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Fluorescent base analogs (FBAs) are powerful probes of nucleic acids’ structures and dynamics. However, previously reported FBAs exhibit relatively low brightness and therefore limited sensitivity of detection. Here we report the hitherto brightest FBA that has ideal molecular rotor properties for detecting local dynamic motions associated with base pair mismatches. The new trans-stilbene annulated uracil derivative “tsT” exhibits bright fluorescence emissions in various solvents (ε × Φ = 3400–29 700 cm–1M–1) and is highly sensitive to mechanical motions in duplex DNA (ε × Φ = 150–4250 cm–1M–1). tsT is thereby a “smart” thymidine analog, exhibiting a 28-fold brighter fluorescence intensity when base paired with A as compared to T or C. Time-correlated single photon counting revealed that the fluorescence lifetime of tsT (τ = 4–11 ns) was shorter than its anisotropy decay in well-matched duplex DNA (θ = 20 ns), yet longer than the dynamic motions of base pair mismatches (0.1–10 ns). These properties enable unprecedented sensitivity in detecting local dynamics of nucleic acids.

Fluorescent nucleoside triphosphates are powerful probes of DNA synthesis, but their potential use in living animals has been previously underexplored. Here, we report the synthesis and characterization of 7-deaza-(1,2,3-triazole)-2′-deoxyadenosine-5′-triphosphate (dATP) derivatives of tetramethyl rhodamine (“TAMRA-dATP”), cyanine (“Cy3-dATP”), and boron-dipyrromethene (“BODIPY-dATP”). Upon microinjection into live zebrafish embryos, all three compounds were incorporated into the DNA of dividing cells; however, their impact on embryonic toxicity was highly variable, depending on the exact structure of the dye. TAMRA-EdATP exhibited superior characteristics in terms of its high brightness, low toxicity, and rapid incorporation and depletion kinetics in both a vertebrate (zebrafish) and a nematode (Caenorhabditis elegans). TAMRA-EdATP allows for unprecedented, real-time visualization of DNA replication and chromosome segregation in vivo.

Metabolic incorporation of bioorthogonal functional groups into chromatin, followed by copper-free conjugation reactions, often gives low yields due to steric hindrance. Here we report that a cationic Sondheimer diyne derivative “DiMOC” rapidly reacts with azide groups in duplex DNA that are otherwise unreactive toward aliphatic cyclooctynes such as bicyclo[6.1.0]nonyne (BCN). DiMOC reversibly intercalates into duplex DNA and undergoes tandem strain-promoted cross-linking of two different azide groups to give DNA-DiMOC-“X” cross-links, where “X” theoretically represents a fluorescent probe, affinity tag, RNA, protein, carbohydrate, and so forth. As a proof of principle, the metabolic incorporation of azide-modified nucleosides into cellular DNA or RNA, followed by treatment with DiMOC and a fluorescent azide enabled visualization of newly synthesized nucleic acids in whole cells.

Previous chemotherapy research has focused almost exclusively on apoptosis. Here, a standard frontline drug combination of cytarabine and idarubicin induces distinct features of caspase-independent, poly(ADP-ribose) polymerase 1 (PARP-1)-mediated programmed cell death “parthanatos” in acute myeloid leukemia (AML) cell lines (n = 3/10 tested), peripheral blood mononuclear cells from healthy human donors (n = 10/10 tested), and primary cell samples from patients with AML (n = 18/39 tested, French-American-British subtypes M4 and M5). A 3-fold improvement in survival rates is observed in the parthanatos-positive versus -negative patient groups (hazard ratio [HR] = 0.28–0.37, p = 0.002–0.046). Manipulation of PARP-1 activity in parthanatos-competent cells reveals higher drug sensitivity in cells that have basal PARP-1 levels as compared with those subjected to PARP-1 overexpression or suppression. The same trends are observed in RNA expression databases and support the conclusion that PARP-1 can have optimal levels for favorable chemotherapeutic responses.

A new fluorescent cytosine analog “tsC” containing a trans-stilbene moiety was synthesized and incorporated into hemiprotonated base pairs that comprise i-motif structures. Unlike previously reported fluorescent base analogs, tsC mimics the acid–base properties of cytosine (pKa≈ 4.3) while exhibiting bright (ε × Φ ≈ 1000 cm–1M–1) and red-shifted fluorescence (λem= 440 → 490 nm) upon its protonation in the water-excluded interface of tsC+:C base pairs. Ratiometric analyses of tsC emission wavelengths facilitate real-time tracking of reversible conversions between single-stranded, double-stranded, and i-motif structures derived from the human telomeric repeat sequence. Comparisons between local changes in tsC protonation with global structure changes according to circular dichroism suggest partial formation of hemiprotonated base pairs in the absence of global i-motif structures at pH = 6.0. In addition to providing a highly fluorescent and ionizable cytosine analog, these results suggest that hemiprotonated C+:C base pairs can form in partially folded single-stranded DNA in the absence of global i-motif structures.

Near-quantitative DNA bioconjugation and detailed mechanistic investigations of reactions involving 5-(vinyl)-2′-deoxyuridine (VdU) and maleimides are reported. According to accelerated reaction rates in solvents with increasing polarity and trends in product stereochemistry, VdU–maleimide reactions proceed via a formal [4 + 2] stepwise cycloaddition. In contrast, 5-(1,3-butadienyl)-2′-deoxyuridine (BDdU) reacts with maleimides in a concerted [4 + 2] Diels–Alder cycloaddition. VdU–maleimide reactions enable high-yielding bioconjugation of duplex DNA in vitro (>90%) as well as metabolic labeling experiments in cells.

A new concept in multifunctional anticancer agents is demonstrated. Tetrakis-(diisopropyl-guanidino) zinc phthalocyanine (Zn-DIGP) exhibits excellent properties as a photodynamic therapy (PDT) agent, as well as potential anti-metastatic activities in vivo. Zn-DIGP exhibits good cellular uptake and low toxicity in the dark (EC50> 80 μM) and is well tolerated upon its intravenous injection into mice at 8 mg/kg. Upon photoexcitation with red laser light (660 nm), Zn-DIGP exhibits a high quantum yield for singlet oxygen formation (Φ ≈ 0.51) that results in potent phototoxicity to cell cultures (EC50≈ 0.16 μM). Zn-DIGP is also capable of inhibiting the formation of tumor colonies in the lungs of C57BL/6 mice injected with B16F10 cells. Zn-DIGP therefore inhibits cancer growth by both light-dependent and light-independent pathways. The anti-metastatic activities of Zn-DIGP possibly result from its ability to interfere with the signaling between chemokine CXCL10 and the G protein-coupled receptor CXCR3. Zn-DIGP is a competitive inhibitor of CXCR3 activation (IC50= 3.8 μM) and selectively inhibits downstream events such as CXCL10-activated cell migration. Consistent with the presence of feedback regulation between CXCR3 binding and CXCL10 expression, Zn-DIGP causes overexpression of CXCL10. Interestingly, Zn-DIGP binds to CXCR3 without activating the receptor yet is able to cause endocytosis and degradation of this GPCR. To the best of our knowledge, Zn-DIGP is the first PDT agent that can facilitate the photodynamic treatment of primary tumors while simultaneously inhibiting the formation of metastatic tumor colonies by a light-independent mode of action.

The missing linking: BCNU is a chemotherapy drug that generates an ethylene bridge between N1of deoxyguanosine and N3of deoxycytidine. No synthesis of a DNA containing this moiety has been reported until now. A new strategy uses a photocaged nucleobase that, when released, generates a highly reactive intermediate which cross‐links the opposing DNA strand in a manner analogous to BCNU (see scheme, NBOC=ortho‐nitrobenzyloxycarbonyl).

Über Kreuz: BCNU ist ein Chemotherapeutikum, das eine Ethylbrücke zwischen N1von Desoxyguanin und N3von Desoxycytidin generiert. Bisher wurde noch über keine Synthese eines solchen DNA‐Addukts berichtet. Eine neue Synthese unter Verwendung einer photoaktivierbaren Nucleobase liefert nach Aktivierung ein hoch reaktives Zwischenprodukt, das mit einem gegenüberliegenden DNA‐Strang analog zu BCNU ein Crosslinking eingeht (siehe Schema; NBOC=ortho‐Nitrobenzyloxycarbonyl).

A synthetic strategy that utilizes O6‐protected 8‐bromoguanosine gives broad access to C8‐guanine derivatives with phenyl, pyridine, thiophene, and furan substituents. The resulting 8‐substituted 2′‐deoxyguanosines are push–pull fluorophores that can exhibit environmentally sensitive quantum yields (Φ=0.001–0.72) due to excited‐state proton‐transfer reactions with bulk solvent. Changes in nucleoside fluorescence were used to characterize metal‐binding affinity and specificity of 8‐substituted 2′‐deoxyguanosines. One derivative, 8‐(2‐pyridyl)‐2′‐deoxyguanosine (2PyG), exhibits selective binding of CuII, NiII, CdII, and ZnIIthrough a bidentate effect provided by the N7 position of guanine and the 2‐pyridyl nitrogen atom. Upon incorporation into DNA, 2‐pyridine‐modified guanine residues selectively bind to CuIIand NiIIwith equilibrium dissociation constants (Kd) that range from 25 to 850 nM; the affinities depend on the folded state of the oligonucleotide (duplex>G‐quadruplex) as well as the identity of the metal ion (Cu>Ni≫Cd). These binding affinities are approximately 10 to 1 000 times higher than for unmodified metal binding sites in DNA, thereby providing site‐specific control of metal localization in alternatively folded nucleic acids. Temperature‐dependent circular‐dichroism studies reveal metal‐dependent stabilization of duplexes, but destabilization of G‐quadruplex structures upon adding CuIIto 2PyG‐modified oligonucleotides. These results demonstrate how the addition of a single pyridine group to the C8 position of guanine provides a powerful new tool for studying the effects of N7 metalation on the structure, stability, and electronic properties of nucleic acids.

No Abstract

The electronic structure of the common intercalating agent ethidium bromide (3,8‐diamino‐5‐ethyl‐6‐phenylphenanthridinium bromide) is dominated by an interplay of electron donating and withdrawing effects mediated by its nitrogen atoms. X‐ray crystallography, UV/Vis and IR absorption, fluorescence emission, and NMR spectroscopy are used to probe the electronic properties of the phenanthridinium “core” of ethidium as well as its exocyclic amines and 6‐phenyl groups. Interestingly, despite its positive charge, most of ethidium's aromatic carbon and hydrogen atoms have highelectron densities (compared to both 6‐phenylphenanthridine and benzene). The data suggest that electron donation by ethidium's exocyclic amines dominates over the electron withdrawing effects of its endocyclic iminium in their combined influence on the electron densities of these atoms. Ethidium's nitrogen atoms are, conversely, electron deficient where the 5‐position is the most electropositive, followed by the 3‐amino, and lastly the 8‐amino group. These results have been used to generate an empirically‐based π‐electron density map of ethidium that may prove useful to understanding its nucleic acid binding specificity.

No Abstract

We have used the backbone cyclic proteinomimetics approach to develop peptides that functionally mimic the arginine-rich motif (ARM) of the HIV-1 Tat protein. This consensus sequence serves both as a nuclear localization signal (NLS) and as an RNA binding domain. Based on the NMR structure of Tat, we have designed and synthesized a backbone cyclic ARM mimetic peptide library. The peptides were screened for their ability to mediate nuclear import of the corresponding BSA conjugates in permeabilized cells. One peptide, designated “Tat11,” displayed active NLS properties. Nuclear import of Tat11-BSA was found to proceed by the same distinct pathway used by the Tat-NLS and not by the common importin α pathway, which is used by the SV40-NLS. Most of the Tat-derived backbone cyclic peptides display selective inhibitory activity as demonstrated by the inhibition of the nuclear import mediated by the Tat-NLS and not by the SV40-NLS. The Tat-ARM-derived peptides, including Tat-11, also inhibited binding of the HIV-1 Rev-ARM to its corresponding RNA element (Rev response element) with inhibition constants of 5 nm. Here we have shown for the first time (a) a functional mimetic of a protein sequence, which activates a nuclear import receptor and (b) a mimetic of a protein sequence with a dual functionality. Tat11 is a lead compound which can potentially inhibit the HIV-1 life cycle by a dual mechanism: inhibition of nuclear import and of RNA binding.

Modified nucleoside triphosphates (NTPs) are powerful probes and medicines, but their anionic character impedes membrane permeability. As such, invasive delivery techniques, transport carriers, or prodrug strategies are required for their in vivouse. Here, we present a fluorescent 2′-deoxyribonucleoside triphosphate “TAMRA-dATP” that exhibits surprisingly high bioavailability in vivo. TAMRA-dATP spontaneously forms nanoparticles in Mg+2-containing buffers that are taken into the vesicles of living cells and animals by energy-dependent processes. In cell cultures, photochemical activation with yellow laser light (561 nm) facilitated endosomal escape of TAMRA-dATP, resulting in its metabolic incorporation into DNA in vitro. In contrast, in vivostudies revealed that TAMRA-dATP is extensively trafficked by active pathways into cellular DNA of zebrafish (Danio rerio) and Caenorhabditis eleganswhere DNA labeling was observed in live animals, even without photochemical release. Metabolic labeling of DNA in whole, living animals can therefore be achieved by simply soaking animals in a buffer containing TAMRA-dATP or a structurally related compound, Cy3-dATP.

Lanthanide ions can mediate both phosphomonoester hydrolysis and β-elimination of inorganic phosphate from polypeptide substrates under near-physiological conditions of pH, temperature, and salt.

No Abstract Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2000/z14440_s.pdf or from the author.

No Abstract Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2000/z14440_s.pdf or from the author.

Symmetrical homometallic dinuclear complexes of the type Rudpq22phen–SOS–phen4, with a flexible 2-mercaptoethyl ether linker joining the two Rudpq2phen2-based sub-units, have DNA dissociation constants Kd in the nM range.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

For Abstract see ChemInform Abstract in Full Text.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.