The Crystal Structure of Non‐Modified and Bipyridine‐Modified PNA Duplexes

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N‐aminoethyl glycine backbone. The crystal structures of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATGCC)₂, and the other containing the same nucleobase pairs and a central pair of bipyridine ligands, have been solved with a resolution of 1.22 and 1.10 Å, respectively. The non‐modified PNA duplex adopts a P‐type helical structure similar to that of previously characterized PNAs. The atomic‐level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and the nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. Our results support the notion that whereas PNA typically adopts a P‐type helical structure, its flexibility is relatively high. For example, the base‐pair rise in the bipyridine‐containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines bulge out of the duplex and are aligned parallel to the major groove of the PNA. In addition, two bipyridines from adjacent PNA duplexes form a π‐stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl‐modified DNA duplexes in solution, where the biphenyls are π stacked with adjacent nucleobase pairs and adopt an intrahelical geometry. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes.     

A Peptide Nucleic Acid (PNA) Heteroduplex Probe Containing an Inosine–Cytosine Base Pair Discriminates a Single‐Nucleotide Difference in RNA

Selective discrimination of a single‐nucleotide difference in single‐stranded DNA or RNA remains a challenge with conventional DNA or RNA probes. A peptide nucleic acid (PNA)‐derived probe, in which PNA forms a pseudocomplementary heteroduplex with inosine‐containing DNA or RNA, effectively discriminates a single‐nucleotide difference in a closely related group of sequences of single‐stranded DNA and/or RNA. The pseudocomplementary PNA heteroduplex is easily converted to a fluorescent probe that distinctively detects a member of highly homologous let‐7 microRNAs.     

Specific Binding of a d‐RNA G‐Quadruplex Structure with an l‐RNA Aptamer

G‐quadruplex (G4) structures are of general importance in chemistry and biology, such as in biosensing, gene regulation, and cancers. Although a large repertoire of G4‐binding tools has been developed, no aptamer has been developed to interact with G4. Moreover, the G4 selectivity of current toolkits is very limited. Herein, we report the first l ‐RNA aptamer that targets a d ‐RNA G‐quadruplex (rG4). Using TERRA rG4 as an example, our results reveal that this l ‐RNA aptamer, Ap3‐7, folds into a unique secondary structure, exhibits high G4 selectivity and effectively interferes with TERRA‐rG4–RHAU53 binding. Our approach and findings open a new door in further developing G4‐specific tools for diverse applications.     

Toehold-Mediated Strand Displacement in a Triplex Forming Nucleic Acid Clamp for Reversible Regulation of Polymerase Activity and Protein Expression

Triplex forming oligonucleotides are used as a tool for gene regulation and in DNA nanotechnology. By incorporating artificial nucleic acids, target affinity and biological stability superior to that of natural DNA may be obtained. This work demonstrates how a chimeric clamp consisting of acyclic (L)-threoninol nucleic acid (aTNA) and DNA can bind DNA and RNA by the formation of a highly stable triplex structure. The (L)-aTNA clamp is released from the target again by the addition of a releasing strand in a strand displacement type of reaction. It is shown that the clamp efficiently inhibits Bsu and T7 RNA polymerase activity and that polymerase activity is reactivated by displacing the clamp. The clamp was successfully applied to the regulation of luciferase expression by reversible binding to the mRNA. When targeting a sequence in the double stranded plasmid, 40 % downregulation of protein expression is achieved.     

Modifying the 5′‐Cap for Click Reactions of Eukaryotic mRNA and To Tune Translation Efficiency in Living Cells

The 5′‐cap is a hallmark of eukaryotic mRNAs and plays fundamental roles in RNA metabolism, ranging from quality control to export and translation. Modifying the 5′‐cap may thus enable modulation of the underlying processes and investigation or tuning of several biological functions. A straightforward approach is presented for the efficient production of a range of N7‐modified caps based on the highly promiscuous methyltransferase Ecm1. We show that these, as well as N²‐modified 5′‐caps, can be used to tune translation of the respective mRNAs both in vitro and in cells. Appropriate modifications allow subsequent bioorthogonal chemistry, as demonstrated by intracellular live‐cell labeling of a target mRNA. The efficient and versatile N7 manipulation of the mRNA cap makes mRNAs amenable to both modulation of their biological function and intracellular labeling, and represents a valuable addition to the chemical biology toolbox.     

Colorimetric Sensing by Using Allosteric‐DNAzyme‐Coupled Rolling Circle Amplification and a Peptide Nucleic Acid–Organic Dye Probe

Target detection by the naked eye : The action of an RNA‐cleaving allosteric DNAzyme in response to ligand binding was coupled to a rolling circle amplification process to generate long single‐stranded DNA molecules for colorimetric sensing (see scheme). Upon hybridization of the resulting DNA with a complementary PNA sequence in the presence of a duplex‐binding dye, the color of the dye changed from blue to purple.

     

Treatment of Human Glioblastoma U251 Cells with Sulforaphane and a Peptide Nucleic Acid (PNA) Targeting miR-15b-5p: Synergistic Effects on Induction of Apoptosis

Glioblastoma multiforme (GBM) is a lethal malignant tumor accounting for 42% of the tumors of the central nervous system, the median survival being 15 months. At present, no curative treatment is available for GBM and new drugs and therapeutic protocols are urgently needed. In this context, combined therapy appears to be a very interesting approach. The isothiocyanate sulforaphane (SFN) has been previously shown to induce apoptosis and inhibit the growth and invasion of GBM cells. On the other hand, the microRNA miR-15b is involved in invasiveness and proliferation in GBM and its inhibition is associated with the induction of apoptosis. On the basis of these observations, the objective of the present study was to determine whether a combined treatment using SFN and a peptide nucleic acid interfering with miR-15b-5p (PNA-a15b) might be proposed for increasing the pro-apoptotic effects of the single agents. To verify this hypothesis, we have treated GMB U251 cells with SFN alone, PNA-a15b alone or their combination. The cell viability, apoptosis and combination index were, respectively, analyzed by calcein staining, annexin-V and caspase-3/7 assays, and RT-qPCR for genes involved in apoptosis. The efficacy of the PNA-a15b determined the miR-15b-5p content analyzed by RT-qPCR. The results obtained indicate that SFN and PNA-a15b synergistically act in inducing the apoptosis of U251 cells. Therefore, the PNA-a15b might be proposed in a “combo-therapy” associated with SFN. Overall, this study suggests the feasibility of using combined treatments based on PNAs targeting miRNA involved in GBM and nutraceuticals able to stimulate apoptosis.     

Investigation of the Structure and Dynamics of the Capsid–Spacer Peptide 1–Nucleocapsid Fragment of the HIV‐1 Gag Polyprotein by Solution NMR Spectroscopy

Structural studies of HIV‐1 Gag, the primary structural polyprotein involved in retroviral assembly, have been challenging, owing to its flexibility and conformational heterogeneity. Using residual dipolar couplings, we show that the four structural units of the capsid (CA)–spacer peptide 1 (SP1)–nucleocapsid (NC) fragment of HIV‐1 Gag (namely, the N‐ and C‐terminal domains of capsid, and the N‐ and C‐terminal Zn knuckles of nucleocapsid) have the same structures as their individually isolated counterparts, and tumble semi‐independently of one another in the absence of nucleic acids. Nucleic acids bind exclusively to the nucleocapsid domain and fix the orientation of the two Zn knuckles relative to one another so that the nucleocapsid domain/nucleic acid complex behaves as a single structural unit. The low ¹⁵N–{¹H} heteronuclear NOE values (≤0.4), the close to zero values for the residual dipolar couplings of the backbone amides, and minimal deviations from random‐coil chemical shifts for the C‐terminal tail of capsid and SP1, both in the absence and presence of nucleic acids, indicate that these regions are intrinsically disordered in the context of CA–SP1–NC.     

Improving Site‐Directed RNA Editing In Vitro and in Cell Culture by Chemical Modification of the GuideRNA

Adenosine‐to‐inosine deamination can be re‐addressed to user‐defined mRNAs by applying phosphothioate/2′‐methoxy‐modified guideRNAs. Dense chemical modification of the guideRNA clearly improves performance of the covalent conjugates inside the living cell. Furthermore, careful positioning of a few modifications controls editing selectivity in vitro and was exploited for the challenging repair of the Factor 5 Leiden missense mutation.     

Exceptionally Selective and Tunable Sensing of Guanine Derivatives and Analogues by Structural Complementation in a G‐Quadruplex

A guanine‐vacancy‐bearing G‐quadruplex (GVBQ) interacts with guanine and derivatives by a structural complementation to form a more stable and intact G‐quadruplex. Sensors using GVBQs are devised to detect guanine and other nucleobases, and their derivatives derived from structurally similar compounds. A strict requirement of Hoogsteen hydrogen bonds between the GVBQ and analyte in the structural complementation confers exceptional selectivity on the analyte. As such, subtle modifications on analytes affecting even a single hydrogen bond can preclude the recognition. In principle, the strategy may also be expanded to detect many planar cyclic compounds. Because nucleobases and derivatives/metabolites are involved in many physiological and pathological processes, this type of sensor may find applications in risk assessment of pathogenesis and therapeutics related to nucleic acid metabolism.     

Functional Nanoparticles with a Reducible Tetrasulfide Motif to Upregulate mRNA Translation and Enhance Transfection in Hard‐to‐Transfect Cells

Effective messenger RNA (mRNA) transfection in hard‐to‐transfect cells delivered by vectors is a long‐standing challenge. Now it is hypothesized that the high intracellular glutathione level is associated with suppressed mRNA translation. This theory leads to a new design principle of next‐generation mRNA vectors: nanoparticles with glutathione depletion chemistry upregulate mRNA translation and enhance transfection, which is beneficial for mRNA delivery in hard‐to‐transfect cells in vitro and in vivo.     

Detoxifying Polyhalogenated Catechols through a Copper‐Chelating Agent by Forming Stable and Redox‐Inactive Hydrogen‐Bonded Complexes with an Unusual Perpendicular Structure

The use of selective metal chelating agents with preference for binding of a specific metal ion to investigate its biological role is becoming increasingly common. We found recently that a well‐known copper‐specific chelator 2,9‐dimethyl‐1,10‐phenanthroline (2,9‐Me₂OP) could completely inhibit the synergistic toxicity induced by tetrachlorocatechol (TCC) and sodium azide (NaN₃). However, its underlying molecular mechanism is still not clear. Here, we show that the protection by 2,9‐Me₂OP is not due to its classic copper‐chelating property, but rather due to formation of a multiple hydrogen‐bonded complex between 2,9‐Me₂OP and TCC, featuring an unusual perpendicular arrangement of the two binding partners. The two methyl groups at the 2,9 positions in 2,9‐Me₂OP were found to be critical to stabilize the 2,9‐Me₂OP/TCC complex due to steric hindrance, and therefore completely prevents the generation of the reactive and toxic semiquinone radicals by TCC/NaN₃. This represents the first report showing that an unexpected new protective mode of action for the copper “specific” chelating agent 2,9‐Me₂OP by using its steric hindrance effect of the two CH₃ groups not only to chelate copper, but also to “chelate” a catechol through multiple H‐bonding. These findings may have broad biological implications for future research of this widely used copper‐chelating agent and the ubiquitous catecholic compounds.     

Conformational Change from a Twisted Figure‐Eight to an Open‐Extended Structure in Doubly Fused 36π Core‐Modified Octaphyrins Triggered by Protonation: Implication on Photodynamics and Aromaticity

Two examples of core‐modified 36π doubly fused octaphyrins that undergo a conformational change from a twisted figure‐eight to an open‐extended structure induced by protonation are reported. Syntheses of the two octaphyrins (in which Ar=mesityl or tolyl) were achieved by a simple acid‐catalyzed condensation of dipyrrane unit containing an electron‐rich, rigid dithienothiophene (DTT) core with pentafluorobenzaldehyde followed by oxidation with 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ). The single‐crystal X‐ray structure of the octaphyrin (in which Ar=mesityl) shows a figure‐eight twisted conformation of the expanded porphyrin skeleton with two DTT moieties oriented in a staggered conformation with a π‐cloud distance of 3.7 Å. Spectroscopic and quantum mechanical calculations reveal that both octaphyrins conform to a [4n]π nonaromatic electronic structure. Protonation of the pyrrole nitrogen atoms of the octaphyrins results in dramatic structural change, which led to 1) a large redshift and sharpening of absorption bands in electronic absorption spectrum, 2) a large change in chemical shift of pyrrole β‐CH and ? NH protons in the ¹H NMR spectrum, 3) a small increase in singlet lifetimes, and 4) a moderate increase in two‐photon absorption cross‐section values. Furthermore, nucleus‐independent chemical shift (NICS) values calculated at various geometrical positions show positive values and anisotropy‐induced current density (AICD) plots indicate paratropic ring‐currents for the diprotonated form of the octaphyrin (in which Ar=tolyl); the single‐crystal X‐ray structure of the diprotonated form of the octaphyrin shows an extended structure in which one of the pyrrole ring of each dipyrrin subunit undergoes a 180 ° ring‐flip. Four trifluoroacetic acid (TFA) molecules are bound above and below the molecular plane defined by meso‐carbon atoms and are held by N? H ??? O, N? H ??? F, and C? H ??? F intermolecular hydrogen‐bonding interactions. The extended‐open structure upon protonation allows π‐delocalization and the electronic structure conforms to a [4n]π Hückel antiaromatic in the diprotonated state.