

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from a variety of multivalent DNAzymes and exhibited the optimal catalytic activity. Yang

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and coworkers33 attributed the optimal catalytic performance of the trivalent DNAzyme to its

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highest ΔTm value, which indicated that the trimeric CatG4: hemin complex possessed the

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most stable peroxidase-mimic structure for H2O2 catalysis.

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Herein, for the first time, a novel aptasensor which used optimized aptamer and multimeric

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DNAzyme for the colorimetric detection of V. parahemolyticus was constructed. The

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detection strategy was based on the competition for an V. parahemolyticus specific aptamer

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between its complementary DNA and V. parahemolyticus. The aptamer-conjugated MNPs

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were used as capture probes, and the G4 DNAzyme was employed as signal amplifying

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element. Thanks to the large surface-to-volume ratio of MNPs, considerable amount of

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aptamer could be conjugated to achieve high capture efficiency. And owing to the superb

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catalytic activity of G4 DNAzyme, high sensitivity could also be obtained. The experimental

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conditions were optimized, furthermore, the specificity and analytical performance of this

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scheme were also explored. The strategy presented high sensitivity, good selectivity, and the

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potential to be used for routine inspection.

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Materials and Methods

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Bacterial Strains and Reagents. Vibrio parahemolyticus ATCC 17802 was grown in

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alkaline peptone with 3% NaCl (w/v) and harvested during logarithmic growth phase. Other

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bacterial strains used in this study included the following: Escherichia coli (E. coli) ATCC

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25922, F's dysentery bacillus ATCC 12022, Staphylococcus aureus (S. aureus) ATCC 29213,

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Salmonella typhimurium (S. typhimurium) ATCC 10420, Listeria monocytogenes (L.

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monocytogenes) ATCC 19115, and Bacillus cereus (B. cereus) CICC 10041. They were all

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grown in Luria-Bertani medium and harvested during logarithmic growth phase. All bacteria

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were cultured under aerobic conditions at 37 °C with shaking at 150 rpm, respectively.

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All chemicals used to prepare the medium and buffers were purchased from Sinopharm

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Chemical Reagent Co. Ltd. (Shanghai, China). The formulations of the different buffers were

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as follows: 1×TE buffer (10 mM Tris-HCl and 1 mM EDTA, pH 7.4); 1×Binding buffer

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(1×BB, 50 mM Tris-HCl, 5 mM KCl, 100 mM NaCl, and 1 mM MgCl2, pH 7.4); 2×Binding

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and washing (B&W) buffer (10 mM Tris-HCl, 1 mM EDTA, and 2 M NaCl, pH 7.5);

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1×Phosphate-buffered saline (1×PBS, 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 2

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mM KH2PO4, pH 7.4). All solutions were prepared with ultra-pure water processed by a

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Millipore Direct-Q® 3 system (Merck Millipore, MA, USA).

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Magnetic beads modified with streptavidin were purchased from Invitrogen (Carlsbad, CA,

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USA). Dimethyl sulfoxide (DMSO) was obtained from Sinopharm Chemical Reagent Co. Ltd.

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(Shanghai, China). Hemin was purchased from Aladdin Industrial Corporation (Shanghai,

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China). 5 mM hemin stock solution was prepared in DMSO, stored in the dark at -20 °C and

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diluted to the required concentrations with PBS buffer. 3,3´-5,5´-Tetramethyl benzidine

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(TMB) solution was purchased from Sangon Biotech Co., Ltd. (Shanghai, China).

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The oligonucleotides were synthesized by Sangon Biotech Co., Ltd. (Shanghai, China), and

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purified using high-performance liquid chromatography. All oligonucleotides were dissolved

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in 1×Tris-EDTA (TE) buffer and stored at -20 °C.

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Identification of Specificity and Affinity by Flow Cytometer. Fluorescently labeled

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aptamer sequences were incubated with different bacteria (V. parahemolyticus, E. coli, F's

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dysentery bacillus, S. aureus, S. typhimurium, L. monocytogenes, and B. cereus) at 37 °C for

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45 min and were analyzed by BD FACSCalibur flow cytometer (BD Biosciences, San Jose,

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CA, USA). Gated fluorescence intensity above control group (cells without aptamers) was

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measured and recorded. Each aptamer sequence modified with FAM group at the 5´ end was

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heat-denatured, followed by the incubation with bacterial cells. Bacteria were washed with

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1×Binding buffer before and after incubation. To identify the binding affinity of the aptamers

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to the target V. parahemolyticus cells, binding assays were carried out using aptamer with

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increasing concentrations (from 25 to 200 nM) and a fixed concentration of cells (108 cfu/mL)

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for each assay. Saturation curves were plotted based on the obtained fluorescence

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measurement values, and the dissociation constant Kd was calculated by nonlinear regression

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analysis using GraphPad Prism 5.0 software. 7



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Colorimetric determination of V. parahemolyticus. The streptavidin-modified MNPs were

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resuspended in 2×B&W buffer to a final concentration of 5 mg/mL. An equal volume of the

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biotinylated aptamer was added to the MNPs suspension prior to incubating at 37 °C for 10

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min using gentle rotation. The MNPs were washed and magnetically collected twice with

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1×B&W buffer to remove excess aptamer from the system. The aptamer-functionalized

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MNPs were preserved at 4 °C in PBS buffer for future use.

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In each assay, a certain amount of aptamer-functionalized MNPs (0.1 mg) was washed and

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magnetically collected twice with 1×B&W buffer. Subsequently, ssDNA was heat-denatured

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at 95 °C and cooled to room temperature, followed by being added in the system. The mixture

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was incubated at 37 °C for 120 min to allow the cDNA part of ssDNA to hybridize

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completely with aptamer. Subsequently, the mixture was washed and magnetically collected

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twice with 1×B&W buffer. By taking these steps, the V. parahemolyticus aptasensor was

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prepared.

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The determination of V. parahemolyticus was carried out by adding different amounts of V.

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parahemolyticus cells to the system. In the presence of target, the V. parahemolyticus specific

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aptamer encountered and captured the target cells, which caused the change of aptamer's

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secondary structure. Thus, the ssDNA could not hybridize with the aptamer anymore. It

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detached from the MNPs and consequently entered the supernatant. Subsequently, the

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supernatant was collected magnetically.

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The supernatant was heated to 95 °C and slowly cooled to room temperature to ensure that

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the G4-DNA therein could fold into stable G4 structure. Then, 5 mM hemin stock solution of

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different volumes were added, and the mixture was kept at 25 °C for 1 h to construct 8


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DNAzyme. Later, TMB solution at a concentration of 80 μg/mL, which contained 0.01%

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H2O2 that could trigger the catalysis reaction, was added. The absorbance signal of the

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resulting products was recorded by a Microplate reader (BioTek Instruments, Tucson, AZ,

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USA).

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Determination of V. parahemolyticus in the salmon samples. Fresh salmon was used as

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realistic sample for the determination of V. parahemolyticus. 25 g aliquots of salmon sample

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were aseptically sampled and immersed in 225 mL saline solution, and gradient dilutions of V.

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parahemolyticus were added to the salmon samples, before the mixture was homogenized for

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2 min to prepare 1:10 homogeneous sample. All samples with different concentrations of V.

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parahemolyticus were simultaneously measured by the plate counting method and the

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developed method, and the results of both were compared.

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Results and Discussion

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Optimization of aptamer. It has been reported that the shorter the ssDNA, the stronger its

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tissue penetration ability, moreover, appropriate truncation of aptamers could remove

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additional bases that might hinder target binding.24,

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aptamer sequence A3P that we obtained through the whole-bacterium SELEX had 87 bases

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(Table S1) ,37 it might not be suitable for further food sample testing due to the relative high

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cost. Hence, it is necessary to optimize the original aptamer.

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The original V. parahemolyticus

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A1 (Fig. S1) was a sequence consisting of 40 bases obtained by removing the primers at

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both ends of the original aptamer A3P. Since its structure was still relatively complicated, A2

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(Fig. S1), which still had good affinity for the target, was obtained through removing some 9



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bases from both ends of A1. Observed that A2 had a one-base-mismatch stem, and base

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mismatch might affect the stability of the secondary structure of the aptamer sequence,

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resulting in a decrease in aptamer affinity, thus the base in stem structure of A2 was replaced,

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thereby making the stem of A2 completely base-paired, which yielded sequence A3 (Fig. S1).

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Just as expected, A3 had a slightly higher affinity for the target than A2 (Table S1).

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Subsequently, one base was removed simultaneously from the 5´ and 3´ ends of the A3

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sequence, generating the desirable sequence A4 (Fig. S1) which was 19 bases less than A1,

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and reducing the Kd value of the sequence to 28.65±3.05 nM (Table S1). Next, both ends of

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the A4 were simultaneously and successively truncated, and sequences A5 and A6 were

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obtained. However, the affinity of these two sequences was not ideal, and their Kd values

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increased by an order of magnitude (Table S1).

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The specificity of fluorescently labeled aptamer sequences against a variety of other

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bacteria, including E. coli, F's dysentery bacillus, S. aureus, S. typhimurium, L.

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monocytogenes, and B. cereus, were also verified. As shown in Fig. 1, A4, namely the

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shortest aptamer, which was got through truncation under the premise of maintaining

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sequence affinity, showed the highest percentage of gated fluorescence intensity among these

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aptamer sequences with 82.21%, and its specificity was generally great. At the same time, A1,

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A2 and A3 preferentially bound to V. parahemolyticus, compared with other types of bacteria,

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while A5 and A6 seemed to bind weakly to F's dysentery bacillus and S. aureus, and did not

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present obvious specificity towards V. parahemolyticus (The gated fluorescence intensity

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above control group was in excess of 20% for A5 incubated with F's dysentery bacillus and S.

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aureus, compared to 41.41% when incubated with V. parahemolyticus; And the gated 10


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fluorescence intensity percentage for A6 incubated with F's dysentery bacillus was 23.25%,

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compared to 37.43% that of A6 incubated with V. parahemolyticus). Considering that longer

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sequences possessed higher odds of forming various secondary structures, which would

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impair the target-binding conformational stability of the aptamer,25 A4 was chosen as the V.

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parahemolyticus binding aptamer in the following experiments.

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After the minimal required sequence for activity was successfully identified by truncation,

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the strategy of single-point mutation was introduced into A4 without changing its basic

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secondary structure. A series of oligonucleotide single-point mutants was obtained with

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mutation sites at the loop region of A4 (Table S1). Although an aptamer sequence with higher

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affinity was failed to get by mutation, the recognition site of A4 was successfully found. The

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binding assay results of A4-1~A4-9 revealed that the six-nucleotide loop sequence

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5´-9CAGTGA14-3´ was crucial for target recognition, when they were replaced with other

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oligonucleotides, the Kd value increased significantly. Moreover, as the remaining three bases

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of the loop were replaced, the affinity decreased but not completely lost. The results indicated

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that the remaining three bases might not directly participate in the recognition and binding of

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the target, but they played an important role in stabilizing the secondary structure of the

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aptamer. Using these results, the corresponding cDNA could be designed reasonably and

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efficiently to obtain a viable and sensitive aptasensor. The sequences used in aptasensor were

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listed in Table S2.

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The scheme of aptasensor for Vibrio parahemolyticus. Taking advantage of the high

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separation efficiency of MNPs, the high affinity and specificity of the optimized aptamer to

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the target, and the excellent catalytic activity of trivalent DNAzyme, an innovative 11



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colorimetric aptasensor for the detection of V. parahemolyticus was constructed. The

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procedure for detecting V. parahemolyticus was shown in Fig. 2. The aptasensor was made up

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of three parts: MNPs modified with streptavidin, biotinylated V. parahemolyticus aptamer,

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and a label-free ssDNA containing cDNA and trimeric CatG4 in its sequence. Aptamer was

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conjugated to MNPs facilely via the biotin-streptavidin interaction. Then the cDNA partly

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hybridized with aptamer, accordingly allowing ssDNA to be immobilized on the surface of

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the magnetic beads. As V. parahemolyticus was introduced into the assay, V. parahemolyticus

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and cDNA would compete for the binding site of the aptamer, and the bacterial cells had

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higher binding affinity to aptamers than cDNA, leading to the dissociation of ssDNA from

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MNPs. Therefore, the more target V. parahemolyticus in the system, the more ssDNA would

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enter the supernatant. After the supernatant was magnetically collected, hemin was added into

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it to form trivalent DNAzyme by interacting with CatG4. 100 μL TMB solution containing

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H2O2 was then added to the supernatant to obtain the absorbance signal at 655 nm. In contrast,

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in the absence of V. parahemolyticus, the supernatant did not show a significant colorimetric

256

signal.

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Feasibility of aptasensor for Vibrio parahemolyticus. The feasibility of the proposed

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colorimetric aptasensor for V. parahemolyticus detection was investigated and shown in Fig. 3.

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The groups without ssDNA (curves a-b) showed extremely weak or slightly enhanced

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background absorbance signal at 655 nm, indicating that these groups only possessed

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inefficient catalytic activity. As for the groups with ssDNA (curves c-d), after the

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participation of V. parahemolyticus, ssDNA detached from the MNPs, and the supernatant

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showed significant absorbance after the addition of hemin. The absorbance for trimeric CatG4

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(curves d) was almost twice more than the value for monomeric CatG4 (curves c). These

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results demonstrated the superior catalytic activity of trivalent DNAzyme, and the feasibility

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of the designed aptasensor for the detection of V. parahemolyticus.

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Optimization of experimental parameters. In order to give full play to the superiority of the

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aptasensor in detection, the following parameters were optimized respectively prior to testing:

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(a) the length of the cDNA; (b) the concentration of ssDNA; (c) the incubation time of V.

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parahemolyticus and aptasensor; (d) the concentration of hemin; and (e) the catalytic reaction

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time.

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For the sake of finding suitable cDNA that could hybridize with the V. parahemolyticus

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aptamer to form stable cDNA-aptamer duplex and could be replaced by target, a set of

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complementary sequences of different lengths was designed, 6-nt, 9-nt, 12-nt and 15-nt,

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respectively (Table S2). The concentrations of the aptamer and each ssDNA were set the same.

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As shown in Fig. 4A, the cDNA3 with 12-nt was evidently the most sensitive one for the V.

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parahemolyticus detection, it exhibited the maximum signal-to-background ratio. When the

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length of cDNA was less than 12-nt, ssDNA was difficult to be immobilized on the surface of

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MNPs due to the instability of the cDNA-aptamer duplex; And when cDNA exceeded 12-nt

280

in length, it closely hybridized with the aptamer and was difficult to be replaced easily by the

281

target. Therefore, ssDNA3 was selected for the subsequent biosensing assay.

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In order to verify the effect of ssDNA concentration on experimental results, the

283

experiments were operated under five different ssDNA3 concentrations, and the difference in

284

absorbance at 260 nm was recorded. As shown in Fig. 4B, as the concentration reached 200

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nM, the figure for △A260 soared to beyond 0.1. The absorbance showed no noticeable

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upward trend as the ssDNA3 concentration was higher than 200 nM. It indicated that under

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the condition of 200 nM, the amount of ssDNA3 had reached saturation. Hence, 200 nM

288

ssDNA3 was selected for colorimetric analysis.

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The effect of incubation time on the aptasensor response was presented in Fig. 4C. The

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absorbance of the supernatant at 655 nm steadily grew along with the increase of incubation

291

time and reached the maximum value at nearly 90 min. However, the absorbance no longer

292

increased after 90 min due to the saturation of the active site of the aptamer for bacteria

293

binding. Therefore, 90 min was chosen as the optimal incubation time for the aptasensor to

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interact with V. parahemolyticus.

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The G-quadruplex DNAzyme possesses high peroxidase-like activity, which is effective in

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catalyzing the H2O2-mediated oxidation of TMB to soluble products, producing a blue

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colorimetric signal that could be simply monitored by naked eyes or spectrophotometer. In G4

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DNAzyme, hemin assists G-quadruplex in folding into a catalytic conformation with much

299

higher catalytic activity than free hemin. Low concentration of hemin was insufficient to

300

fabricate DNAzyme, while high concentration of hemin would produce strong background

301

signals, so it was necessary to optimize the hemin concentration. As shown in Fig. 4D, the

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absorbance at 655 nm reached a plateau as 400 nM hemin was added to the test solution.

303

Therefore, 400 nM hemin was selected as the adequate concentration of hemin.

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The catalytic reaction time directly affected the signal that changed over time. Kinetic

305

study was performed to determine an appropriate detection time with clear and stable color

306

signal. Fig. 4E showed that it took about 20 min to form stable hemin/G-quadruplex

307

complexes with high catalytic activity.

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Specificity evaluation and analytical performance. To evaluate the selectivity of the

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proposed aptasensor for V. parahemolyticus, some other pathogenic bacteria, including E. coli,

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F's dysentery bacillus, S. aureus, S. typhimurium, L. monocytogenes and B. cereus, at a

311

concentration of 104 cfu/mL, were examined under the same detection conditions. Fig. 5

312

revealed that the absorbance signals produced by the other bacteria were close to the negative

313

control, while V. parahemolyticus showed a significantly darker color than the other bacteria.

314

The results indicated that the proposed aptasensor had good selectivity to V. parahemolyticus,

315

and the detection of V. parahemolyticus was not interfered by other pathogenic bacteria.

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Fig. 6A and B presented a typical result of detecting different concentrations of V.

317

parahemolyticus utilizing the proposed aptasensor. It could be seen that as the concentration

318

of V. parahemolyticus increased to 102 cfu/mL, a light blue color signal which was discernible

319

to the naked eye appeared, moreover, as the concentration of V. parahemolyticus further

320

increased, the blue color gradually became darker, and the absorbance at 655 nm increased

321

correspondingly. The absorbance signal intensity was plotted against the logarithmic of

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bacterial concentration in the range of 102 to 107 cfu/mL in Fig. 6C, illustrating a good linear

323

relationship between the intensity of the signals and the concentration of V. parahemolyticus

324

(y ＝ 0.1929x － 0.0957) with a correlation coefficient (R2) of 0.9941. The limit of detection

325

(LOD) was calculated to be 10 cfu/mL using the equation LOD ＝ 3 × σ/S. Compared to

326

previously reported detection methods for V. parahemolyticus (Table S3), the proposed

327

aptasensor showed great potential for sensitive detection of V. parahemolyticus of wide

328

concentration range in real food samples.

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In order to verify its analytical performance, both the traditional plate counting method and

330

the proposed method were used to detect V. parahemolyticus in salmon samples. The results

331

were summarized in Table 1. There was no significant difference between the results obtained

332

by the two methods. The recoveries of V. parahemolyticus in the salmon samles ranged from

333

93.9% to 104.7%, which confirmed that the proposed method using truncated aptamer and

334

trivalent DNAzyme could be used for the determination of V. parahemolyticus in complex

335

food samples.

336

In summary, after optimizing the V. parahemolyticus aptamer by truncation to make it

337

more suitable for downstream applications, and identifying the binding site of the aptamer by

338

site-directed mutation to design the appropriate cDNA, a novel colorimetric aptasensor for V.

339

parahemolyticus detection with high sensitivity and selectivity was developed. As V.

340

parahemolyticus was introduced into the system, the ssDNA containing cDNA and G4 DNA

341

would be replaced by the target and dissociated from the surface of the MNPs. Later, after

342

hemin was added to the supernatant, it interacted with the G4 DNA to form DNAzyme, which

343

could catalyze peroxidase substrate to produce color signal. Benefiting from the high

344

separation efficiency of MNPs, the high affinity and specificity of the optimized aptamer to

345

the target, and the excellent catalytic activity of trivalent DNAzyme, the aptasensor exhibited

346

an obvious colorimetric response to V. parahemolyticus, rendering it a promising alternative

347

to routine detection of V. parahemolyticus. Furthermore, with the capability of producing

348

specific aptamers for any type of food-borne pathogen, this scheme possesses the potential of

349

monitoring other pathogens by simply replacing aptamers.

350

16


Page 16 of 33

Page 17 of 33

351


Acknowledgments

352

This work was partly funded by the National Natural Science Foundation of China

353

(31871881, 31871721), S&T Support Program of Jiangsu Province (BE2017623), Jiangsu

354

Agriculture Science and Technology Innovation Fund (CX(18)2025), the National First-class

355

Discipline Program of Food Science and Technology (JUFSTR20180303), Ministry of

356

Education of the People's Republic of China (JUSRP51714B) and the Distinguished Professor

357

Program of Jiangsu Province.

358 359

Supporting Information. Secondary structure of aptamers predicted by Mfold software,

360

sequence and dissociation constants (Kd values) for the studied V. parahemolyticus-binding

361

aptamers, sequences used in the aptasensor, an overview of main method reported recently for

362

the determination of V. parahemolyticus

363 364 365 366 367 368 369 370 371 372

17



373

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490 491 492 493 494 495 496 497 498 499 500 501 502 503 504

23



505 506

Figure captions

507

Fig. 1 Identification of the specificity of truncated aptamers against V. parahemolyticus: (A)

508

histogram of the percentage of gated fluorescence intensity above background for individual

509

aptamers. (B) Flow cytometry assay for the binding of aptamers to bacteria.

510

Fig. 2 Schematic illustration of the colorimetric detection method for V. parahemolyticus

511

based on aptamer recognition, MNPs, and trivalent DNAzyme.

512

Fig. 3 Absorbance spectra of the catalytic reaction product under different conditions: only

513

hemin (a); hemin and 104 cfu/mL target (b); hemin, 104 cfu/mL target, and ssDNA with

514

monomeric CatG4 (c); hemin, 104 cfu/mL target, and ssDNA with trimeric CatG4 (d). 400

515

nM hemin was applied in each group.

516

Fig. 4 The optimization of detection condition. (A) The optimization of the length of duplex:

517

S/B = (A-Abackground)/(A0 -Abackground), where A and A0 are the absorbance of the catalysis of

518

the aptasensor with and without the target at 655 nm, respectively. The assays were measured

519

in the conditions: [ssDNA] = 200 nM, [Hemin] = 400 nM, and lg[V. parahemolyticus] = 8. (B)

520

Plot for optimizing the concentration of ssDNA3. The assays were measured in the conditions:

521

[Hemin] = 400 nM and lg[V. parahemolyticus] = 8. (C) The optimization of the incubation

522

time of target and aptasensor: the catalysis absorbance spectra of different incubation time.

523

The assays were measured in the conditions: [ssDNA] = 200 nM, [Hemin] = 400 nM, and

524

lg[V. parahemolyticus] = 8. (D) Effect of hemin concentration. The assays were measured in

525

the conditions: [ssDNA] = 200 nM and lg[V. parahemolyticus] = 8. (E) Kinetic

526

absorbance-time curves measured at 655 nm of different systems: (a) aptasensor and (b) free

527

hemin with the experimental conditions: [ssDNA] = 200 nM, [Hemin] = 400 nM, and lg[V.

528

parahemolyticus] = 8.

529

Fig. 5 Specificity studies against other bacteria. (A) The photograph of the specificity for 24


Page 24 of 33

Page 25 of 33


530

blank (a), V. parahemolyticus (b), B. cereus (c), E. coli (d), S. aureus (e), S. typhimurium (f),

531

F's dysentery bacillus (g), L. monocytogenes (h). (B) The intensity of the signals measured for

532

blank and different bacteria. The concentration of V. parahemolyticus was 103 cfu/mL, while

533

that of other bacteria was 104 cfu/mL.

534

Fig. 6 (A) Photograph and (B) UV-vis absorption spectra for colorimetric detection of V.

535

parahemolyticus at 100, 101, 102, 103, 104, 105, 106, 107 and 108 cfu/mL (from a to i); (C)

536

Standard correlation curve between the intensity of the signals and the concentration of V.

537

parahemolyticus.

538 539 540 541 542 543 544 545 546 547 548 549 550 551 552

25



Page 26 of 33

553

Table 1 Comparison of salmon sample results obtained from classical plate counting method and the proposed method. concentration measured by the

concentration measured by the

recovery

plate counting method (cfu•mL-1)

proposed method (cfu•mL-1)

(%)

(3.58±0.15)×102

（3.47±0.11）×102

96.9

(3.40±0.10)×103

（3.42±0.08）×103

100.6

(3.49±0.22)×104

（3.56±0.14）×104

102.0

(3.62±0.06)×102

（3.40±0.19）×102

93.9

(3.79±0.16)×103

（3.97±0.20）×103

104.7

(3.55±0.18)×104

（3.52±0.23）×104

99.2

sample

salmon 1

salmon 2

26


Page 27 of 33


(A)

(B)

Fig. 1

27



Fig. 2

28


Page 28 of 33

Page 29 of 33


Fig. 3

29



Fig. 4

30


Page 30 of 33

Page 31 of 33


(A)

(B)

Fig. 5

31



(A)

(B)

(C)

Fig.6

32


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For Table of Contents Only

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Colorimetric aptasensor based on truncated aptamer and trivalent

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