I wanted to talk a little about the selection characteristics of Agencourt’s AMPure beads, a bead-reagent combination that purifies PCR reactions.
The suppliers of these kits recommend AMPure XP often as the sole cleanup option. AMPure XP has also been cited in over 21,000 articles on Google Scholar. Using AMPure XP as your cleanup kit, you can keep your sequencing projects on track and continue to provide the best results possible to your customers, patients and journals.
Table 1 Purification efficiency data using automated AMPure XP. 1000 bp pGEM plasmid DNA PCR fragments were purified using the Biomek 4000 AMPure XP method and a manual process. Yield (95.4%) and purity (102.5%) obtained in triplicate by automation using three columns were compared to those obtained from manual purification. Faster manual and automated processing as compared to traditional post-PCR cleanup methods Requires no centrifugation or filtration step, Agencourt AMPure XP can be easily used in manual and automated 96- or 384-well formats. ICELL8 Human TCR a/b Profiling User Manual (072219) takarabio.com Takara Bio USA, Inc. Page 7 of 61 - Figure 2. Protocols for ICELL8 Human TCR a/b Profiling. Library Validation and Quantification (Section IV.L) Purification of Amplified Libraries Using Agencourt AMPure XP Beads (Section IV.K). AMPure XP for PCR Purification Cleanup and Size Selection You can use our proprietary SPRI paramagnetic bead-based chemistry to remove contaminants (dNTPs, salts, primers, primer dimers) throughout your NGS workflows. Used in a variety of NGS library prep chemistries.
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This stuff is incredible in terms of simplicity, efficiency, and high-throughput compatibility. I have a sneaking suspicion that AMPure, not unlike fire to Prometheus, was handed down from the gods to benefit humanity. You just dunk it into your sample, slosh it around, stick it to a magnet, wash, wash again, and elute in your favorite buffer. No muss, no fuss.
![Ampure Ampure](/uploads/1/3/4/9/134900900/986228920.jpg)
We were wondering, though, about its selection process. What size fragments are selected by the AMPure beads, specifically at which ratio of beads to sample? So, like diligent scientists, we rolled up the sleeves of our labcoats and… read the protocol.
The protocol recommends washing your sample in a 1.8:1 ratio of beads to sample, although it says that fragments less than 100bp will be omitted at this ratio, it doesn’t say which sized fragments will be selected. We found this remarkably helpful technical bulletin, which describes calibrating each batch of AMPure beads with various ratios of DNA ladder.
![Ampure xp beads beckman protocol Ampure xp beads beckman protocol](/uploads/1/3/4/9/134900900/197928350.png)
Ampure Xp Beads Manual
So I did our very own calibration with AMPure beads using Fermentas’s GeneRuler™ Low Range DNA Ladder (25-700 bp). I added 30ul ladder to various concentrations of AMPure beads according to Agencourt’s instructions.
(Actually, if you’re looking for good AMPure instructions, I recommend looking at Illumina’s TruSeq™ Sample Preparation Guide. Borderlands 2: assassin madness pack download. Honestly, their instructions are more comprehensive than Agencourt’s, and easier to read.) After purifying each sample, I bookended the various AMPure:ladder ratios with 10ul non-purified ladder on a 2% TBE gel for easy comparison.
Beckman Ampure Xp Beads
Without any further ado, here are the results: