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NucleoSpin cfDNA XS purification kit catalog page NucleoSpin cfDNA XS
Product overview

NucleoSpin cfDNA XS

An ideal solution for purifying circulating DNA from plasma

  • Highly reliable silica membrane technology provides high purity
    Ready to use for real-time PCR
  • Optimized column design yields highly concentrated DNA without a speedvac
    Reduced column membrane area allows elution in only 5–20 µl
  • High recovery for fragments >50 bp
    Ideally suited for fragmented circulating DNA
  • Works with up to 240 µl of plasma
    Ideal solution for routine analyses

Increased amounts of circulating DNA in plasma have been found in a variety of disorders, including cancer, autoimmune diseases, infections, certain fetal diseases, trauma, stroke, and others. Circulating DNA is known to be highly fragmented and low in concentration, which makes it difficult to purify.

NucleoSpin cfDNA XS is designed for the isolation of fragmented DNA larger than 50 bp from human EDTA blood plasma. This kit overcomes the limitations of conventional kits: a large membrane diameter associated with large default elution volumes and a resulting DNA concentration which is too low to be directly used as PCR template. NucleoSpin cfDNA XS allows you to perform PCR directly on your purified DNA, because it allows elution in only 5–20 µl, resulting in highly concentrated DNA.

Column design  

Optimized column design offers unique advantages

The innovative internal funnel design (Figure 1) allows standard miniprep spin columns to hold a silica membrane of very small diameter. The small diameter of the NucleoSpin cfDNA XS membrane allows efficient elution in only 5–20 μl, resulting in highly concentrated DNA that is ready for all typical downstream applications. The ability to purify highly concentrated circulating DNA allows for increased sensitivity and better results.

Design of NucleoSpin Plasma XS column membrane

Figure 1. Design of the NucleoSpin cfDNA XS column membrane.

Elution volume depends on membrane diameter

The Xtra Small diameter of the NucleoSpin cfDNA XS column membrane (Figure 2) allows efficient elution in only 5–20 μl, compared to at least 20–30 µl using the Competitor Q kit designed for very small samples.

Diameter of NucleoSpin Plasma XS column membrane

Figure 2. The exceptionally small diameter of the NucleoSpin cfDNA XS (MN) column membrane is optimized for elution in smaller volumes than a competitor kit (Q).

Protocol overview  

The NucleoSpin Plasma XS procedure

Figure 3. The NucleoSpin cfDNA XS procedure.

Fetal DNA detection  

NucleoSpin cfDNA XS is ideally suited for the detection of fetal DNA in maternal plasma

Duplex PCR amplification of an RHD fragment (rhesus gene) and an amelogenin fragment specific for the male Y chromosome was used to detect fetal DNA purified from human maternal plasma with either NucleoSpin cfDNA XS or a kit from Competitor R (Figure 4). The NucleoSpin cfDNA XS kit displayed significantly better performance than the Competitor R kit, as demonstrated by PCR signals that were detectable 2.6 cycles earlier for the RHD fragment and 2.1 cycles earlier for the amelogenin fragment.

More sensitive detection of fetal DNA in maternal plasma

Figure 4. NucleoSpin cfDNA XS enables more sensitive detection of fetal DNA in maternal plasma than a competitor kit. DNA was purified from human maternal plasma used for fetal DNA diagnostics with either NucleoSpin cfDNA XS (formerly known as NucleoSpin Plasma XS) or a kit from Competitor R. In each case, DNA from approximately 100 µl of plasma (40% of a NucleoSpin cfDNA XS eluate derived from 240 µl of starting material, or 10% of a Competitor R eluate derived from 1,000 µl of starting material) was used for duplex PCR analysis. Amplification of an RHD fragment (rhesus gene) and an amelogenin fragment specific for the male Y chromosome produced 150–180-bp amplicons. PCR signals were detectable 2.6 cycles earlier for the RHD fragment and 2.1 cycles earlier for the amelogenin fragment with the NucleoSpin cfDNA XS kit than with the Competitor R kit. Data kindly provided by Dr. Doescher, DRK Blutspendedienst NSTOB, Oldenburg, Germany.

Higher recovery  

Higher recovery of DNA spikes from plasma

When NucleoSpin cfDNA XS and a kit from Competitor Q were each used to purify a series of DNA spikes ranging in size from 50–1,000 bp (Figure 5), only the NucleoSpin cfDNA XS kit was able to recover fragments smaller than 100 bp, and it showed higher recovery rates of all the remaining fragment sizes than the Competitor Q kit.

Higher recovery of DNA spikes from plasma samples

Figure 5. Higher recovery of DNA spikes from plasma samples than a competitor kit. DNA spikes of 50, 100, 150, 250, and 1,000 bp were mixed with plasma samples. The DNA was subsequently purified with NucleoSpin cfDNA XS (MN) and a kit from Competitor Q (Q) in parallel. The Competitor Q kit completely failed to show recovery of fragments smaller than 100 bp and performed more poorly overall compared to NucleoSpin cfDNA XS, which showed significantly higher recovery rates.

Better PCR  

Better PCR performance than a competitor midiprep kit

PCR amplification of a 165-bp fragment of the k-ras gene (often involved in cancer) was used to compare DNA purified from rat plasma using NucleoSpin cfDNA XS with DNA purified from a larger volume of the same plasma sample using a kit from Competitor Q (Figure 6). The NucleoSpin cfDNA XS kit displayed significantly better performance than the Competitor Q kit, as demonstrated by a PCR signal that was detectable 2.1 cycles earlier, even though the PCR input was 2.7-fold greater for the Competitor Q kit.

Better PCR performance with smaller plasma volumes

Figure 6. NucleoSpin cfDNA XS provides better PCR performance using smaller volumes of plasma than a competitor midiprep kit. DNA was purified from plasma samples derived from rat EDTA blood using either NucleoSpin cfDNA XS (formerly known as NucleoSpin Plasma XS) using 240 µl of starting material or a kit from Competitor Q using 1,000 µl of starting material, and analyzed using PCR amplification of a 165-bp fragment of the k-ras gene. The NucleoSpin cfDNA XS sample was purified according to the user manual (high sensitivity protocol), and eluted in a volume of 20 µl, 2 µl of which were used for PCR. The Competitor Q sample was purified according to the user manual, with the following modification: 100 µl of elution buffer was preheated to 56°C and incubated on the membrane for 5 min prior to elution. The elution fraction was concentrated to 30 µl, 2 µl of which were used for PCR. Although the PCR input was 2.7-fold greater for the Competitor Q kit, a PCR signal was detectable 2.1 cycles earlier for the NucleoSpin cfDNA XS kit. Data kindly provided by Dolores C. García Olmo, PhD, Unidad de Investigación del Complejo Hospitalario Universitario de Albacete, Albacete, Spain.

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