Aptasensor designed via the stochastic tunneling-basin hopping method for biosensing of vascular endothelial growth factor

Hung-Wei Yang; Shin-Pon Ju; Che-Hao Cheng; Ying-Tzu Chen; Yu-Sheng Lin; See-Tong Pang

doi:10.1016/j.bios.2018.07.073

Aptasensor designed via the stochastic tunneling-basin hopping method for biosensing of vascular endothelial growth factor

Biosens Bioelectron. 2018 Nov 15:119:25-33. doi: 10.1016/j.bios.2018.07.073. Epub 2018 Aug 2.

Authors

Hung-Wei Yang¹, Shin-Pon Ju², Che-Hao Cheng³, Ying-Tzu Chen¹, Yu-Sheng Lin³, See-Tong Pang⁴

Affiliations

¹ Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.
² Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan; Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan. Electronic address: jushin-pon@mail.nsysu.edu.tw.
³ Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.
⁴ Division of Urology, Department of Surgery, Linkou Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan; School of Medicine, Chang Gung University, Taoyuan 33302, Taiwan.

PMID: 30098463
DOI: 10.1016/j.bios.2018.07.073

Abstract

The Systematic Evolution Ligands by Exponential Enrichment (SELEX) is common used for selection of high affinity single-stranded DNA (ssDNA) aptamer with target protein. However, we do not know what the most stable configuration of the selected aptamer bound with target protein is. Therefore, a systematic search process using the stochastic tunneling-basin hopping (STUN-BH) method is proposed to find the most stable configuration of the ssDNA aptamer specific for vascular endothelial growth factor (VEGF) capture (Apt_VEGF; 5'-TGTGGGGGTGGACGGGCCGGGTAGA-3'). After the most stable configuration was obtained by the STUN-BH method, molecular dynamics (MD) simulation was carried out to investigate the thermal stability of Apt_VEGF/VEGF at 300 K in both vacuum and water. All molecular simulations were conducted with the large-scale atomic/molecular massively parallel simulator (LAMMPS), and the AMBER99SB force field was used to describe the atomic interactions for the current Apt_VEGF/VEGF system. The three most stable Apt_VEGF/VEGF configurations obtained by the STUN-BH method indicated that Apt_VEGF residues exhibit greater affinity for VEGF surface loop fragments as compared with surface alpha helix and beta sheet fragments. Results indicated that after the first Apt_VEGF (Apt_VEGF I) occupies most of the VEGF loop fragment, the second Apt_VEGF (Apt_VEGF II) is adsorbed by the rest of the VEGF loop fragment and the VEGF Chain B beta sheet fragment, resulting in a 24.8% reduction in binding strength as compared to that of Apt_VEGF I. Furthermore, when Apt_VEGF I and Apt_VEGF II chains were stably adsorbed by VEGF, the third Apt_VEGF (Apt_VEGF III) chain can only partially attach to VEGF, as confirmed by real Apt_VEGF-VEGF binding experiments. Lastly, we demonstrated that the aptasensor constructed according to MD simulation is highly sensitive for VEGF with a linear detection range of 10 pg/mL-10 ng/mL.

Keywords: Aptasensor; Molecular dynamics simulation; Single-stranded DNA aptamer; Stochastic tunneling-basin hopping method; VEGF.

MeSH terms

Aptamers, Nucleotide / chemistry*
Biosensing Techniques / methods*
DNA, Single-Stranded / chemistry
Limit of Detection
Molecular Dynamics Simulation
Protein Binding
SELEX Aptamer Technique
Vascular Endothelial Growth Factor A / chemistry*
Vascular Endothelial Growth Factor A / isolation & purification*

Substances

Aptamers, Nucleotide
DNA, Single-Stranded
Vascular Endothelial Growth Factor A