OPTIMASI SUHU ANNEALING PRIMER DEGENERATE UNTUK MENGAMPLIFIKASI FRAGMEN GEN ARGININE DECARBOXYLASE (ADC) GENOM UBI KAYU LOKAL MALUKU TENGGARA

Siti Kurniawati, N. Sri Hartati

Sari


Abstract

Arginine decarboxylase (ADC) is an enzyme that plays a role in polyamine biosynthesis and has been shown to increase resistance to biotic and abiotic stress. Woody oak (Manihot esculenta Crantz) is known to grow and produce well in dry and poor nutrient conditions. The purpose of this study was to obtain optimum conditions in PCR reaction process to obtain candidate gene fragment of ADC. Four pairs of primers to amplify the gene fragments of ADC are degenerate from several plants that have been deposited on NCBI databases, namely Jatropa curcas (Acc XM_022220421), Populus trichocarpa (Acc XM_002306105.2), Capsicum annuum cv Nockwang (Acc KC160547.1) and Lycopersicon esculentum (Acc L16582.1). The success in amplifying a gene by PCR technique using a specially designed primer is determined by the precision of the primary attachment temperature with the DNA mold. Four primer pairs are designed to successfully amplify DNA sequence fragments from the local cassava genome from Malra, namely Malra012 and Malra016 genotypes. The MeadC1 primary pair can amplify the DNA mold and produce bands of less than 1,000 base pairs at a fixed temperature of 46 ° C.47 ° C. and 48 ° C. Nucleotide base sequence analysis using primary pair MeadC1 has been done, but based on bioinformatic analysis using NCBI BLAST program, the obtained fragment did not show the encoding fragment of ADC gene.

 

Keywords : cassava, arginine decarboxylase, AADC

 

Abstrak

Arginine decarboxylase (ADC) merupakan enzim yang berperan dalan biosintesis poliamin dan telah terbukti dapat meningkatkan ketahanan terhadap cekaman biotik dan abiotik.Ubi kayu (Manihot esculenta Crantz) dikenal mampu tumbuh dan berproduksi dengan baik meski pada kondisi kering dan miskin hara. Tujuan dari penelitian ini adalah untuk mendapatkan kondisi optimum pada proses reaksi PCR untuk memperoleh kandidat fragmen gen ADC. Empat pasang primer untuk mengamplifikasi fragmen gen ADC dirancang secara degenerate dari beberapa tanaman yang telah terdeposit pada database NCBI yaitu Jatropa curcas (Acc XM_012229042.1), Populus trichocarpa (Acc XM_002306105.2), Capsicum annuum cv Nockwang (Acc KC160547.1) dan Lycopersicon esculentum (Acc L16582.1). Keberhasilan dalam amplifikasi suatu gen dengan teknik PCR menggunakan primer yang dirancang khusus sangat ditentukan oleh ketepatan suhu penempelan primer dengan cetakan DNA. Empat pasang primer yang didesain berhasil mengampifikasi fragmen sekuen DNA dari genome ubi kayu lokal asal Malra yaitu genotipe Malra012 dan Malra016. Pasangan primer MeADC1 dapat mengampifikasi cetakan DNA dan menghasilkan pita dengan ukuran kurang dari 1.000 pasang basa pada suhu penempelan 46°C.47°C dan 48°C. Analisis sekuen basa nukleotida menggunakan pasangan primer MeADC1 telah dilakukan, namun berdasarkan analisis bioinformatik menggunakan program BLAST NCBI, fragmen yang diperoleh tidak menunjukkan fragmen penyandi gen ADC.

 

Kata kunci: ubi kayu, arginine decarboxylase, ADC


Referensi


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