The Application of Nucleic Acid Probe-Based Fluorescent Sensing and Imaging in Cancer Diagnosis and Therapy

Ultra-stable threose nucleic acid-based biosensors for rapid and sensitive nucleic acid detection and in vivo imaging

The human genome's nucleotide sequence variation, such as single nucleotide mutations, can cause numerous genetic diseases. However, detecting nucleic acids accurately and rapidly in complex biological samples remains a major challenge. While natural deoxyribonucleic acid (DNA) has been used as biorecognition probes, it has limitations like poor specificity, reproducibility, nuclease-induced enzymatic degradation, and reduced bioactivity on solid surfaces. To address these issues, we introduce a stable and reliable biosensor called graphene oxide (GO)- threose nucleic acid (TNA). It comprises chemically modified TNA capture probes on GO for detecting and imaging target nucleic acids in vitro and in vivo, distinguishing single nucleobase mismatches, and monitoring dynamic changes in target microRNA (miRNA). By loading TNA capture probes onto the GO substrate, the GO-TNA sensing platform for nucleic acid detection demonstrates a significant 88-fold improvement in the detection limit compared to TNA probes alone. This platform offers a straightforward preparation method without the need for costly and labor-intensive isolation procedures or complex chemical reactions, enabling real-time analysis. The stable TNA-based GO sensing nanoplatform holds promise for disease diagnosis, enabling rapid and accurate detection and imaging of various disease-related nucleic acid molecules at the in vivo level. STATEMENT OF SIGNIFICANCE: The study's significance lies in the development of the GO-TNA biosensor, which addresses limitations in nucleic acid detection. By utilizing chemically modified nucleic acid analogues, the biosensor offers improved reliability and specificity, distinguishing single nucleobase mismatches and avoiding false signals. Additionally, its ability to detect and image target nucleic acids in vivo facilitates studying disease mechanisms. The simplified preparation process enhances practicality and accessibility, enabling real-time analysis. The biosensor's potential applications extend beyond healthcare, contributing to environmental analysis and food safety. Overall, this study's findings have substantial implications for disease diagnosis, biomedical research, and diverse applications, advancing nucleic acid detection and its impact on various fields.

DNA and Nanomaterials: A Functional Combination for DNA Sensing

Recent decades have experienced tough situations due to the lack of reliable diagnostic facilities. The most recent cases occurred during the pandemic, where researchers observed the lack of diagnostic facilities with precision. Microorganisms and viral disease's ability to escape diagnosis has been a global challenge. DNA always has been a unique moiety with a strong and precise base-paired structure. DNA in human and foreign particles makes identification possible through base pairing. Since then, researchers have focused heavily on designing diagnostic assays targeting DNA in particular. Moreover, DNA nanotechnology has contributed vastly to designing composite nanomaterials by combining DNA/nucleic acids with functional nanomaterials and inorganic nanoparticles exploiting their physicochemical properties. These nanomaterials often exhibit unique or enhanced properties due to the synergistic activity of the many components. The capabilities of DNA and additional nanomaterials have shown the combination of robust and advanced tailoring of biosensors. Preceding findings state that the conventional strategies have exhibited certain limitations such as a low range of target detection, less biodegradability, subordinate half-life, and high susceptibility to microenvironments; however, a DNA-nanomaterial-based biosensor has overcome these limitations meaningfully. Additionally, the unique properties of nucleic acids have been studied extensively due to their high signal conduction abilities. Here, we review recent studies on DNA-nanomaterial-based biosensors, their mechanism of action, and improved/updated strategies in vivo and in situ. Furthermore, this review highlights the recent methodologies on DNA utilization to exploit the interfacial properties of nanomaterials in DNA sensing. Lastly, the review concludes with the limitations/challenges and future directions.

Nanotechnology and Cancer Bioelectricity: Bridging the Gap Between Biology and Translational Medicine

Bioelectricity is the electrical activity that occurs within living cells and tissues. This activity is critical for regulating homeostatic cellular function and communication, and disruptions of the same can lead to a variety of conditions, including cancer. Cancer cells are known to exhibit abnormal electrical properties compared to their healthy counterparts, and this has driven researchers to investigate the potential of harnessing bioelectricity as a tool in cancer diagnosis, prognosis, and treatment. In parallel, bioelectricity represents one of the means to gain fundamental insights on how electrical signals and charges play a role in cancer insurgence, growth, and progression. This review provides a comprehensive analysis of the literature in this field, addressing the fundamentals of bioelectricity in single cancer cells, cancer cell cohorts, and cancerous tissues. The emerging role of bioelectricity in cancer proliferation and metastasis is introduced. Based on the acknowledgement that this biological information is still hard to access due to the existing gap between biological findings and translational medicine, the latest advancements in the field of nanotechnologies for cellular electrophysiology are examined, as well as the most recent developments in micro- and nano-devices for cancer diagnostics and therapy targeting bioelectricity.

Recent advances in small-molecule fluorescent probes with the function of targeting cancer receptors

Cancer is "the sword of Damocles" that threatens human life and health. Therefore, the diagnosis and treatment of cancer have been receiving much attention. Many overexpressed receptors on the surface of cancer cells provide us with an effective way to specifically identify the cancer cells, and receptor targeting strategies are becoming one of the hot ideas to enhance the ability of fluorescent probes to target tumors. Fluorescent probes connected to ligands are targeted at cancer cell surfaces through receptor-mediated endocytosis. Receptor-targeting probes can image and track cancer cells, determine tumor boundaries, monitor deep lesions, and play a role in clinical medicine, such as fluorescent imaging-guided surgery. In this review, based on the perspective of small molecule fluorescent probes, we reviewed the design ideas, photophysical properties, and applications of receptor-targeting probes for detecting biomarkers in imaging and tracing cancer cells and prospected the future developmental direction of such probes. We hope that this review will provide more ideas for the design and development of active targeting probes for receptors and lead to more applications in the medical field.

Nucleic Acid Probes in Bio-Imaging and Diagnostics: Recent Advances in ODN-Based Fluorescent and Surface-Enhanced Raman Scattering Nanoparticle and Nanostructured Systems

Raman nanoparticle probes are a potent class of optical labels for the interrogation of pathological and physiological processes in cells, bioassays, and tissues. Herein, we review the recent advancements in fluorescent and Raman imaging using oligodeoxyribonucleotide (ODN)-based nanoparticles and nanostructures, which show promise as effective tools for live-cell analysis. These nanodevices can be used to investigate a vast number of biological processes occurring at various levels, starting from those involving organelles, cells, tissues, and whole living organisms. ODN-based fluorescent and Raman probes have contributed to the achievement of significant advancements in the comprehension of the role played by specific analytes in pathological processes and have inaugurated new possibilities for diagnosing health conditions. The technological implications that have emerged from the studies herein described could open new avenues for innovative diagnostics aimed at identifying socially relevant diseases like cancer through the utilization of intracellular markers and/or guide surgical procedures based on fluorescent or Raman imaging. Particularly complex probe structures have been developed within the past five years, creating a versatile toolbox for live-cell analysis, with each tool possessing its own strengths and limitations for specific studies. Analyzing the literature reports in the field, we predict that the development of ODN-based fluorescent and Raman probes will continue in the near future, disclosing novel ideas on their application in therapeutic and diagnostic strategies.

Optofluidic Particle Manipulation: Optical Trapping in a Thin-Membrane Microchannel

We demonstrate an optofluidic device which utilizes the optical scattering and gradient forces for particle trapping in microchannels featuring 300 nm thick membranes. On-chip waveguides are used to direct light into microfluidic trapping channels. Radiation pressure is used to push particles into a protrusion cavity, isolating the particles from liquid flow. Two different designs are presented: the first exclusively uses the optical scattering force for particle manipulation, and the second uses both scattering and gradient forces. Trapping performance is modeled for both cases. The first design, referred to as the orthogonal force design, is shown to have a 80% capture efficiency under typical operating conditions. The second design, referred to as the gradient force design, is shown to have 98% efficiency under the same conditions.

Imaging of Hepatitis B Virus Nucleic Acids: Current Advances and Challenges

Hepatitis B virus infections are the main reason for hepatocellular carcinoma development. Current treatment reduces the viral load but rarely leads to virus elimination. Despite its medical importance, little is known about infection dynamics on the cellular level not at least due to technical obstacles. Regardless of infections leading to extreme viral loads, which may reach 10¹⁰ virions per mL serum, hepatitis B viruses are of low abundance and productivity in individual cells. Imaging of the infections in cells is thus a particular challenge especially for cccDNA that exists only in a few copies. The review describes the significance of microscopical approaches on genome and transcript detection for understanding hepatitis B virus infections, implications for understanding treatment outcomes, and recent microscopical approaches, which have not been applied in HBV research.

Pre-miRNA-149 G-quadruplex as a molecular agent to capture nucleolin

One of the most significant challenges in capturing and detecting biomarkers is the choice of an appropriate biomolecular receptor. Recently, RNA G-quadruplexes emerged as plausible receptors due to their ability to recognize with high-affinity proteins. Herein, we have unveiled and characterized the capability of the precursor microRNA 149 to form a G-quadruplex structure and determined the role that some ligands may have in its folding and binding capacity to nucleolin. The G-quadruplex formation was induced by K+ ions and stabilized by ligands, as demonstrated by nuclear magnetic resonance and circular dichroism experiments. Surface plasmon resonance measurements showed a binding affinity of precursor microRNA 149 towards ligands in the micromolar range (10-5-10-6 M) and a strong binding affinity to nucleolin RNA-binding domains 1 and 2 (8.38 × 10-10 M). Even in the presence of the ligand PhenDC3, the binding remains almost identical and in the same order of magnitude (4.46 × 10-10 M). The molecular interactions of the RNA G-quadruplex motif found in precursor miRNA 149 (5'-GGGAGGGAGGGACGGG- 3') and nucleolin RNA-binding domains 1 and 2 were explored by means of molecular docking and molecular dynamics studies. The results showed that RNA G-quadruplex binds to a cavity between domains 1 and 2 of the protein. Then, complex formation was also evaluated through polyacrylamide gel electrophoresis. The results suggest that precursor microRNA 149/ligands and precursor microRNA 149/nucleolin RNA-binding domains 1 and 2 form stable molecular complexes. The in vitro co-localization of precursor microRNA 149 and nucleolin in PC3 cells was demonstrated using confocal microscopy. Finally, a rapid and straightforward microfluidic strategy was employed to check the ability of precursor microRNA 149 to capture nucleolin RNA-binding domains 1 and 2. The results revealed that precursor microRNA 149 can capture nucleolin RNA-binding domains 1 and 2 labeled with Fluorescein 5-isothiocyanate in a concentration-dependent manner, but PhenDC3 complexation seems to decrease the ability of precursor microRNA 149 to capture the protein. Overall, our results proved the formation of the G-quadruplex structure in the precursor microRNA 149 and the ability to recognize and detect nucleolin. This proof-of-concept study could open up a new framework for developing new strategies to design improved molecular receptors for capture and detection of nucleolin in complex biological samples.

Efficient Photoacoustic Imaging With Biomimetic Mesoporous Silica-Based Nanoparticles

Indocyanine green (ICG), a near-infrared (NIR) fluorescent dye approved by the Food and Drug Administration (FDA), has been extensively used as a photoacoustic (PA) probe for PA imaging. However, its practical application is limited by poor photostability in water, rapid body clearance, and non-specificity. Herein, we fabricated a novel biomimetic nanoprobe by coating ICG-loaded mesoporous silica nanoparticles with the cancer cell membrane (namely, CMI) for PA imaging. This probe exhibited good dispersion, large loading efficiency, good biocompatibility, and homologous targeting ability to Hela cells in vitro. Furthermore, the in vivo and ex vivo PA imaging on Hela tumor-bearing nude mice demonstrated that CMI could accumulate in tumor tissue and display a superior PA imaging efficacy compared with free ICG. All these results demonstrated that CMI might be a promising contrast agent for PA imaging of cervical carcinoma.

Organic Fluorophores for 1064 nm Excited NIR-II Fluorescence Imaging

Second near-infrared window (NIR-II) fluorescence imaging has shown great potential in the field of bioimaging. However, the excitation wavelengths of most NIR-II fluorescence dyes are in the first near-infrared (NIR-I) region, which leads to limited imaging depth and resolution. To address such issue, NIR-II fluorescence dyes with 1,064 nm excitation have been developed and applied for in vivo imaging. Compared with NIR-I wavelength excited dyes, 1,064 nm excited dyes exhibit a higher tissue penetration depth and resolution. The improved performance makes these dyes have much broader imaging applications. In this mini review, we summarize recent advances in 1,064 nm excited NIR-II fluorescence fluorophores for bioimaging. Two kinds of organic fluorophores, small molecule dye and semiconducting polymer (SP), are reviewed. The general properties of these fluorophores are first introduced. Small molecule dyes with different chemical structures for variety of bioimaging applications are then discussed, followed by the introduction of SPs for NIR-II phototheranostics. Finally, the conclusion and future perspective of this field is given.