Primer Design and Analysis for Detection of mecA gene
DOI:
https://doi.org/10.25026/jtpc.v5i3.297Keywords:
MecA gene, PCR, Primer, AmplificationAbstract
MecA is a gene that causes antibiotic resistance and it contained in Staphylococcus aureus. The gene can be detected using pairs of primer (forward and reverse). Primes is short nucleotide that are used as attachment point for DNA polymerase and as a barrier for the fragment DNA target to be amplified with Polymerase Chain Reaction (PCR). The aims of this study were to design and analysis the nucleotide primer sequences of MecA. This research using in silico method of NCBI (National Center of Biotechnology Information) application, clone manager10, oligoanalyzer3.1, perlprimer and primer3plus. The results of design and candidate primer analysis showed that the first candidate of forward and reverse primer that falls with in the criteria with base sequences 18-30, 40-60 GC%, Tm 50-60, 3’ dimer ?3, stability ?1,2, secondary structure >-16 Kcal/mol, runs ?5, repeats ?4, hairpins>-3 Kcal/mol. The conclusion is the first candidate of forward primer with 19 base pair (5’GTGAAGCAACCATCGTTAC'3), %GC 47Tm 58oC, 3’dimer 2, stability 1.6, secondary structure -1,95 dan -3,61 Kcal/mol, runs 2, hairpins -0,1 start 53844 and the first candidate of reverse primer with 21 base pair (5’CCTTCTACACCTCCATATCAC'3), %GC 47, Tm 58oC, 3’dimer 0, stability 1.3, secondary structure -4,74 dan -5,38 Kcal/mol, runs 2, hairpins -2.5 dan start 55852. The both of primer can be use for identification of MecA gene by PCR methodDownloads
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References
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[3] Wilson, D. N. (2014). Ribosome-targeting antibiotics and mechanisms of bacterial resistance. Nature Reviews Microbiology, 12(1), 35–48. https://doi.org/10.1038/nrmicro3155
[4] Sudiogdadi, sunarjati. 2015. Mekanisme Timbulnya Resistensi Pada Antibiotik Pada Infeksi Bakteri :Mikrobiologi Fakultas Kedokteran Universitas Pedjajaran
[5] Handoyo D, Rudiretna A. General Principles and Implementation of Polymerase. 2001;9(1):17–29
[6] Borah P. Primer designing for PCR. Sci Vis. 2011
[7] Li Z, Chen JH, Hao Y, Nair SK. Structures of the PelD cyclic diguanylate effector involved in pellicle formation in Pseudomonas aeruginosa PAO1. J Biol Chem. 2012;287(36):30191–204.
[8]Baker P, Hill PJ, Snarr BD, Alnabelseya N, Pestrak MJ, Lee MJ, et al. Exopolysaccharide biosynthetic glycoside hydrolases can be utilized to disrupt and prevent Pseudomonas aeruginosa biofilms. Sci Adv. 2016
[9] Rafika Sari , Mawarnursavira K, Apridamayanti P. metode. OPTIMASI MELTING Temp Prim DEGENERATE PADA SUHU 60°C GEN ERM(T) (ERYTHROMYCIN RIBOSOME METHYLASE) YANG Resist TERHADAP BAKTERI Streptococcus pyogenes[Internet].2019;4:1.Availablefrom:http://jurnal.untan.ac.id/index.php/jmfarmasi/article/view/32895/75676581195
[10] Luh Ketut Budi M, I Nengah W, Sagung Chandra Y. DESAIN PRIMER UNTUK AMPLIFIKASI FRAGMEN GEN inhA ISOLAT 134 MULTIDRUG RESISTANCE TUBERCULOSIS (MDR-TB) DENGAN METODE POLYMERASE CHAIN REACTION. 2014;2:20–4.
[11] Wirajana IN. DESAIN PRIMER SECARA IN SILICO UNTUK AMPLIFIKASI FRAGMEN GEN rpoB Mycobacterium tuberculosis DENGAN POLYMERASE CHAIN REACTION ( PCR ). 2016;(July).
[12] Marshall OJ. PerlPrimer: Cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics. 2004;20(15):2471–2.
[13] Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 2007;35(SUPPL.2):71–4.
[14] Oliveira, D. C., & de Lencastre, H. (2011). Methicillin-resistance in Staphylococcus aureus is not affected by the overexpression in trans of the mecA gene repressor: A surprising observation. PLoS ONE, 6(8). https://doi.org/10.1371/journal.pone.0023287.
[15] Hiramatsu, K. (2004). Elucidation of the Mechanism of Antibiotic Resistance Acquisition of Methicillin-Resistant Staphylococcus Aureus (MRSA) and Determination of Its Whole Genome Nucleotide Sequence. Japanese Medical Association Journal, 47(4), 153–159. Retrieved from http://www.med.or.jp/english/journal/pdf/jmaj/v47no04.pdf
[16] Bambang, H., Harlis, Muswita, Aina, M., & Ali, S. (2011). PELATIHAN PENGGUNAAN GEN BANK NCBI (National Center for Biotechnology Information) DAN PROGRAM MEGA 4.0 (Molecular Evolutionary Genetics Analysis Version 4.0) UNTUK PENELITIAN. 0(52), 55–60.
[17] Marlina, Ramadhani, P., Eka Putra, A., Rustini, & Aldi, Y. (2015). Desain Primer Multiplex Polymerase Chain Reaction ( PCR ) Gen E6 HPV Tipe 45 dan HPV Tipe 52. Prosiding Seminar Nasional Dan Workshop “Perkembangan Terkini Sains Farmasi Dan Klinik,”52, 158–165
[18] Solanki, G. (2012). Polimerase Chain Reaction. International Journal of Pharmacological Research
[19] Yustin, P. D., & adewi, Putu Sanna Yustiantara, I. N. (2018). MDR-1 GENE 1199 VARIANT PRIMER DESIGN TECHNIQUES IN PEDIATRIC PATIENT BUFFY COAT SAMPLES WITH LLA. The Journal of Ecology, 1(3), 105–111. https://doi.org/10.2307/2257356
[20] Judelson, H. (2013). Guidelines for designing primers. Primer Guidelines.
[21] Widowati, E. W. (2013). DESAIN PRIMER SITOKROM B (cyt b) SEBAGAI SALAH SATU KOMPONEN PCR (polymerase chain reaction)UNTUK DETEKSI DNA BABI. Laporan Penelitian Individual, 1–64
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Published
2021-06-30
How to Cite
Syamsidi, A., Aanisah, N., Fiqram, R. ., & Jultri, I. A. (2021). Primer Design and Analysis for Detection of mecA gene . Journal of Tropical Pharmacy and Chemistry, 5(3), 245–253. https://doi.org/10.25026/jtpc.v5i3.297
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