Direct plasmonic detection of circulating RAS mutated DNA in colorectal cancer patients

D’Agata, Roberta; Bellassai, Noemi; Allegretti, Matteo; Rozzi, Andrea; Korom, Saša; Manicardi, Alex; Melucci, Elisa; Pescarmona, Edoardo; Corradini, Roberto; Giacomini, Patrizio; Spoto, Giuseppe

doi:10.1016/j.bios.2020.112648

Cited by 27 publications

(19 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… 56 A PNA surface coverage of 3 × 10 12 molecules cm –2 has been shown to allow ultrasensitive nanoparticle-enhanced SPRI detection of the DNA target. 15 …”

Section: Resultsmentioning

confidence: 99%

“…PNA selectivity and cross-reactivity in the PBS buffer have been already tested for similar systems, as reported elsewhere. 15 The use of PNA clamp sequences and the fine-tuning of the assay temperature may be evaluated to improve the discrimination between AuNP@KRAS enhanced signals.…”

Section: Resultsmentioning

confidence: 99%

“…The new platform also introduces substantial improvements compared to the recently introduced nanoparticle-enhanced SPRI assay for detecting ctDNA in plasma samples. 15 The preanalytical processing of the plasma sample no longer involves the 1.5 h lasting treatment of plasma samples with proteinase K, and the SPRI sensor surface is not treated with dithiothreitol or other blocking additives after the plasma adsorption as a consequence of the surface fouling resistance introduced by PLL-mal(26%)-PNA-CEEEEE.…”

Section: Resultsmentioning

confidence: 99%

“…The AuNP dispersion was passivated with poly(vinylpyrrolidone) (PVP) as previously reported 15 and modified with streptavidin (SA) and then with a biotinylated oligonucleotide sequence (DNA sequence: 5′-CAAGTTTATATTCAGTCAT-3′). Briefly, 500 μL of citrate-stabilized AuNPs (5 nM in water) was added to 500 μL of PVP (50 μM in water).…”

Section: Experimental Sectionmentioning

confidence: 99%

See 3 more Smart Citations

Detection of Tumor DNA in Human Plasma with a Functional PLL-Based Surface Layer and Plasmonic Biosensing

et al. 2021

Self Cite

View full text Add to dashboard Cite

Standard protocols for the analysis of circulating tumor DNA (ctDNA) include the isolation of DNA from the patient’s plasma and its amplification and analysis in buffered solutions. The application of such protocols is hampered by several factors, including the complexity and time-constrained preanalytical procedures, risks for sample contamination, extended analysis time, and assay costs. A recently introduced nanoparticle-enhanced surface plasmon resonance imaging-based assay has been shown to simplify procedures for the direct detection of tumor DNA in the patient’s plasma, greatly simplifying the cumbersome preanalytical phase. To further simplify the protocol, a new dual-functional low-fouling poly- l -lysine (PLL)-based surface layer has been introduced that is described herein. The new PLL-based layer includes a densely immobilized CEEEEE oligopeptide to create a charge-balanced system preventing the nonspecific adsorption of plasma components on the sensor surface. The layer also comprises sparsely attached peptide nucleic acid probes complementary to the sequence of circulating DNA, e.g., the analyte that has to be captured in the plasma from cancer patients. We thoroughly investigated the contribution of each component of the dual-functional polymer to the antifouling properties of the surface layer. The low-fouling property of the new surface layer allowed us to detect wild-type and KRAS p.G12D-mutated DNA in human plasma at the attomolar level (∼2.5 aM) and KRAS p.G13D-mutated tumor DNA in liquid biopsy from a cancer patient with almost no preanalytical treatment of the patient’s plasma, no need to isolate DNA from plasma, and without PCR amplification of the target sequence.

show abstract

“… 56 A PNA surface coverage of 3 × 10 12 molecules cm –2 has been shown to allow ultrasensitive nanoparticle-enhanced SPRI detection of the DNA target. 15 …”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Experimental Sectionmentioning

confidence: 99%

See 2 more Smart Citations

Detection of Tumor DNA in Human Plasma with a Functional PLL-Based Surface Layer and Plasmonic Biosensing

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…The minimization of the non-specific adsorption of biological fluids' components [101] on the surface of a biosensor improves sensitivity and selectivity of biosensing assays, thus allowing the detection of ultra-low-concentrated biomarkers in complex biofluids [102,103]. The ability to detect biomarkers directly in the biological fluids is a pre-requisite to developing challenging biosensing applications for clinical diagnostics [104][105][106]. With this perspective, surface plasmon resonance (SPR) has been used to detect human thrombin with a 3D DNA origami structure modified with an aptamer [107].…”

Section: Origami-based Structure Design and Mechanismsmentioning

confidence: 99%

Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

2021

Self Cite

View full text Add to dashboard Cite

Nucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami. Graphical abstract

show abstract

Engineering of a DNA/γPNA Hybrid Nanoreporter for ctDNA Mutation Detection via γPNA Urinalysis

Xiang,

Lu,

Ming

et al. 2024

Advanced Science

View full text Add to dashboard Cite

Detection of circulating tumor DNA (ctDNA) mutations, which are molecular biomarkers present in bodily fluids of cancer patients, can be applied for tumor diagnosis and prognosis monitoring. However, current profiling of ctDNA mutations relies primarily on polymerase chain reaction (PCR) and DNA sequencing and these techniques require preanalytical processing of blood samples, which are time‐consuming, expensive, and tedious procedures that increase the risk of sample contamination. To overcome these limitations, here the engineering of a DNA/γPNA (gamma peptide nucleic acid) hybrid nanoreporter is disclosed for ctDNA biosensing via in situ profiling and recording of tumor‐specific DNA mutations. The low tolerance of γPNA to single mismatch in base pairing with DNA allows highly selective recognition and recording of ctDNA mutations in peripheral blood. Owing to their remarkable biostability, the detached γPNA strands triggered by mutant ctDNA will be enriched in kidneys and cleared into urine for urinalysis. It is demonstrated that the nanoreporter has high specificity for ctDNA mutation in peripheral blood, and urinalysis of cleared γPNA can provide valuable information for tumor progression and prognosis evaluation. This work demonstrates the potential of the nanoreporter for urinary monitoring of tumor and patient prognosis through in situ biosensing of ctDNA mutations.

show abstract

Direct plasmonic detection of circulating RAS mutated DNA in colorectal cancer patients

Cited by 27 publications

References 51 publications

Detection of Tumor DNA in Human Plasma with a Functional PLL-Based Surface Layer and Plasmonic Biosensing

Detection of Tumor DNA in Human Plasma with a Functional PLL-Based Surface Layer and Plasmonic Biosensing

Novel nucleic acid origami structures and conventional molecular beacon–based platforms: a comparison in biosensing applications

Engineering of a DNA/γPNA Hybrid Nanoreporter for ctDNA Mutation Detection via γPNA Urinalysis

Contact Info

Product

Resources

About