The Nanopore-Tweezing-Based, Targeted Detection of Nucleobases on Short Functionalized Peptide-Nucleic Acid Sequences

Dragomir, Isabela; Asandei, Alina; Schiopu, Irina; Bucataru, Ioana C.; Mereuta, Loredana; Luchian, Tudor

doi:10.20944/preprints202103.0514.v1

Cited by 3 publications

(2 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, to reach these goals, a lot of optimization steps are required. Applications of AGPs will be further improved through the use of special dedicated software [174], detection of PNAs using nanopore platforms [175], and with rational improvements in reducing side effects such as hepatotoxicity [176]. Machine learning algorithms partially help alleviate this problem by predicting possible side effects of experimental drugs, however, a lot of work needs to be done in this direction [177][178][179] In terms of exciting perspectives that may open sometimes for oncological applications of AGPs, arming of oncolytic viruses with transgenes encoding AGP-synthesizing polymerases inside the cancer cells would be of great interest, since such an approach may greatly boost the action of cytotoxic drugs.…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Artificial genetic polymers against human pathologies

et al. 2022

View full text Add to dashboard Cite

Originally discovered by Nielsen in 1991, peptide nucleic acids and other artificial genetic polymers have gained a lot of interest from the scientific community. Due to their unique biophysical features these artificial hybrid polymers are now being employed in various areas of theranostics (therapy and diagnostics). The current review provides an overview of their structure, principles of rational design, and biophysical features as well as highlights the areas of their successful implementation in biology and biomedicine. Finally, the review discusses the areas of improvement that would allow their use as a new class of therapeutics in the future.

show abstract

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Artificial genetic polymers against human pathologies

et al. 2022

View full text Add to dashboard Cite

show abstract

“…Examples included the use of peptides with a negative glutamine or aspartic acid chain on the N-terminus and a positive arginine or lysine chain on the C-terminus. [117][118][119] The introduced dipole balanced the peptide at the centre of the nanopore near the sensitive region of the nanopore and differences between singular amino acid substitutions, containing either a neutral, hydrophobic or hydrophilic side chain, were determined. 120,121 It was also shown previously that such designed peptides allow the detection and localisation of post-translational modifications.…”

Section: Protein Detection Using Nanopore Spectrometrymentioning

confidence: 99%

Engineering nanopore sensors for proteomic and metabolomic analysis

Lucas¹

View full text Add to dashboard Cite

Single-molecule analysis is a new emerging field of science, allowing the detection of analytes on the smallest biologically-relevant scale. 28 Whereas most methods require an ensemble of molecules to interact with the detector, single-molecule techniques require theoretically only one.In recent years, single-molecule analysis has excelled in oligonucleotide sequencing, maturing into commercial products capable of sequencing long stretches of oligonucleotides. These techniques are collectively known as third-generation (DNA) sequencing, not to be confused with NGS which also includes second-generation sequencing techniques. At the time of writing, two third-generation methods have reached the stage of commercialisation, namely: zero-mode waveguided sequencing by synthesis, and nanopore based sequencing.The first technique, zero-mode waveguided sequencing by synthesis, utilises nanostructures smaller than the wavelength of light in order to reduce the detection volume to less than the diffraction limit of visible light. 29 A polymerase is immobilised in the nanostructure, which elongates single stranded DNA using fluorescently labelled nucleotides. 30 The nucleotides are added in 0.1 to 10 µM range, such that (on average) there is only a single nucleotide present in the sampling volume which is in the attoto zeptoliter range (10 -18 -10 -23 L). The nucleotides are excited using a laser, causing nucleotide emission which is optically detected. The time of emission is an indication of binding, as unbound nucleotides enter and exit the sampling volume more rapidly. The laser excitation is, however, the main limitation of the system, as this causes photo-oxidation of the polymerase, rendering it inactive over-time.Contrary to other sequencing techniques, nanopores provide a polymerase-and label-free platform.The principle working of nanopore based sequencing is similar to nanometer-sized Coulter counters.They allow the differentiation of nucleotides (and other molecules)-due to ion displacement-based on the size and interaction of the analyte with the nanopore and it's environment. 31 For the purpose of oligonucleotide sequencing, an ATP-dependent helicase (e.g. Phi29) is brought on top of a nanopore (e.g. an engineered α-hemolysin or Mycobacterium smegmatis porin A nanopore). 32 The nucleobases are fed through the pore using the helicase, controlling speed by ATP concentration, and the nucleobases are read as a decrease in ionic current. Nucleobases translocating through the nanopore are not measured one-by-one. At any given time, there will be several nucleobases excluding ionic current, such that a chain of nucleobases is measured. Sequencing is performed by re-constructing the most probable sequence of nucleotides causing the excluded current over time.Events•s -1 where β > 0 Events•s -1 where β > 1 Events•s -1 where β > 10

show abstract

Probing the Hepatitis B Virus E-Antigen with a Nanopore Sensor Based on Collisional Events Analysis

et al. 2022

View full text Add to dashboard Cite

Real-time monitoring, simple operation, and cheaper methods for detecting immunological proteins hold the potential for a solid influence on proteomics and human biology, as they can promote the onset of timely diagnoses and adequate treatment protocols. In this work we present an exploratory study suggesting the applicability of resistive-pulse sensing technology in conjunction with the α-hemolysin (α-HL) protein nanopore, for the detection of the chronic hepatitis B virus (HBV) e-antigen (HBeAg). In this approach, the recognition between HBeAg and a purified monoclonal hepatitis B e antibody (Ab(HBeAg)) was detected via transient ionic current spikes generated by partial occlusions of the α-HL nanopore by protein aggregates electrophoretically driven toward the nanopore’s vestibule entrance. Despite the steric hindrance precluding antigen, antibody, or antigen–antibody complex capture inside the nanopore, their stochastic bumping with the nanopore generated clear transient blockade events. The subsequent analysis suggested the detection of protein subpopulations in solution, rendering the approach a potentially valuable label-free platform for the sensitive, submicromolar-scale screening of HBeAg targets.

show abstract

The Nanopore-Tweezing-Based, Targeted Detection of Nucleobases on Short Functionalized Peptide-Nucleic Acid Sequences

Cited by 3 publications

References 59 publications

Artificial genetic polymers against human pathologies

Artificial genetic polymers against human pathologies

Engineering nanopore sensors for proteomic and metabolomic analysis

Probing the Hepatitis B Virus E-Antigen with a Nanopore Sensor Based on Collisional Events Analysis

Contact Info

Product

Resources

About