References
for correlation with normalized photocurrent densities. As shown in Figure 5D, a
positive correlation was observed using the C-LAMP/1O2-driven PEC platform in the analysis
of FFT samples, indicating that PEC output reflects allelic burden across clinically relevant
VAF ranges (approximately 5-40% in the evaluated cohort). Notably, FFT samples with VAF
values as low as 5-20% were distinguishable from WT tissues.
ROC analysis was performed to evaluate diagnostic classification performance. Within the
evaluated cohort (n = 16), complete discrimination was achieved between WT and mutant FFT
samples, offering a cut -off value of 1.23 nA mm -2 (Figure 5E). While larger clinical studies
are required to establish definitive diagnostic performance metrics, these preliminary results
demonstrate full concordance with gold-standard ddPCR in the analyzed samples and support
the translational potential of the C -LAMP/1O2-driven PEC platform for decentralized KRAS
mutation analysis.
Figure 5. Clinical validation of the C -LAMP/1O2-driven PEC platform in FFT samples. (A) Agarose
gel electrophoresis of C-LAMP products obtained from representative WT controls (FFT-2 and FFT-8)
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and KRAS-mutant patients carrying G12C (FFT-11) and G12V (FFT-15). M: 100-1,000 bp DNA ladder.
(B) Photocurrent densities obtained with b-CPs specific for WT (orange), G12C (turquoise) and G12V
(dark blue), confirming genotype -specific detection depending on probe complementarity. (C)
Comparison of conventional LAMP and C-LAMP in a representative WT sample (FFT-5), confirming
efficient WT suppression upon inclusion of LNA clamp probes during amplification. Error bars
represent the standard deviation of the mean (n = 3). (D) Correlation between normalized photocurrent
densities and VAF values determined by ddPCR. (E) ROC analysis for discrimination between WT and
mutant FFT samples with ROC-defined threshold (*Cut-off) enabling complete separation of WT and
mutant samples within the evaluated cohort (n = 16).
3. Discussion
Recent advances in pan-KRAS inhibitors underscore the growing importance of comprehensive
KRAS genotyping in clinical oncology (Choate et al. 2024), highlighting the need for analytical
platforms capable of selectively identifying activating mutations within heterogeneous DNA
backgrounds. While NGS and ddPCR remain reference standards for KRAS mutation analysis,
their implementation in decentralized or resource -limited settings is constrained by
instrumentation requirements, workflow complexity and the need for specialized infrastructure.
Recent (photo)electrochemical approaches, frequently coupled with isothermal amplification,
have been explored for KRAS mutation detection (Table S3) . Although these approaches
demonstrate notable analytical sensitivity, many rely on enzymatic reporters, involve complex
or time-consuming workflows and, critically, lack validation in patient -derived samples. Most
LAMP-based KRAS assays employ fluorescent or colorimetric readouts combined with PNA -
modified primers or ligation -based designs (Fu et al. 2019; Islam et al. 2025; Itonaga et al.
2016; Mirlohi et al. 2024). Because mutant alleles may constitute only a small fraction of total
DNA, simultaneous enrichment of mutant sequences and suppression of WT amplification are
essential to achieve robust discrimination. While PNA clamps offer strong binding affinity and
mismatch discrimination, their synthesis cost and solubility limitations can complicate routine
implementation(Ondraskova et al. 2023). Moreover, optical detection systems remain relatively
costly and less compatible with decentralized testing than (photo)electrochemical readouts. In
contrast, the present approach introduces a practical alternative based on commercially
available, water -soluble LNA -modified oligonucleotides that act both as allele -specific
blockers during amplification and as capture probes for SNV recognition in the PEC
transduction stage, thereby providing a scalable and clinically relevant route toward
decentralized testing.
C-LAMP effectively mitigates WT interference, which has historically limited the selectivity
of isothermal amplification methods. The dual implementation of LNA chemistry constitutes a
key molecular design feature underlying the platform’s specificity. In the amplification stage,
LNA incorporation within the clamp probes increases duplex stability and mismatch
discrimination, enabling complete WT suppression under isothermal conditions. In the PEC
transduction stage, LNA substitutions in the capture probes enhance hybridization affinity
toward mutant amplicons while minimizing off -target binding. Nevertheless, limited cross -
reactivity between closely related variants (e.g., G12C and G12V) was observed, consistent
with the high sequence homology (>93%) shared among b -CPs and the inherent
thermodynamic constraints of single -mismatch discrimination under isothermal conditions.
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Importantly, such partial cross -reactivity did not result in false -positive classification of WT
samples and therefore does not compromise mutant-versus-WT discrimination, which
represents the primary clinical requirement for diagnosis and many therapeutic decision
pathways.
The enzyme-free 1O2-driven PEC readout further contributes to assay robustness by avoiding
enzymatic reporters such as horseradish peroxidase (HRP), which require external substrates to
generate electrochemical signals and controlled storage conditions. Photosensitizers such as
Ce6 generate 1O2 directly under visible -light excitation, promoting HQ/BQ redox cycling
without enzymatic intermediates. This photochemical transduction simplifies reagent handling,
eliminates instability associated with enzyme stora ge and reduces per -test cost, key
considerations for decentralized implementations.
Comparison with state-of-the-art diagnostic methods (Table S4) highlights the complementary
positioning of the C -LAMP/¹O₂-driven PEC platform. Whereas ddPCR and NGS provide
absolute quantification and base -level sequence resolution, the proposed system offers a
simplified hardware configuration requiring a constant -temperature heater, a low -power light
source and a portable potentiostat. With total amplification and detection times close to one
hour, the workflow may serve as a rapid screening or triage tool in molecular oncology settings.
Importantly, the positive correlation between photocurrents and VAF values in both cell lines
and patient-derived samples indicates that PEC output reflects mutation burden, enabling semi-
quantitative assessment without sequencing. Moreover, although the clinical dataset is limited
(n = 16), the absence of misclassification within this cohort suggests high discriminative
capability for potential adoption in decentralized testings.
Regarding potential interference effects from complex biological matrices, it is important to
note that the majority of experiments were conducted using purified gDNA extracted from
clinically characterized samples. Such DNA extracts reflect standard diagnostic workflows and
avoid reliance on synthetic constructs, thereby providing a clinically relevant evaluation
environment. The successful discrimination of KRAS mutation status under these conditions
supports the practical applicability of the proposed as say within routine genomic testing
frameworks.
Several aspects warrant further refinement. Hybridization kinetics between C-LAMP products
and capture probes could be optimized to shorten assay time, and expansion to additional KRAS
variants (e.g., G12D, G13D) will require probe design and validation. Although partial cross -
reactivity was observed between certain codon 12 variants, activating KRAS mutations are
typically mutually exclusive within individual tumors, reducing the likelihood of
misclassification in routine screening contexts. Nevertheless, applications requiring strict
mutation-specific stratification (e.g., allele -targeted inhibitor selection) would benefit from
further probe optimization to enhance discrimination stringency.
Finally, while the present study relies on pre -extracted gDNA in accordance with standard
molecular diagnostic workflows (such as ddPCR), integration with simplified sample -
preparation modules or microfluidic cartridges may further streamline the assay arc hitecture.
Larger clinical validation studies will be necessary to establish definitive diagnostic
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13
performance metrics. Within the evaluated cohort, however, full concordance with ddPCR was
achieved, supporting the translational potential of this C-LAMP/PEC platform.
Overall, the integration of clamp -mediated isothermal amplification with enzyme -free 1O2-
driven PEC detection establishes a stable and analytically robust biosensing framework. By
merging molecular selectivity with light -driven electrochemical transduction, this approach
provides a versatile strategy for mutation detection that may be extende d to other actionable
oncogenic variants and nucleic-acid biomarkers.
4. Experimental/methods section
4.1 Instrumentation and electrode configuration
1O2-driven PEC measurements were performed at room temperature using a PalmSens4
potentiostat operated with PSTrace 5.9 software (PalmSens, The Netherlands). Screen -printed
carbon electrodes (DRP-110, ф = 0.4 cm) served as transducers and were connected through a
DSC box connector (Metrohm DropSens, Spain). Illumination was provided by a 660 nm LED
integrated into a pE -4000 system (CoolLED, UK) synchronized with the potentiostat via the
digital I/O lines of PSTrace. The LED power (30 mW) was calibrated using a PM100D optical
power meter (Thorlabs, USA). Real -time C -LAMP experiments were conducted on the
QuantStudio 5 device with direct analysis by the QuantStudio software (Thermo Fisher
Scientific, USA).
4.2 Oligonucleotide design and sequences
The complete list of oligonucleotide sequences and terminal modifications is provided in Table
S4. LAMP primers (F3, B3, FIP and BIP) were designed using PrimerExplorer V.5 (Eiken
Chemical Co., Japan) and synthesized by Integrated DNA Technologies (USA). LNA-modified
clamp probes (CL1 and CL2) and capture probes (a -CPs and b-CPs), were obtained from t he
same supplier. DPs were synthesized and purified by reverse -phase HPLC, and subsequently
labelled with Ce6 as the photosensitizer (Eurogentec, Belgium). All oligonucleotides were
dissolved in nuclease-free PCR-grade water (VWR, Avantor®, USA) and stored at -20 °C until
use.
The initial C-LAMP primer set was designed to amplify multiple KRAS SNVs without targeting
a specific mutation, with downstream discrimination achieved through hybridization with
mutation-specific capture probes. However, this design exhibited reduced amplification
efficiency for WT templates, primarily due to the backwar d inner primer (BIP.V2; Table S4).
To address this limitation, alternative BIP sequences (BIP and BIP.V3) were designed to anneal
closer to the mutation hotspot. The original primer contain ed only a single guanine overlap at
the KRAS mutation site, whereas the new sequences spanned both codons, either with
(GGTGGCG) or without (GGTGGC) additional nucleotides. The most consistent performance
was obtained with the latter design, in which the BIP primer hybridized across both codons
without consecutive mismatches. This optimized sequence (BIP) was selected for the final C -
LAMP protocol.
4.3 Cancer cell lines
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Cancer cell lines used as models for KRAS mutation detection are listed in Table S1 . The
selected cell lines were chosen to represent homozygous (WT and mutant) and heterozygous
KRAS mutation backgrounds, enabling systematic evaluation of WT suppression and mutation-
specific amplification across different allelic compositions. HT -29 and A2780 (WT/WT),
SW837 (G12C/WT) and SW620 (G12V/G12V) were cultured in Dulbecco’s Modified Eagle’s
Medium (DMEM) supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and
1% sodium pyruvate under standard conditions (37 °C, 5% CO 2 and 100% humidity). Cells
were collected by scraping, centrifuged (1,500 rpm, 5 min) and the resulting pellets stored at -
80 °C until use. gDNA was extracted using the Tissue DNA Preparation Column Kit (Jena
Bioscience, Germany) according to the manufacturer’s protocol. DNA purity was assessed by
NanoDrop UV -Vis spectrophotometry (Thermo Fisher Scientific, USA) an d concentrations
were determined using a Qubit 4 fluorometer (Invitrogen, USA) with the dsDNA HS Assay
Kit.
KRAS amplicons were sequenced using the MinION platform (Oxford Nanopore Technologies,
UK) with primers listed in Table S4 (ddPCR Fwd and SEQ Rev). Amplicons were generated
with LongAmp ® Hot Start Taq 2X Master Mix (New England Biolabs, USA), purified with
AMPure XP magnetic beads (Beckman Coulter, USA) and barcoded using the Rapid Barcoding
Kit 14 (SQK -RBK114.24, Oxford Nanopore) following the manufacturer's instructions.
Libraries were cleaned with AMPure XP beads, quantified, pooled and loaded onto a MinION
flow cell (R10.4.1). Sequencing was performed using MinKNOW software; basecalling and
demultiplexing were conducted in Guppy (high -accuracy mode). Reads were aligned to the
KRAS reference sequence ((NCBI) 2025) using EPI2ME and IGV platforms. Nucleotide
substitutions detected at codons 12 and 13 matched the expected genotypes for each cell line
(Table S1).
Droplet digital PCR (ddPCR) was performed on SW620 gDNA using the QX200 AutoDG
system (Bio-Rad, USA) with KRAS-specific primers (Table S6). Each 22 µL reaction contained
1×QX200™ EvaGreen Supermix; 0.45 µM ddPCR Fwd and ddPCR Rev primers, PCR -grade
water, and 25, 50 or 100 ng of gDNA. Droplets were generated using the Automated Droplet
Generator and thermal cycling was conducted as follows: 94 °C for 10 min; 35 cycles of 94 °C
for 30 s; 62 °C for 30 s; 72 °C for 40 s; final extension at 72 °C for 10 min; ho ld at 4 °C.
Fluorescence was measured with the QX200 Droplet Reader and data were processed using
QuantaSoft 1.7.4.0917 software (Bio-Rad).
To determine the KRAS copy number in 100 ng of gDNA, copy numbers per microliter of
reaction mixture were multiplied by 22 (total reaction volume, 22 µL). The 25 ng and 50 ng
samples used to reduce bias caused by distribution of DNA into the droplets were normalized
to 100 ng of gDNA. The mean value across replicates corresponded to 5,666 KRAS copies per
100 ng of SW620 gDNA, which was used to construct the SW620 calibration curve and
estimate the LOD of the biosensing platform (Figure 3F).
4.4 Patient-derived tissues
All procedures involving human material were approved by the institutional ethics committee
of the University Hospital Antwerp (UZA/University of Antwerp, BUN B3002023000515) and
informed consent was obtained from all participants prior to sample collectio n. Biobank
Antwerp (ID: BE 71030031000) was also involved in this study. FFT samples, including tumor
type, percentage of neoplastic cells and VAF are summarized in Table S2. Hematoxylin–eosin
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(H&E)-stained sections were prepared from each specimen and examined by a pathologist to
confirm tumor content and estimate neoplastic-cell percentage.
gDNA was extracted from the remaining FFT material using the QIAamp DNA Mini Kit with
a QIAshredder column (Qiagen, Germany). Briefly, pre -chopped tissue was lysed in ATL/AL
buffer with Proteinase K, homogenized, incubated at 70 °C and clarified using QIAs hredder
columns. The lysates were combined with ethanol, transferred onto QIAamp Mini spin
columns, washed with AW1 and AW2 buffers, and eluted in nuclease -free water. DNA
concentration was quantified using a Qubit fluorometer (Thermo Fisher Scientific, USA).
KRAS mutation analysis was performed on a QX200 ddPCR system (Bio-Rad, USA). Each 20
µL reaction contained 10 µL 2× ddPCR ™ Supermix for Probes (no dUTP, Bio -Rad), 1 µL of
20× KRAS primer/probe mix (FAM + HEX, Bio-Rad), nuclease-free water and 50 fg-130 ng of
gDNA. Droplets were generated using the QX200 Automated Droplet Generator and amplified
in a Veriti™ thermal cycler (Applied Biosystems, USA) under the following conditions: 95 °C
for 10 min; 40 cycles of 94 °C for 30 s and 55 °C for 1 min; 98 °C for 10 min; hold at 4 °C.
End-point fluorescence was recorded using the QX200 Droplet Reader and data were analyzed
in multiplex mode with QuantaSoft™ software. While ddPCR allowed discrimination between
WT and mutant alleles, the specific KRAS subtype (e.g., G12C, G12V) was determined from
parallel NGS of matched FFPE tissue performed during routine clinical diagnostics. This
combined workflow ensured accurate confirmation of mutation status across the FFT cohort.
4.5 C-LAMP protocol
C-LAMP was performed in two sequential steps: selective suppression of WT alleles followed
by amplification of mutant alleles carrying SNVs. The optimized 10 µL reaction mixture
contained 100 ng of gDNA (10 ng µL-1); 0.6 µM each of clamp probes (CL1 and CL2); 0.2 µM
each of outer primers (F3 and B3); 1.6 µM each of inner primers (FIP and BIP); 1x LAMP
Master Mix (STM), and nuclease-free water.
In the first step, DNA templates were incubated with clamp probes at 40 °C for 10 min to
promote hybridization to WT regions, followed by rapid cooling on ice. In the second step,
LAMP primers and STM were added to the clamped DNA mixture, and amplificatio n was
performed at 62 °C for 35 min. Amplicons were verified by 1.5% agarose gel electrophoresis
(TBE buffer, GelRed ® staining) and subsequently used directly for 1O2-driven PEC
measurements or stored at -20 °C until use.
4.6 Real-time C-LAMP protocol
The Real time C-LAMP experiments were performed using a QuantStudio™ 5 Real-Time PCR
System (Applied Biosystems). The reaction mixture contained the same components as the
designed C-LAMP protocol, with the exception of the amplification master mix. Instead of the
conventional STM Master Mix (containing SYBR Green), an STM High-ROX Master Mix
(Jena Bioscience, Germany) was used. This formulation has identical amplification components
but includes ROX dye as a passive reference for fluorescence normalization.
Clamp pre-incubation was carried out for 10 min at three different temperatures (38, 40, and 42
°C) to evaluate thermal tolerance. Following pre -incubation, the DNA –clamp mixture was
transferred to qPCR tube strips and combined with the remaining reaction components. Real-
time amplification was performed at 62 °C using 30 s acquisition intervals, with fluorescence
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16
recorded at the end of each segment for a total of 70 cycles (35 min). Cycle threshold (Ct)
values were automatically calculated using QuantStudio™ Design and Analysis Software with
default baseline and threshold settings.
4.7 Preparation of the 1O2-driven PEC platform
A 5 µL aliquot of Strep -MBs was washed twice with 200 µL of hybridization buffer on a
magnetic rack (2 min per wash). Beads were then incubated with 100 µL of 100 nM b -CP
solution in hybridization buffer for 10 min at 25 °C under constant agitation (950 rp m). After
two additional washes, functionalized Strep -MBs were hybridized with denatured C -LAMP
products. The amplicons were denatured at 95 °C for 10 min and rapidly cooled on ice before
use. For hybridization, 95 µL of 50 nM DP solution was mixed with 5 µL of denatured C -
LAMP products and incubated with the Strep -MB/b-CP complexes at 40 °C for 15 min with
shaking (950 rpm). The resulting biofunctionalized beads were washed twice with 200 µL of
measuring solution and resuspended for 1O2-driven PEC analysis.
For electrode assembly, 100 µL of 1 mM HQ in measuring solution was deposited onto a
screen-printed carbon electrode, covering the three -electrode system. Biofunctionalized beads
were resuspended in 10 µL of the HQ droplet, transferred onto the electrode s urface and
magnetically captured at the working electrode using a neodymium magnet positioned beneath
the screen -printed electrode. PEC measurements followed the 1O2-mediated detection
strategy(Daems et al. 2024; Shanmugam et al. 2024; Stratulat et al. 2025; Trashin et al. 2017) .
A potential of -0.20 V was applied to the Ag pseudo -reference electrode to reduce BQ to HQ
under a light cycle of 60 s dark, 10 s illumination and 30 s dark; completing total measurement
times below two minutes.
Further details on instrumentation, magnetic microbeads, reagents, and statistical analyses are
provided in the Supplementary Information.
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