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LAMP Reaction Lab

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LAMP reaction
The LAMP reaction was performed by using Loopamp DNA amplification kit, Eiken chemical CO., LTD., JAPAN. The 2X reaction mix composed of 40 mM Tris-HCl (pH 8.8), 20 mM MgSO4, 16 mM (NH4)2SO4, 0.2% Tween 20, 1.6 M Betaine and 2.8 mM dNTPs each. The LAMP reaction was optimized by incorporating different concentrations of primers and temperature. The LAMP reaction of total 25µl volume consisted of 2X reaction mixture (12.5µl), 2.0 μM FIP and BIP; 0.8 μM LF and LB; 0.2 μM F3 and B3 each, 1µl (8 units) of Bst DNA polymerase, Template DNA and PCR grade nuclease free water. Primer concentrations were optimized by using 0.8 μM or 1.2 μM or 1.6 μM or 2.0 μM of FIP and BIP primers each, 0.8 μM or 1 μM of LF and LB primers each, 0.2 μM …show more content…
Primer concentrations for 2X reaction mix containing individual buffer components were optimized using 2.0 μM of FIP and BIP primers each, 0.4 μM, 0.48 μM ,0.6 μM and 0.8 μM of LF and LB primers each, 0.2 μM or 0.28 μM of F3 and B3 each.
Analysis of LAMP products:
The amplified products of LAMP assay were detected using Eiken Loopamp Real-time Turbidimeter LA-500 which detects the turbidity of amplified product with respect to time (Mori et al., 2004). Turbidimeter records the time (Tt) required to attained the turbidity level above 0.1 OD (optical density). Readings were recorded in form of turbidity curves with time at 650 nm in every 6 seconds. The turbidity of amplified product was dependent on the amount of amplified product. The visual end point detection of amplified products was observed by using 1 μl of 1000X SYBR green I dye …show more content…
mallei NCTC 10245 from 10000 pico gram (pg)/reaction to 0.1 pg/reaction through 1000 pg, 100 pg, 10 pg, 1pg, 0.5 pg, 0.25 pg and 0.1 pg/reaction and in terms of number of plasmid DNA copies of B. mallei NCTC 10245 from 106, 105, 104, 103, 102 and 10 plasmid DNA copies/reaction for real time monitoring and visual detection of endpoint of assay from SYBR green I dye.
Determination of specificity of LAMP assay
The specificity of LAMP assay were determined by incorporating 10,000 pg of genomic DNA isolated from Burkholderia and non- Burkholderia strains in 25 μl of LAMP reaction containing strictly same conditions as before mentioned.

Detection of B. mallei in spiked blood by LAMP assay
One ml of human blood was spiked with 2.1 Χ 109 CFU to 21 CFU of B. mallei NCTC 10245 through 2.1×108, 2.1×107, 2.1×106, 2.1×105, 2.1×104, 2.1×103 and 2.1×102 CFU Genomic DNA from the blood samples and water samples spiked with B. mallei were isolated using DNeasy blood and tissue kit (Qiagen, Germany) in 50 µl elution buffer and 2 µl of the genomic DNA was used as template

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