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In addition, the enhanced thermo-stability of the Stoffel fragment results in better efficiency when used with G+C rich templates or templates having complex secondary structure [22].
In addition to ours, a number of protocols for difficult or GC rich templates are published [ 36, 37], supplemented by several commercial kits.
Several additives were tested as denaturation reagents in the PCR protocols for MIRUs, VNTR and SSRs in an attempt to improve the amplification efficiency for the GC rich templates.
Analysis of sequence data obtained from RPA-amplified libraries showed reduced bias towards GC rich templates compared to standard Illumina libraries for both P. falciparum 3D7 and the clinical isolate.
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Two μl of template was amplified using High Fidelity Platinum Taq (Invitrogen Cat #11304-102) and the PCRx enhancer system to facilitate amplification of CG rich template (Cat# 11495 017), with the following thermocycling conditons: 95° for 5 minutes, (95° for 30s, 58° for 30s and 72° for 45 seconds) x 45 cycles, 72° for 7 minutes, 4° indefinitely.
Southern blotting of long-range PCR products, optimized for amplification of a long and GC rich template, requires less DNA, as small as 15 pg [ 108], even of lower quality, and gives reliable information about repeat copy number with using a few replicate of PCRs with 180 300 pg of DNA [ 88].
The reason is that GC-rich templates frequently generate local secondary structures leading to an inefficient PCR amplification [50].
We first optimized the LASL method (Figure 1) by reducing template contamination during shearing, and taking steps to minimize cloning biases, particularly for AT-rich templates.
While techniques are available to manage these difficult regions during PCR amplification of plasmid and genomic DNA [20], [21], to our knowledge no method for de novo synthesis of GC-rich templates has been clearly defined.
Additives betaine (1 M, Sigma) and/or DMSO (7%, Sigma) were used for GC-rich templates.
They also made possible more efficient amplification of GC-rich templates than betaine and other previously described additives.
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