Magnetic bead-based DNA and RNA purification is technically straightforward but performance-sensitive. Yield, purity, and downstream compatibility depend on the accuracy and precision of pipetting throughout each liquid handling step. The Myra liquid handler automates the extraction workflow across a growing range of sample types, including whole blood, clinical swabs, tissue, plant material, and environmental specimens.
NUCLEIC ACID EXTRACTION
Automated Nucleic Acid Extraction
OVERVIEW
Myra is an automated nucleic acid extraction and liquid handling system designed to perform the critical pipetting, mixing, magnetic bead handling, and transfer steps involved in DNA and RNA purification.
THE CHALLENGE
Why bead-based extraction is harder to automate reliably than it appears
Magnetic bead extraction workflows look deceptively simple on paper: bind, wash, elute. In practice, the steps that determine yield and purity are the ones most sensitive to how liquid handling is executed, and the failure modes differ depending on whether you are working manually or on an automated platform.
Manual workflows suffer from the well-documented sources of operator variability: inconsistent bead resuspension before binding, incomplete supernatant removal during wash steps, and elution volume imprecision that compounds across a full plate of samples. These manifest as sample-to-sample variability in A260/A280 ratios, Cq scatter in downstream qPCR, and coverage non-uniformity in sequencing data.
Automated workflows introduce a different and less obvious failure mode specific to robotic liquid handling: bead loss during supernatant aspiration. When a pipette tip seals against the base of a well or tube during aspiration, negative pressure builds within the tip. When the tip finally releases from the base, either by retracting or completing the aspirate, the pressure differential creates a brief but significant fluidic suction event. This suction can physically pull beads from the pellet into the tip, removing them from the extraction and reducing nucleic acid yield. The event is silent, nothing flags it as an error, and the yield loss is attributed to protocol variability rather than the mechanical event that caused it.
Myra addresses bead loss at the mechanical level.
Dynamic Retract detects tip sealing against the well base during aspiration and retracts the tip incrementally before negative pressure has the opportunity to build to the point of causing fluidic suction. By breaking the seal progressively rather than suddenly, the pressure differential that drives bead loss is avoided, protecting pellet integrity throughout washing and supernatant removal steps.
Myra's niche in extraction automation.
Processing up to 48 samples per run using the 96-well magnetic station, the Myra automated liquid handling system occupies a well-defined position in the extraction automation landscape, delivering research-grade extraction quality in a compact, accessible platform without the capital cost, dedicated floorspace, and specialist maintenance overhead of large robotic systems. For medium and smaller labs where full-scale robotics is neither practical nor economically justified, the Myra portable liquid handler provides a credible automated alternative to manual extraction that does not require compromising on sample quality or throughput for typical batch sizes.
SAMPLE TYPES
Extraction across the full range of sample inputs
Magnetic bead chemistry is adaptable across sample types, but each input presents different challenges for liquid handling. Viscosity, inhibitor load, cell density, and fragment fragility all affect how the extraction protocol needs to be executed. Pressure-based liquid level sensing, intelligent mixing, and swab-aware aspiration make Myra well suited to the broad range of sample types encountered in research and applied laboratory settings.
Whole blood
A high-viscosity sample requires precise aspiration to keep blood within the tip and prevent deck contamination. Validated with SwiftX™ technology, it is compatible with EDTA, citrate, and heparin anticoagulated samples.
Swabs in VTM
Oropharyngeal, nasopharyngeal, and other swab types in viral transport medium. Myra’s swab-aware aspiration detects and avoids Rhinoswab and Flocked swab bodies, aspirating from clear areas of the tube without collision.
Tissue and FFPE
Post-lysis supernatant from homogenised fresh-frozen or formalin-fixed paraffin-embedded tissue. High inhibitor loads from FFPE processing require thorough wash steps. Consistent execution is critical for PCR-compatible eluates.
Plant material
Polyphenol and polysaccharide co-purification is the primary challenge for plant DNA extraction. Consistent binding and wash execution improves inhibitor removal for downstream PCR and sequencing applications.
Cultured cells
Cell pellets from mammalian, bacterial, or yeast culture. Consistent lysis buffer addition and mixing are the primary variables Myra controls for yield and fragment integrity.
Environmental samples
Soil, water, and air filter eluates for environmental DNA (eDNA) and microbial community profiling. High inhibitor loads and variable input concentrations benefit from consistent automated handling before 16S amplification or metagenomic sequencing.
Food and feed
Homogenised food matrices are used for GMO screening, allergen detection, and microbial contamination testing. Consistent DNA extraction is a prerequisite for reliable qPCR quantification against certified reference materials.
Serum and plasma
Cell-free DNA and viral RNA extraction for liquid biopsy, oncology research, and viral load quantification. Low input concentrations require precise low-volume handling throughout the extraction workflow.
WORKFLOW
How Myra automates the magnetic bead extraction workflow
The automated nucleic acid extraction workflow follows the same core structure across sample types and extraction kits: lysis, binding, washing, and elution. Myra handles all liquid transfers, mixing, and magnetic bead management on-deck, with a single off-deck heating step where required by the protocol chemistry.
Step 1. Sample lysis
Chemical or thermal lysis to release nucleic acids from the sample matrix. For protocols requiring heat lysis (e.g. 95°C incubation), lysis is performed off-deck on a thermal block or heat cycler. Lysis buffer addition and mixing are performed by Myra before transfer. Custom Simple Prep and Independent Prep modes support on-deck lysis buffer dispensing for liquid-based lysis workflows.
Step 2. Binding (bead and sample mixing)
Paramagnetic bead suspension dispensed into sample wells. Myra’s intelligent mixing ensures complete bead resuspension and homogeneous contact between beads and sample before magnetic capture. Thorough resuspension at this step is the primary determinant of binding efficiency. Settled or clumped beads reduce the available surface area for capture and directly reduce yield.
Step 3. Myra magnetic separation and supernatant removal
96-well magnetic station engages to capture beads against the well wall. Supernatant is aspirated to very low residual volumes. MyraSense pressure sensing detects liquid at levels below the dead volume of wells and tubes, maximising the volume of supernatant removed, while the Dynamic Retract prevents the tip from sealing against the well base. Tip sealing during aspiration creates negative pressure that, on sudden release, produces a fluidic suction event capable of pulling beads from the pellet. Dynamic Retract breaks any developing seal incrementally before this pressure differential builds.
Step 4. Wash steps
Sequential wash buffer additions with full bead resuspension occur between each step. Consistent wash buffer volumes and mixing execution across all wells removes residual proteins, salts, and PCR inhibitors. The same Dynamic Retract protection applies during each wash supernatant removal step. Bead loss risk is not limited to the initial separation but recurs at every aspiration over the pellet.
Step 5. Air-dry
A controlled air-dry period follows the final wash to eliminate residual ethanol before elution. Timing is scripted and consistent across all wells. Over-drying reduces elution efficiency by increasing bead aggregation. Under-drying carries ethanol into the eluate, inhibiting downstream polymerase activity.
Step 6. Elution
Elution buffer is dispensed onto dried beads and magnets released. Bead resuspension and incubation at ambient or elevated temperature (protocol-dependent) followed by magnetic recapture. Purified nucleic acid aspirated and transferred to a clean output plate or tubes. Dynamic Retract remains active throughout elution. At these small volumes, tip sealing is most likely, and the consequences for yield are most direct.
Step 7. QC and downstream analysis
Eluate quality assessed by NanoDrop (A260/A280, A260/A230), Qubit fluorometry, or capillary electrophoresis (DIN by TapeStation). Myra sets up qPCR reactions for downstream amplification, including full integration with the Mic cycler and export to QuantStudio, CFX, Rotor-Gene Q, and Qiagen 384-well platforms.
KEY CAPABILITIES
What makes Myra suited to nucleic acid extraction workflows
96-well magnetic station
Integrated automated magnet control for bead capture and release across up to 48 samples per run. Consistent magnet engagement timing eliminates the variable bead separation that manual handling introduces between samples in a plate.
Pressure-based liquid level sensing
MyraSense detects liquid levels below the dead volume of wells and tubes, maximising supernatant removal during wash steps and confirming the completeness of eluate transfer during elution. It does so without relying on programmed height offsets that may not reflect actual liquid levels.
Dynamic Retract
Detects tip sealing against the well base during aspiration and retracts incrementally before negative pressure builds. Prevents the fluidic suction event on tip release that pulls beads from the pellet into the tip, protecting yield at every supernatant removal and elution step throughout the workflow.
Intelligent mixing
Vortex, advanced, and simple mixing strategies selected automatically by volume and labware. Ensures complete bead resuspension at binding and wash steps, the most direct determinant of binding efficiency and inhibitor removal effectiveness.
Non-contact dispensing
Wash and elution buffer are dispensed without tip contact, protecting pellet integrity during buffer addition and reducing cross-contamination risk between adjacent wells in high-density plates.
Swab-aware aspiration
Collision detection and repositioning for Rhinoswab and Flocked swab types in VTM. The pipette head oscillates to detect swab position and aspirates from a clear area of the tube, directly relevant to diagnostic respiratory sample processing workflows.
VALIDATED SCRIPTS
Extraction scripts for Myra
| Kit | Verified By |
|---|---|
 attomol® Attosorb 3×96 | Community |
| QIAGEN MagAttract HMW DNA Tissue Extraction Protocol | Community |
| Medicinal Genomics MaGiC™ Lysis Kit | Community |
| sbeadex™ Lightning Nucleic Acid Purification Kit | Community |
| MagSi-DNA Plant CLS | BMSCommunity |
| SwiftX™ DNA Extraction (Blood Samples) | BMS |
CASE STUDY
SwiftX™ DNA extraction from whole blood is 50% faster than manual and competitor methods
BMS application development, the Xpedite Diagnostics SwiftX™ technology is validated on Myra
TECHNOLOGY
SwiftX™ reverse purification is a different approach to inhibitor removal
Conventional magnetic bead DNA extraction captures nucleic acids onto bead surfaces and washes away contaminants. SwiftX™ by Xpedite Diagnostics inverts this logic using paramagnetic beads with broad binding affinity to capture cells and proteins, rather than DNA, actively removing inhibitors and cell debris while the nucleic acid remains in solution. Cell lysis is then performed by heat at 95°C in the presence of a lysis buffer, releasing DNA directly into the eluate without an adsorption-desorption cycle.
This reverse purification approach simplifies the bead handling steps and reduces the number of wash cycles required. This makes it well-suited for automation on Myra, where the 96-well magnetic station manages bead capture and the single off-deck step is the heat lysis incubation.
EXPERIMENTAL SETUP
Whole blood DNA extraction compared to manual and competitor methods
Whole blood was collected into 6 mL BD Vacutainer® K2 EDTA tubes and aliquoted into 2 mL screw-cap tubes. Extraction was performed in parallel using three methods: SwiftX™ on Myra, a competitor magnetic bead extraction kit prepared manually, and a manual preparation using the same SwiftX™ reagents. Eluate quality was assessed by qPCR targeting the human RNaseP reference gene, and by allelic discrimination genotyping of the HIF-1α sports performance gene. The reaction setup for both assays was performed on Myra; amplification was run on the Mic qPCR Cycler.
The SwiftX™ protocol uses 100 µL Buffer EN, 30 µL paramagnetic beads A, and 50 µL whole blood per reaction in a 200 µL PCR tube. Following bead binding and magnetic capture, two wash steps with Buffer EN remove impurities. After a 1-minute air-dry, Buffer DL is added, and samples are heat-lysed at 95°C for 5 minutes off-deck. Beads are recaptured, and 40 µL purified DNA are eluted into new tubes.
RESULTS
Extraction quality on par with competitor, with significantly faster processing
Myra generated consistent dilution series for both assay formats. Replicate MIC plates showed well-defined growth inhibition patterns with clear endpoints, and checkerboard matrices produced interpretable FICI gradients across the full concentration range. Operator-to-operator variability (a persistent challenge in manual AST at scale) was substantially reduced compared to equivalent manual preparation.
50%
Faster than manual and competitor methods
RNaseP
Successful amplification confirms eluate quality
HIF-1α
Allelic discrimination genotyping from Myra eluates
Cq values for RNaseP were comparable across all three methods, confirming that SwiftX™ on Myra produces eluates of equivalent quality to those from manual competitor extraction. Myra’s automated protocol extracted samples approximately 50% faster than both the competitor and manual SwiftX™ methods.
Eluates prepared on Myra successfully resolved heterozygous CT genotypes in the HIF-1α allelic discrimination assay, confirming compatibility with allele-specific PCR chemistries in addition to standard amplification.
Myra’s pipette aspiration maintained whole blood within the tip throughout the protocol, preventing deck contamination, an important practical consideration for high-viscosity biological samples processed in an open-deck liquid-handling environment.
“SwiftX DNA on the Myra enables fast, plug-and-play DNA extraction without the need to study complex operating manuals beforehand.”
Dr Stéphen Hennart – Xpedite Diagnostics, Hallbergmoos, Germany
More Case Studies
Automating plant DNA extraction with MagSi-DNA Plant CLS
A magnetic bead-based workflow for consitent DNA purification from plant seeds using MagiSi-DNA Plant CLS and automated liquid handling.
Medicinal Genomics MaGiCTM Lysis on Myra
Medicinal Genomics partnered with Bio Molecular Systems to simplify, accelerate, and consolidate qPCR testing for Cannibis and Hemp Microbial Contamination, Plant Pathogens, and Matural Products.
DOWNSTREAM INTEGRATION
Extraction as the first step in a broader automated workflow
Nucleic acid extraction is the upstream step that determines the quality of everything that follows. The broader benefits of automated liquid handling include reduced manual intervention, more consistent execution, and a smoother transition between extraction and downstream analysis. Myra connects extraction directly with applications such as quantification, amplification, and sequencing preparation, allowing multiple stages of the process to be completed on a single platform.
qPCR setup
Eluates loaded directly as sample inputs. Reaction plates exported to Mic, QuantStudio, CFX, Rotor-Gene Q, or Qiagen 384-well.
NGS library preparation
Extracted gDNA or total RNA used as input for library prep across Illumina, ONT, and PacBio platforms.
Bead cleanup
SPRI-based fragment purification and size selection are performed following library prep or PCR amplification from the extracted template.
Normalization and pooling
Post-quantification molar normalization, equimolar pooling, and Illumina loading preparation on the same platform.
Frequently Asked Questions
How does Dynamic Retract prevent bead loss during automated extraction?
When a pipette tip seals against the base of a well during aspiration, negative pressure builds within the tip. When the tip releases (by retracting or completing the aspirate), the pressure differential between the tip interior and the surrounding liquid creates a brief fluidic suction event. This suction can pull beads from the pellet into the tip, removing them from the extraction and reducing nucleic acid yield without generating any error or flag. Dynamic Retract addresses this issue by monitoring tip pressure during aspiration and detecting the resistance signature of tip sealing. It then retracts the tip incrementally, just a small distance at a time, rechecking pressure after each increment until free flow is confirmed before completing the aspirate. This breaks the seal gradually rather than suddenly, preventing the pressure differential from reaching the level required to cause fluidic suction and bead loss.
How many samples can Myra process per extraction run?
Up to 48 samples per run using the 96-well magnetic station. This positions Myra for the medium and smaller batch sizes typical of research and applied diagnostic laboratories, delivering the consistency and reproducibility expected from automated extraction workflows without the capital cost, floor space, or specialist maintenance requirements of many larger robotic platforms.
What sample types can Myra handle for nucleic acid extraction?
Validated scripts currently cover whole blood (SwiftX™) and VTM swab samples (QIAGEN QIAprep& Viral RNA UM Kit). Scripts in development cover tissue and FFPE, plant material, additional blood and plasma workflows including cell-free DNA, environmental samples, and total RNA from cells and tissue. Custom extraction protocols for additional sample types can be implemented using Python-based MyraScripts with the Independent Prep configuration.
How does Myra handle high-viscosity samples like whole blood?
MyraSense pressure-based sensing monitors the aspiration of viscous samples in real time, adjusting for the higher resistance of high-viscosity liquids and ensuring that the sample is fully drawn into the tip rather than being partially aspirated. In the SwiftX™ validation, automated whole blood handling maintained blood within the tip throughout the protocol, with no deck contamination events observed.
What is SwiftX™ technology and how does it differ from standard magnetic bead extraction?
SwiftX™ by Xpedite Diagnostics uses a reverse purification approach. Paramagnetic beads capture cells and proteins rather than nucleic acids, actively removing inhibitors and cell debris while DNA remains in solution. Heat lysis at 95°C then releases DNA directly into the eluate without an adsorption-desorption cycle. This simplifies bead handling steps and reduces wash cycle requirements. In BMS validation, SwiftX™ on Myra produced RNaseP Cq values comparable to a competitor extraction kit while processing samples approximately 50% faster.
Can Myra perform both extraction and downstream qPCR setup in a single workflow?
Yes. Following extraction and elution, Myra loads eluates directly as sample inputs into qPCR reaction setup, setting up plates for the Mic cycler or exporting layouts to QuantStudio, CFX, Rotor-Gene Q, or Qiagen 384-well instruments. This was demonstrated in the SwiftX™ validation, where reaction setup for both RNaseP qPCR and HIF-1α allelic discrimination was performed on Myra immediately following extraction.
Does Myra support RNA extraction as well as DNA?
Yes. The QIAGEN QIAprep and Viral RNA UM Kit is validated for viral RNA extraction from VTM samples. Additional RNA extraction scripts for total RNA from cells and tissue are in development. For RNA workflows, consistent non-contact dispensing and complete supernatant removal are particularly important. Carry-over RNases from incompletely removed wash buffer can degrade RNA yield during the elution step.
Automate your nucleic acid extraction workflow on Myra
Every laboratory has different sample types, extraction chemistries, and downstream applications.
To determine whether Myra is the right automated nucleic acid extraction instrument for your sample types, extraction chemistry, and downstream applications, request a demo or submit an enquiry to discuss your protocol with the Bio Molecular Systems team.
You can also browse Myra’s applications to learn more about the workflows already supported, or explore Myra by Bio Molecular Systems for a broader overview of the platform and its capabilities.