2'-Bispyrene-modified 2'-O-methyl RNA probes as useful tools for the detection of RNA: synthesis, fluorescent properties, and duplex stability

Convenient Solid-Phase Attachment of Small-Molecule Ligands to Oligonucleotides via a Biodegradable Acid-Labile P-N-Bond

One of the key problems in the design of therapeutic and diagnostic oligonucleotides is the attachment of small-molecule ligands for targeted deliveries in such a manner that provides the controlled release of the oligonucleotide at a certain moment. Here, we propose a novel, convenient approach for attaching ligands to the 5'-end of the oligonucleotide via biodegradable, acid-labile phosphoramide linkage. The method includes the activation of the 5'-terminal phosphate of the fully protected, support-bound oligonucleotide, followed by interaction with a ligand bearing the primary amino group. This technique is simple to perform, allows for forcing the reaction to completion by adding excess soluble reactant, eliminates the problem of the limited solubility of reagents, and affords the possibility of using different solvents, including water/organic media. We demonstrated the advantages of this approach by synthesizing and characterizing a wide variety of oligonucleotide 5'-conjugates with different ligands, such as cholesterol, aliphatic oleylamine, and p-anisic acid. The developed method suits different types of oligonucleotides (deoxyribo-, 2'-O-methylribo-, ribo-, and others).

5'-Monopyrene and 5'-Bispyrene 2'-O-methyl RNA Probes for Detection of RNA Mismatches

Progress in synthesis of novel fluorescent oligonucleotides has provided effective instruments for nucleic acid detection. Pyrene conjugated oligonucleotides have demonstrated their effectiveness as fluorescent hybridization probes. Here we describe the synthesis, isolation, and analysis of 5'-monopyrene and 5'-bispyrene conjugates of oligo(2'-O-methylribonucleotides) and their application as probes for fluorescent detection of mismatches in RNA targets.

2'-O-Methyl molecular beacon: a promising molecular tool that permits elimination of sticky-end pairing and improvement of detection sensitivity

An innovative 2'-O-methyl molecular beacon (MB) has been designed and prepared with improved thermal stability and unique nuclease resistance. The employment of 2'-O-methyl MBs helps efficiently suppress the background signal, while DNase I is responsible for the signal amplification and elimination of sticky-end pairing. The coupled use of 2'-O-methyl MBs and DNase I makes it possible to develop an enzyme-aided strategy for amplified detection of DNA targets in a sensitive and specific fashion. The analysis requires only mix-and-measure steps that can be accomplished within half an hour. The detection sensitivity is theoretically determined as 27.4 pM, which is nearly 200-fold better than that of the classic MB-based assay. This proposed sensing system also shows desired selectivity. All these features are of great importance for the design and application of MBs in biological, chemical, and biomedical fields.

Novel near-infrared fluorescent probe with a large Stokes shift for sensing hypochlorous acid in mitochondria

Hypochlorous acid (HOCl) plays a crucial role in various physiological and pathological processes. However, it is still a challenge to design a xanthene-based near-infrared (NIR) fluorescent probe with a large Stokes shift for sensing HOCl. In this work, a novel mitochondria-targeted fluorescent probe, MXS, with a large Stokes shift based on a xanthene-hemicyanine dyad structure, has been successfully designed and synthesized for the specific detection of HOCl. Gratifyingly, the peak-to-peak Stokes shift of MXS was found to be 130 nm, which was obviously larger than those of conventional rhodamine dyes and most reported xanthene-based hypochlorous acid probes. As expected, MXS exhibited high selectivity, high sensitivity, and fast response time (30 s) for the detection of HOCl via a specific HOCl-promoted intramolecular charge transfer process. The detection limit of MXS for HOCl is calculated to be as low as 72 nM, enabling its use within the physiological concentration range of HOCl (5-25 μM). Importantly, MXS is able to permeate cell membranes and accumulate in the mitochondria, which is convenient for monitoring the variation of hypochlorous acid concentration in the mitochondria of living cells.

Postsynthetic On-Column 2' Functionalization of RNA by Convenient Versatile Method

We report a universal straightforward strategy for the chemical synthesis of modified oligoribonucleotides containing functional groups of different structures at the 2' position of ribose. The on-column synthetic concept is based on the incorporation of two types of commercial nucleotide phosphoramidites containing orthogonal 2'-O-protecting groups, namely 2'-O-thiomorpholine-carbothioate (TC, as "permanent") and 2'-O-tert-butyl(dimethyl)silyl (tBDMS, as "temporary"), to RNA during solid-phase synthesis. Subsequently, the support-bound RNA undergoes selective deprotection and follows postsynthetic 2' functionalization of the naked hydroxyl group. This convenient method to tailor RNA, utilizing the advantages of solid phase approaches, gives an opportunity to introduce site-specifically a wide range of linkers and functional groups. By this strategy, a series of RNAs containing diverse 2' functionalities were synthesized and studied with respect to their physicochemical properties.

A highly sensitive turn-on fluorescent probe for real-time detecting hypochlorite and its application in living cells

It is very necessary to develop real-time, highly sensitive and selective fluorescent probes for hypochlorite (ClO^-) in living cells owing to hypochlorite's important role in pathological and physiological processes and its short life. Herein, a pyrene Schiff's base derivative was successfully developed for real-time (within seconds), highly sensitive detecting ClO^- with a low detection limit (5.7 nM) and wide pH range (4.0-11.0) based on nucleophilic addition and subsequent hydrolysis mechanism. The probe has aggregation-induced emission properties and emits yellow fluorescence (544 nm) in PBS solution, while it exhibits blue fluorescence in other organic solvents (426 nm (THF) - 460 nm (MeOH)). The probe can be used to response ClO^- in A549 cells with low cytotoxicity, a good cell membranes penetration and good biocompatibility. Cell uptake experiment indicates that probe getting into the cells is energy-dependent and is not attributed to endocytosis. Moreover, the probe is successfully used in real water sample to detect ClO^- and it can be expected to be applied to ClO^- participated biological and pathological functions in biological systems.

A mitochondria-targeted near-infrared fluorescent probe with a large Stokes shift for real-time detection of hypochlorous acid

A real-time mitochondria-targeted near-infrared fluorescent probeLhas been synthesized with large Stokes shifts, and high selectivity and sensitivity.

Conformational studies of 10-23 DNAzyme in solution through pyrenyl-labeled 2'-deoxyadenosine derivatives

10-23 DNAzyme is a small catalytic DNA molecule. Studies on its conformation in solution are critical for understanding its catalytic mechanism and functional optimization. Based on our previous research, two fluorescent nucleoside analogues 1 and 2 were designed for the introduction of a pyrenyl group at one of the five dA residues in the catalytic core and the unpaired adenosine residue in its full-DNA substrate, respectively. Ten pyrenyl-pyrenyl pairs are formed in the DNAzyme-substrate complexes in solution for sensing the spacial positions of the five dA residues relative to the cleavage site using fluorescence spectra. The position-dependent quenching effect of pyrene emission fluorescence by nucleobases, especially the pyrenyl-pyrenyl interaction, was observed for some positions. The adenine residues in the 3'-part of the catalytic loop seem to be closer to the cleavage site than the adenine residues in the 5'-part, which is consistent with the molecular dynamics simulation result. The catalytic activities and T_m changes also confirmed the effect of the pyrenyl-nucleobase and pyrenyl-pyrenyl pair interactions. Together with functional group mutations, catalytically relevant nucleobases will be identified for understanding the catalytic mechanism of 10-23 DNAzyme.

A convenient solid phase approach to obtain lipophilic 5'-phosphoramidate derivatives of DNA and RNA oligonucleotides

This paper explores the potential of a modified phosphotriester approach to the synthesis of 5'-phosphoramidate derivatives of DNA and RNA oligonucleotides. The modification of 5'-deprotected support-bound oligonucleotides is done in two steps: i) conversion of the 5'-OH group of an oligonucleotide into an activated phosphodiester, and ii) treatment of the activated phosphodiester with an aminocompound. The approach is efficient and compatible with conventional solid phase oligonucleotide synthesis. It can be used for the conjugation of therapeutically relevant oligonucleotides with functional moieties or carrier constructions, which are to be removed after endocytosis.

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

Rational design and studies of excimer forming novel dual probes to target RNA

In this paper, we report structure-based rational design and physico-chemical and biological studies of novel pyrene excimer forming dual probes for visualization of intracellular RNAs. Herein, the probes based on 2'-O-methyl RNA with linkers of different structure and length between pyrene moiety and ribose are studied with respect to their hybridization and spectral properties. We found optimal linkers that provide more intense excimer emission (at ∼480nm) of RNA-bound probes; particularly, the length of the linker arm of the 3'-component of dual probes plays a key role in formation of pyrene excimer. Calculated molecular dynamics trajectories and probability distributions of pyrene-pyrene dimer formation upon hybridization of the dual probes with RNA target are in agreement with the obtained fluorescence spectroscopy data for the corresponding duplexes. Our study demonstrates the excellent binding properties of new dual probes to structured RNA and their feasibility for the visualization of intracellular RNA targets.

Design of a synthetic luminescent probe from a biomolecule binding domain: selective detection of AU-rich mRNA sequences

We report the design of a luminescent sensor based upon the zinc finger protein TIS11d, that allows for the selective time-resolved detection of the UUAUUUAUU sequence of the 3′-untranslated region of messenger RNA.

We report the design of a luminescent sensor based upon the zinc finger (ZF) protein TIS11d, that allows for the selective time-resolved detection of the UUAUUUAUU sequence of the 3′-untranslated region of messenger RNA. This sensor is composed of the tandem ZF RNA binding domain of TIS11d functionalized with a luminescent Tb³⁺ complex on one of the ZFs and a sensitizing antenna on the other. This work provides the proof of principle that an RNA binding protein can be re-engineered as an RNA sensor and, more generally, that tunable synthetic luminescent probes for biomolecules can be obtained by modifying biomolecule-binding domains.

Synthesis, Thermal Stability, Biophysical Properties, and Molecular Modeling of Oligonucleotides of RNA Containing 2'-O-2-Thiophenylmethyl Groups

Dodecamers of RNA [CUACGGAAUCAU] were functionalized with C2'-O-2-thiophenylmethyl groups to obtain oligonucleotides 10-14 and 17. The modified nucleotides were incorporated into RNA strands via solid-phase synthesis. The biophysical properties of these ONs were used to quantify the effects of this modification on RNA:RNA and RNA:DNA duplexes. A combination of UV-vis and circular dichroism were used to determine thermal stabilities of all strands, which hybridized into A-form geometries. Destabilization of the double stranded RNA was measured as a function of number of consecutive modifications, reflected in decreased thermal denaturation values (ΔT_m, ca. 2.5-11.5 °C). Van't Hoff plots on a duplex containing one modification (10:15) displayed a ca. ΔΔG° of +4 kcal/mol with respect to its canonical analogue. Interestingly, hybridization of two modified strands (13:17, containing a total of eight modifications) resulted in increased stability and a distinct secondary structure, reflected in its CD spectrum. Molecular modeling based on DFT calculations shed light on the nature of this stability, with induced changes in the torsional angle δ (C5'-C4'-C3'-O3) and phosphate-phosphate distances that are in agreement with a compacted structure. The described synthetic methodology and structural information will be useful in the design of thermodynamically stable structures containing chemically reactive modifications.