A solid-phase CuAAC strategy for the synthesis of PNA containing nucleobase surrogates

Exploring Nucleobase Modifications in Oligonucleotide Analogues for Use as Environmentally Responsive Fluorophores and Beyond

Over the past two decades, it has become abundantly clear that nucleic acid biochemistry, especially with respect to RNA, is more convoluted and complex than previously appreciated. Indeed, the application and exploitation of nucleic acids beyond their predestined role as the medium for storage and transmission of genetic information to the treatment and study of diseases has been achieved. In other areas of endeavor, utilization of nucleic acids as a probe molecule requires that they possess a reporter group. The reporter group of choice is often a luminophore because fluorescence spectroscopy has emerged as an indispensable tool to probe the structural and functional properties of modified nucleic acids. The scope of this review spans research done in the Hudson lab at The University of Western Ontario and is focused on modified pyrimidine nucleobases and their applications as environmentally sensitive fluorophores, base discriminating fluorophores, and in service of antisense applications as well as tantalizing new results as G-quadruplex destabilizing agents. While this review is a focused personal account, particularly influential work of colleagues in the chemistry community will be highlighted. The intention is not to make a comprehensive review, citations to the existing excellent reviews are given, any omission of the wonderful and impactful work being done by others globally is not intentional. Thus, this review will briefly introduce the context of our work, summarize what has been accomplished and finish with the prospects of future developments.

Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

Simultaneous ultrasound- and microwave-assisted one-pot 'click' synthesis of 3-formyl-indole clubbed 1,2,3-triazole derivatives and their biological evaluation

An environment friendly, high yielding, promising one-pot protocol for the click reaction of N-propargyl-3-formylindole 2(a-b), chloroacetic acid/ester 3(a-b) and sodium azide, leading to the formation of 3-formyl-indole clubbed 1,4-disubstituted-1,2,3-triazole derivatives 4(a-b), 5(a-b) and 6(a-f) aided by CuI catalyst accomplished under acceleration of simultaneous ultrasound and microwave irradiation in a very short reaction time has been described. Further, acid derivative 4(a-b) is subjected to acid-amine coupling reaction with secondary amine (p-t) in the presence of HATU to afford 6(p-t) and 7(p-t). The perspective of this protocol is to get rid of the hectic preparation and handling of organic azide which are generated in situ. Consequently, this protocol blossoms the click process by making it environment benign, user-friendly, safe and clean technique. All the synthesized compounds have been preliminarily screen for their in vitro antimicrobial activity against a panel of pathogenic strains. The majority of compounds possess noticeably inhibitory action against E. Coli, S. Typhi, P. Aeruginosa, C. tetani, S. aureus and B. subtillis. Among all compounds, 6p and 7q exhibit excellent inhibitory action against E.Coli and P. Aeruginosa strain, respectively, as compared to standard drug. One compound 5b shows remarkable potency against fungal strain. Molecular docking study was carried out to understand binding of compound with protein. In silico ADME prediction was carried out to check physicochemical properties of synthesized compound.

Semiflexible polymer scaffolds: an overview of conjugation strategies

Semiflexible polymers are excellent scaffolds for the presentation of a wide variety of (bio)molecules. This manuscript reviews advantages and challenges of the most common conjugation strategies for the major classes of semiflexible polymers.

Clickable PNA Probes for Imaging Human Telomeres and Poly(A) RNAs

The ability to bind strongly to complementary nucleic acid sequences, invade complex nucleic acid structures, and resist degradation by cellular enzymes has made peptide nucleic acid (PNA) oligomers as very useful hybridization probes in molecular diagnosis. For such applications, the PNA oligomers have to be labeled with appropriate reporters as they lack intrinsic labels that can be used in biophysical assays. Although solid-phase synthesis is commonly used to attach reporters onto PNA, development of milder and modular labeling methods will provide access to PNA oligomers labeled with a wider range of biophysical tags. Here, we describe the establishment of a postsynthetic modification strategy based on bioorthogonal chemical reactions in functionalizing PNA oligomers in solution with a variety of tags. A toolbox composed of alkyne- and azide-modified monomers were site-specifically incorporated into PNA oligomers and postsynthetically click-functionalized with various tags, ranging from sugar, amino acid, biotin, to fluorophores, by using copper(I)-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, and Staudinger ligation reactions. As a proof of utility of this method, fluorescent PNA hybridization probes were developed and used in imaging human telomeres in chromosomes and poly(A) RNAs in cells. Taken together, this simple approach of generating a wide range of functional PNA oligomers will expand the use of PNA in molecular diagnosis.

Facile functionalization of peptide nucleic acids (PNAs) for antisense and single nucleotide polymorphism detection

In this report, we show how a convenient on-resin copper-click functionalization of azido-functionalized peptide nucleic acids (PNAs) allows various PNA-based detection strategies. Firstly, a thiazole orange (TO) clicked PNA probe facilitates a binary readout when combined with F/Q labeled DNA, giving increased sensitivity for antisense detection. Secondly, our TO-PNA conjugate also allows single nucleotide polymorphism detection. Since antisense detection is also possible in the absence of the TO label, our sensing platform based on azido-d-ornithine containing PNA even allows for additional and more advanced functionalization and sensing strategies.

Synthesis of a poly(Gd(iii)-DOTA)–PNA conjugate as a potential MRI contrast agent via post-synthetic click chemistry functionalization

An operationally easy method provides poly(Gd³⁺chelate) PNA conjugates that form comb-like complexes with poly(rA) and demonstrate increased relaxivity.

Furan-PNA: a mildly inducible irreversible interstrand crosslinking system targeting single and double stranded DNA

We here report on the design and synthesis of tailor-made furan-modified peptide nucleic acid (PNA) probes for covalent targeting of single stranded DNA through a crosslinking strategy. After introducing furan-containing building blocks into a PNA sequence, hybridization and furan-oxidation based crosslinking to DNA is investigated. The structure of the crosslinked products is characterized and preliminary investigations concerning the application of these systems to double stranded DNA are shown.

PNA Molecular Beacons Assembled by Post-Synthetic Click Chemistry Functionalization

To avoid the tedious synthesis of functionalized peptide nucleic acid (PNA) monomers for probe development, we proposed a simple approach to modify PNA oligomers by post-synthetic on-resin click chemistry. PNA molecular beacons (MBs) were prepared by incorporation of azide-containing monomers into the oligomer by automatic solid-phase peptide synthesis and subsequent derivatization with pyrene moieties by copper-catalyzed azide-alkyne cycloaddition. Two pyrene-based quencher-free PNA molecular beacons, a stemless MB and one possessing a stem-loop structure, targeting a portion of the cystic fibrosis gene, were successfully synthesized by using this method. Fluorescence studies showed that the stem-loop MB exhibited better discrimination of changes in excimer/monomer ratios as compared to the stemless MB construct.