Preparation of alkyne-labeled 2-nitroimidazoles for identification of tumor hypoxia by Raman spectroscopy

Biomedical applications, perspectives and tag design concepts in the cell - silent Raman window

Spectroscopic studies increasingly employ Raman tags exhibiting a signal in the cell - silent region of the Raman spectrum (1800-2800 cm-1), where bands arising from biological molecules are inherently absent. Raman tags bearing functional groups which contain a triple bond, such as alkyne and nitrile or a carbon-deuterium bond, have a distinct vibrational frequency in this region. Due to the lack of spectral background and cell-associated bands in the specific area, the implementation of those tags can help overcome the inherently poor signal-to-noise ratio and presence of overlapping Raman bands in measurements of biological samples. The cell - silent Raman tags allow for bioorthogonal imaging of biomolecules with improved chemical contrast and they have found application in analyte detection and monitoring, biomarker profiling and live cell imaging. This review focuses on the potential of the cell - silent Raman region, reporting on the tags employed for biomedical applications using variants of Raman spectroscopy.

A review of surface-enhanced Raman spectroscopy in pathological processes

With the continuous growth of the human population and new challenges in the quality of life, it is more important than ever to diagnose diseases and pathologies with high accuracy, sensitivity and in different scenarios from medical implants to the operation room. Although conventional methods of diagnosis revolutionized healthcare, alternative analytical methods are making their way out of academic labs into clinics. In this regard, surface-enhanced Raman spectroscopy (SERS) developed immensely with its capability to achieve single-molecule sensitivity and high-specificity in the last two decades, and now it is well on its way to join the arsenal of physicians. This review discusses how SERS is becoming an essential tool for the clinical investigation of pathologies including inflammation, infections, necrosis/apoptosis, hypoxia, and tumors. We critically discuss the strategies reported so far in nanoparticle assembly, functionalization, non-metallic substrates, colloidal solutions and how these techniques improve SERS characteristics during pathology diagnoses like sensitivity, selectivity, and detection limit. Moreover, it is crucial to introduce the most recent developments and future perspectives of SERS as a biomedical analytical method. We finally discuss the challenges that remain as bottlenecks for a routine SERS implementation in the medical room from in vitro to in vivo applications. The review showcases the adaptability and versatility of SERS to resolve pathological processes by covering various experimental and analytical methods and the specific spectral features and analysis results achieved by these methods.

Changes of C≡C Triple Bond Vibration that Disclosed Non-Canonical Cytosine Protonation in i-Motif-Forming Oligodeoxynucleotides

Non-canonical protonation at cytosine (C) in DNA is related to a formation of second order DNA structures such as i-motif, which has a role in gene regulation. Although the detailed structural information is indispensable for comprehension of their functions in cells, the protonation status of C in complicated environments is still elusive. To provide a reporter system of non-canonical protonation, we focused on the molecular vibration that could be monitored using the Raman spectroscopy. We prepared a cytosine derivative (^PC) with an acetylene unit as a Raman tag, and found that the Raman signal of acetylene in ^PC in oligodeoxynucleotides (ODNs) changed due to protonation at the cytosine ring which shortened an acetylene bond. The signal change in i-motif-forming ODNs was also observed in crowded environments with polyethylene glycol, evidencing protonation in i-motif DNA in complicated environments. This system would be one of tracking tools for protonation in DNA structures.

Monitoring intracellular metal ion complexation with an acetylene-tagged ligand by Raman spectroscopy

We propose to monitor molecular vibrations to identify metal ion-ligand complexation by means of Raman spectroscopy, which has been applied to track vibrational modes of molecules and to obtain a structural fingerprint. We prepared ligand molecules for Zn²⁺ ion complexation with a dipycolylaminoethyl aniline (DPEA) skeleton and phenylacetylene unit as the Raman tag which showed a typical band around 2200 cm^-1. Among the labeled ligands synthesized in this study, A-DPEA showed a strong band attributed to the acetylene unit at 2212 cm^-1, while the addition of Zn²⁺ ion resulted in a band shift to 2220 cm^-1 due to complex formation. The addition of other metal ions and titration experiments showed that A-DPEA bound with Zn²⁺ selectively with a dissociation constant (K _d) that was estimated to be 0.22 μM. We also conducted cellular experiments and found that complexation between A-DPEA and Zn²⁺ also occurred in cells, with a shift in the Raman signal of the ligand from 2212 to 2215 cm^-1. Thus, complex formation of the metal ion was identified by monitoring the Raman band shift.

Live Intracellular Biorthogonal Imaging by Surface Enhanced Raman Spectroscopy using Alkyne-Silver Nanoparticles Clusters

Live intracellular imaging is a valuable tool in modern diagnostics and pharmacology. Surface Enhanced Raman Spectroscopy (SERS) stands out as a non-destructive and multiplexed technique, but intracellular SERS imaging still suffers from interfering background from endogenous components. Here we show the assembly of small colloidal SERS probes with Raman signal in the cell-silent window of 1800–2900 cm⁻¹ for biorthogonal intracellular SERS imaging of dopamine that was undistinguishable from the endogenous cell background. By linking colloidal silver nanoparticles with alkyne-dopamine adducts, clusters are formed by 2–6 nanoparticles spaced by tight interparticle gaps that exhibited high electric field enhancement and strong SERS signals of alkyne and dopamines. Due to the cell-silent signals of the alkyne, intracellular in-vitro Raman imaging shows that the dopamines on the internalized clusters remain distinguishable across the cytoplasm with good spatial resolution. Our method can be a general-purpose method for real-time imaging of biomolecules, such as proteins, peptides, DNA and drugs.

Nitroimidazoles with a halogen-containing side-chain

Syntheses are reported for: nine 2-nitroimidazoles, the abbreviated names all beginning with E, based on derivation from Etanidazole); five 2-methyl-5-nitroimidazoles (M compounds, derived from Metronidazole); and five 2-methyl-4-nitroimidazoles (labelled 2M4N compounds). The nitroimidazoles all have an amide side-chain at the N1 atom of the imidazole, with 17 of them containing one to five halogen atoms. The aim is to study compounds for comparison with EF5 (the number showing the presence of five F-atoms), a previously reported, pentafluoropropylacetamide derivative of 2-nitroimidazole that is currently used as a hypoxia marker drug to detect cancerous tumours. The new compounds are characterized by standard methods, including X-ray structural data for the fluorinated MF5, 2M4NF5, and 2M4NF1(−1) species, with the “–1” indicating two C-atoms in an alkylamide chain rather than the three C-atoms in the propylacetamide of EF5. Intra- and inter-molecular H-bonding is seen in the solid state structures, likely an important property in biological use; another key property of the nitroimidazoles is their reduction potentials, and the measured CV data confirm that 2NO2Im compounds with longer side-chains and more F-atoms (like EF5) are worth investigating for possible activity as hypoxia-selective, bioreductive agents.