Fluorescent Sequence-Specific dsDNA Binding Oligomers

Sequence-specific detection methods for double-stranded DNA that obviate the need for denaturation would provide a powerful tool for bioorganic chemistry and genetics. As part of a sustained effort to develop sequence-specific fluorescent DNA detection methods, two programmable oligomers have been synthesized which target their respective sequences 5‘-WTACGW-3‘ and 5‘-WGGGGW-3‘ (W = A or T). The two oligomers were found to fluoresce weakly in the absence of DNA but showed significant fluorescence enhancement by the addition of match DNA. The fluorescence is shown to increase in a concentration-dependent manner, and the intensity varies depending on the number of mismatch sites incorporated into the DNA hairpins. This new class of oligomers provides a method to detect DNA sequences without denaturation and in the absence of conjugation to a dye molecule. This is a first step toward sequence-specific DNA-binding molecules containing a fluorescent switch integrated as part of the recognition modules

Exploring the limits of benzimidazole DNA-binding oligomers for the hypoxia inducible factor (HIF) site

The vascular endothelial growth factor (VEGF) and its receptors have been implicated as key-factors in tumor angiogenesis and are major targets in cancer therapy. New oligomers which mimic the architecture of DNA-binding polyamides have been designed to target the hypoxia inducible factor (HIF-1alpha) binding site on the promoter of VEGF gene. These oligomers incorporate an increasing number of six-five fused rings such as hydroxybenzimidazole-imidazole, benzimidazole-pyrrole, benzimidazole-chlorothiophene, and imidazopyridine-pyrrole, and bind the VEGF hypoxia response element (HRE) 5'-TACGT-3' with high affinity and selectivity

Exploring the limits of benzimidazole DNA-binding oligomers for the hypoxia inducible factor (HIF) site

The vascular endothelial growth factor (VEGF) and its receptors have been implicated as key-factors in tumor angiogenesis and are major targets in cancer therapy. New oligomers which mimic the architecture of DNA-binding polyamides have been designed to target the hypoxia inducible factor (HIF-1alpha) binding site on the promoter of VEGF gene. These oligomers incorporate an increasing number of six-five fused rings such as hydroxybenzimidazole-imidazole, benzimidazole-pyrrole, benzimidazole-chlorothiophene, and imidazopyridine-pyrrole, and bind the VEGF hypoxia response element (HRE) 5'-TACGT-3' with high affinity and selectivity

F-19 Magic Angle Spinning Dynamic Nuclear Polarization Enhanced NMR Spectroscopy

WOS:000474803100008The introduction of high-frequency, high-power microwave sources, tailored biradicals, and low-temperature magic angle spinning (MAS) probes has led to a rapid development of hyperpolarization strategies for solids and frozen solutions, leading to large gains in NMR sensitivity. Here, we introduce a protocol for efficient hyperpolarization of F-19 nuclei in MAS DNP enhanced NMR spectroscopy. We identified trifluoroethanol-d(3) as a versatile glassy matrix and show that 12mm AMUPol (with microcrystalline KBr) provides direct F-19 DNP enhancements of over 100 at 9.4T. We applied this protocol to obtain DNP-enhanced F-19 and F-19-C-13 cross-polarization (CP) spectra for an active pharmaceutical ingredient and a fluorinated mesostructured hybrid material, using incipient wetness impregnation, with enhancements of approximately 25 and 10 in the bulk solid, respectively. This strategy is a general and straightforward method for obtaining enhanced F-19 MAS spectra from fluorinated materials

Atomic-Scale Description of Interfaces between Antigen and Aluminum-Based Adjuvants Used in Vaccines by Dynamic Nuclear Polarization (DNP) Enhanced NMR Spectroscopy

The addition of aluminum-based adjuvants in vaccines enhances the immune response to antigens. The strength of antigen adsorption on adjuvant gels is known to modulate vaccine efficacy. However, a detailed understanding of the mechanisms of interaction between aluminum gels and antigens is still missing. Herein, a new analytical approach based on dynamic nuclear polarization (DNP) enhanced NMR spectroscopy under magic angle spinning (MAS) is implemented to provide a molecular description of the antigen-adjuvant interface. This approach is demonstrated on hepatitis B surface antigen particles in combination with three aluminum gels obtained from different suppliers. Both noncovalent and covalent interactions between the phospholipids of the antigen particles and the surface of the aluminum gels are identified by using MAS DNP (NMRAl)-Al-27 and(31)P correlation experiments. Although covalent interactions were detected for only one of the formulations, dipolar recoupling rotational echo adiabatic passage double resonance (REAPDOR) experiments reveal significant differences in the strength of weak interactions

The Structure of Molecular and Surface Platinum Sites Determined by DNP-SENS and Fast MAS 195Pt Solid-State NMR Spectroscopy

The molecular level characterization of heterogeneous catalysts is challenging due to the low concentration of surface sites and the lack of techniques that can selectively probe the surface of a heterogeneous material. Here, we report the joint application of room temperature proton-detected NMR spectroscopy under fast magic angle spinning (MAS) and dynamic nuclear polarization surface enhanced NMR spectroscopy (DNP-SENS), to obtain the 195Pt solid-state NMR spectra of a prototypical example of highly dispersed Pt sites (single site or single atom), here prepared via surface organometallic chemistry, by grafting [(COD)Pt(OSi(OtBu)3)2] (1, COD = 1,5-cyclooctadiene) on partially dehydroxylated silica (1@SiO2). Compound 1@SiO2 has a Pt loading of 3.7 wt %, a surface area of 200 m2/g, and a surface Pt density of around 0.6 Pt site/nm2. Fast MAS 1H{195Pt} dipolar-HMQC and S-REDOR experiments were implemented on both the molecular precursor 1 and on the surface complex 1@SiO2, providing access to 195Pt isotropic shifts and Pt–H distances, respectively. For 1@SiO2, the measu red isotropic shift and width of the shift distribution constrain fits of the static wide-line DNP-enhanced 195Pt spectrum, allowing the 195Pt chemical shift tensor parameters to be determined. Overall the NMR data provide evidence for a well-defined, single-site structure of the isolated Pt sites. © 2020 American Chemical Society.ISSN:0002-7863ISSN:1520-512

Reactive surface organometallic complexes observed using dynamic nuclear polarization surface enhanced NMR spectroscopy

Dynamic Nuclear Polarization Surface Enhanced NMR Spectroscopy (DNP SENS) is an emerging technique that allows access to high-sensitivity NMR spectra from surfaces. However, DNP SENS usually requires the use of radicals as an exogenous source of polarization, which has so far limited applications for organometallic surface species to those that do not react with the radicals. Here we show that reactive surface species can be studied if they are immobilized inside porous materials with suitably small windows, and if bulky nitroxide bi-radicals (here TEKPol) are used as the polarization source and which cannot enter the pores. The method is demonstrated by obtaining significant DNP enhancements from highly reactive complelxes [(equivalent to Si-O-)W(Me)(5)] supported on MCM-41, and effects of pore size (6.0, 3.0 and 2.5 nm) on the performance are discussed