3D Structural Prediction of Catechin Specific Aptamer

Arinaasna Mat Tamidi; Nor Azlina Ahmad; Razauden Zulkifli; Huszalina Hussin; Muhammad Helmi Nadri

doi:10.38001/ijlsb.961138

Research Article

3D Structural Prediction of Catechin Specific Aptamer

Year 2022, , 21 - 28, 15.04.2022

Arinaasna Mat Tamidi Nor Azlina Ahmad Razauden Zulkifli , Huszalina Hussin Muhammad Helmi Nadri

https://doi.org/10.38001/ijlsb.961138

Abstract

Catechin has been reported to possess many advantageous for practical application due to its distinctive antioxidant and anti-inflammatory performance. This paper reports the in-silico characterization of single stranded-DNA (ssDNA) aptamers, speciﬁc for catechin. 28 primary sequences from DNA-aptamers library screened via systemic evolution of ligands by exponential enrichment (SELEX) from previous research were predicted and constructed into 3D structural conformation using several bioinformatics tools. Blind docking was performed to all 28 aptamer candidates and resulted in 4 noticeable aptamer with highest binding energy, namely Aptamer 24, 18, 9 and 27 as catechin specific aptamer. Influence of environmental factors towards catechin specific aptamers also was taken in consideration. It was predicted that aptamer 24, 18, 9 and 27 were the most potential aptamer for catechin recognition tool at laboratory scale based on the docking result. However, further in vitro experimental study in laboratory needs to be done as validation.

Keywords

3D, DNA aptamer, catechin, molecular docking

Project Number

This project was funded by Ministry of Higher Education (MOE), Malaysia and Innovation and Commercialization Centre (ICC), Universiti Teknologi Malaysia (UTM) [PRGS:ICC (PY/2020/03762)]

Thanks

We also would like to acknowledge Department of Bioscience, Faculty of Science, UTM for supporting this project

References

1. Mbaveng AT, Hamm R, Kuete V. Harmful and Protective Effects of Terpenoids from African Medicinal Plants. Toxicological Survey of African Medicinal Plants. Elsevier Inc.; 2014. 557-576 p.
2. Zanwar AA, Badole SL, Shende PS, Hegde M V., Bodhankar SL. Antioxidant Role of Catechin in Health and Disease. Vol. 1, Polyphenols in Human Health and Disease. Elsevier Inc.; 2013. 267-271 p.
3. Heiat M, Ranjbar R, Fasihi-ramandi M, Mohammad A. Characterization of pharmacological properties of isolated single- stranded DNA aptamers against angiotensin II. 2016;30:238–45.
4. Hermann T, Patel DJ. Biochemistry - Adaptive recognition by nucleic acid aptamers [Review]. Science (80- ). 2000;287(5454):820–5.
5. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406–15.
6. Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, et al. Automated 3D structure composition for large RNAs. Nucleic Acids Res. 2012;40(14):1–12.
7. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–12.
8. Jeddi I, Saiz L. Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors. Sci Rep. 2017;7(1):1–13.
9. Tuma Sabah J, Zulkifli RM, Shahir S, Ahmed F, Abdul Kadir MR, Zakaria Z. In vitro selection and characterization of single stranded DNA aptamers for luteolin: A possible recognition tool. Anal Biochem. 2018;549(March):72–9.
10. Oleg Trott and Arthur J Olson. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Isr J Psychiatry Relat Sci. 2012;49(3):151–8.
11. Owczarzy R, Moreira BG, You Y, Behlke MA, Wälder JA. Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations. Biochemistry. 2008;47(19):5336–53.
12. Tan ZJ, Chen SJ. Nucleic acid helix stability: Effects of salt concentration, cation valence and size, and chain length. Biophys J. 2006;90(4):1175–90.
13. Driessen RPC, Sitters G, Laurens N, Moolenaar GF, Wuite GJL, Goosen N, et al. Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins. Biochemistry. 2014;53(41):6430–8.
14. Sharma TK, Bruno JG, Dhiman A. ABCs of DNA aptamer and related assay development. Biotechnol Adv. 2017;35(2):275–301.
15. Hianik T, Ostatná V, Sonlajtnerova M, Grman I. Influence of ionic strength, pH and aptamer configuration for binding affinity to thrombin. Bioelectrochemistry. 2007;70(1):127–33.
16. Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK. Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity. Front Mol Biosci. 2018;5(May):1–16.
17. Duss O, Michel E, Yulikov M, Schubert M, Jeschke G, Allain FHT. Structural basis of the non-coding RNA RsmZ acting as a protein sponge. Nature. 2014;509(7502):588–92.
18. Jung J, Ihiy R, Scott E, Yu M, Van Orden A. Probing the complete folding trajectory of a DNA hairpin using dual beam fluorescence fluctuation spectroscopy. J Phys Chem B. 2008;112(1):127–33.
19. Lamoureux M, Patard L, Hernandez B, Couesnon T, Santini GPH, Cognet JAH, et al. Spectroscopic and structural impact of a stem base-pair change in DNA hairpins: GTTC-ACA-GAAC versus GTAC-ACA-GTAC. Spectrochim Acta - Part A Mol Biomol Spectrosc. 2006;65(1):84–94.