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To date, there are limited approaches for the direct and rapid visualization (on site) of tumor tissues for pathological assessment and for aiding cytoreductive surgery. Herein, we have designed FIT-PNAs (forced-intercalation-peptide nucleic acids) to detect two RNA cancer biomarkers. Firstly, a lncRNA (long noncoding RNA) termed CCAT1, has been shown as an oncogenic lncRNA over-expressed in a variety of cancers. The latter, an mRNA termed KRT20, has been shown to be over-expressed in metastases originating from colorectal cancer (CRC). To these FIT-PNAs, we have introduced the bis-quinoline (BisQ) cyanine dye that emits light in the red region (605–610 nm) of the visible spectrum. Most strikingly, spraying fresh human tissue taken from patients during cytoreductive surgery for peritoneal metastasis of colon cancer with an aqueous solution of CCAT1 FIT-PNA results in bright fluorescence in a matter of minutes. In fresh healthy tissue (from bariatric surgeries), no appreciable fluorescence is detected. In addition, a non-targeted FIT-PNA shows no fluorescent signal after spraying this FIT-PNA on fresh tumor tissue emphasizing the specificity of these molecular sensors. This study is the first to show on-site direct and immediate visualization of an RNA cancer biomarker on fresh human cancer tissues by topical application (spraying) of a molecular sensor.

Cyclopentane modified FIT-PNA (cpFIT-PNA) probes are reported as highly emissive RNA sensors with the highest reported brightness for FIT-PNAs. Compared to FIT-PNAs, cpFIT-PNAs have improved mismatch discrimination for several pyrimidine-pyrimidine single nucleotide variants (SNVs).

Intrinsically disordered regions (IDRs) in proteins are highly abundant, but they are still commonly viewed as long stretches of polar, solvent-accessible residues. Here we show that the disordered C-terminal domain (CTD) of HIV-1 Rev has two subregions that carry out two distinct complementary roles of regulating protein oligomerization and contributing to stability. We propose that this takes place through a delicate balance between charged and hydrophobic residues within the IDR. This means that mutations in this region, as well as the known mutations in the structured region of the protein, can affect protein function. We suggest that IDRs in proteins should be divided into subdomains similarly to structured regions, rather than being viewed as long flexible stretches.

The forced-intercalation peptide nucleic acid (FIT-PNA) concept, introduced by Seitz and co-workers, is based on replacing a nucleobase of the PNA sequence with a cyanine dye (such as thiazole orange). The cyanine dye is thus a surrogate base that is forced to intercalate in the duplex (e.g., PNA:DNA). This allows single-mismatch sensitivity as the introduction of a mismatch in the vicinity of the dye increases freedom of motion and leads to a significant depletion of its fluorescence because of the free rotation of the monomethine bond separating the two π-systems of the cyanine dye. Herein, we designed and synthesized six FIT-PNA probes, featuring bisquinoline (BisQ), a red-emitting cyanine dye recently developed in our laboratory for FIT-PNAs. By following PNA–DNA duplex fluorescence, we found new sequence-based factors governing the fluorescence response to the mismatched FIT-PNA:DNA duplex. Fluorogenic properties are correlated with the π-stacking energy of three distinctive base pair steps (BPSs) in the PNA:DNA duplex. The first two are the two BPSs opposite BisQ, whereas the third is the BPS of the mismatch position, which presumably becomes unstacked due to the mismatch. We suggest a predictive model for FIT-PNA single-mismatch detection mechanism, a model that can be used in future research to improve FIT-PNA design.

Efficient delivery of nucleic acids into cells still remains a great challenge. Peptide nucleic acids (PNAs) are DNA analogues with a neutral backbone and are synthesized by solid phase peptide chemistry. This allows a straightforward synthetic route to introduce a linear short peptide (a.k.a. cell-penetrating peptide) to the PNA molecule as a means of facilitating cellular uptake of PNAs. Herein, we have devised a synthetic route in which a cyclic peptide is prepared on a solid support and is extended with the PNA molecule, where all syntheses are accomplished on the solid phase. This allows the conjugation of the cyclic peptide to the PNA molecule with the need of only one purification step after the cyclic peptide–PNA conjugate (C9–PNA) is cleaved from the solid support. The PNA sequence chosen is an antimiR-155 molecule that is complementary to mature miR-155, a well-established oncogenic miRNA. By labeling C9–PNA with fluorescein isothiocyanate, we observe efficient cellular uptake into glioblastoma cells (U87MG) at a low concentration (0.5 μM), as corroborated by fluorescence-activated cell sorting (FACS) analysis and confocal microscopy. FACS analysis also suggests an uptake mechanism that is energy-dependent. Finally, the antimiR activity of C9–PNA was shown by analyzing miR155 levels by quantitative reverse transcription polymerase chain reaction and by observing a reduction in cell viability and proliferation in U87MG cells, as corroborated by XTT and colony formation assays. Given the added biological stability of cyclic versus linear peptides, this synthetic approach may be a useful and straightforward approach to synthesize cyclic peptide–PNA conjugates.

Alternative splicing, a fundamental step in gene expression, is deregulated in many diseases. Splicing factors (SFs), which regulate this process, are up- or down regulated or mutated in several diseases including cancer. To date, there are no inhibitors that directly inhibit the activity of SFs. We designed decoy oligonucleotides, composed of several repeats of a RNA motif, which is recognized by a single SF. Here we show that decoy oligonucleotides targeting splicing factors RBFOX1/2, SRSF1 and PTBP1, can specifically bind to their respective SFs and inhibit their splicing and biological activities both in vitro and in vivo. These decoy oligonucleotides present an approach to specifically downregulate SF activity in conditions where SFs are either up-regulated or hyperactive., Alternative splicing, critical for gene expression, is deregulated in many diseases. Here the authors develop decoy oligonucleotides to specifically downregulate splicing factors activity.

The DNA mimic, PNA (peptide nucleic acid), has been with us now for almost 3 decades [...]

Efficient delivery of oligonucleotides still remains a challenge in the field of oligonucleotide based therapy. Peptide nucleic acid (PNA), a DNA analogue that is typically synthesized by solid phase peptide chemistry, has been conjugated to a variety of cell penetrating peptides (CPP) as a means of improving its cellular uptake. These CPPs typically deliver their cargoes into cells by an endosomal-dependent mechanism resulting in lower bioavailability of the cargo. Herein, we designed and synthesized PNA-peptide conjugates as splice switching oligonucleotides (SSO) targeting the Mnk2 gene, a therapeutic target in cancer. In humans, the MKNK2 gene, is alternatively spliced, generating isoforms with opposite biological activities: Mnk2a and Mnk2b. It was found that the Mnk2a isoform is down-regulated in breast, lung, brain, and colon tumors and is a tumor suppressor, whereas MnK2b is oncogenic. We have designed and synthesized PNAs that were conjugated to either of the following peptides: a nuclear localization sequence (NLS) or a cytosol localizing internalization peptide (CLIP6). CLIP6-PNA demonstrates effective cellular uptake and exclusively employs a nonendosomal mechanism to cross the cellular membranes of glioblastoma cells (U87). Simple incubation of PNA-peptide conjugates in human glioblastoma cells up-regulates the Mnk2a isoform leading to cancer cell death.

Carboxylates and dicarboxylates are important phosphate mimics. Herein, we present a simple synthetic route for the preparation of RNA carboxylate/dicarboxylate conjugates, starting from suitably protected NH2- and COOH-containing molecules that are coupled to the RNA on the solid support. The key point in our method was the use of trimethylsilylethanol (TMSE-OH) protecting group, which is removed simultaneously with the silyl protecting group on the 2'-OH of the RNA ribose (e.g. t-Butyldimethylsilyl) during the final RNA cleavage/deprotection steps. The usefulness of this method was demonstrated by preparing different RNA-phosphate mimics oligos.

To improve visualization of malignant regions in the colon epithelium during diagnostic procedures, we have recently suggested a multimodal system comprising the water-soluble cationized polyacrylamide, tagged with the near infrared dye derivative IR-783-S-Ph-COOH [fluorescent-cationized polyacrylamide (Flu-CPAA)] and conjugated to the recognition peptide VRPMPLQ to form Flu-CPAA-Pep. The fluorescent-cationized polyacrylamide-peptide conjugate (Flu-CPAA-Pep) is then incorporated into echogenic microbubbles (MBs) made of polylactic acid (PLA) to protect it from pre-mature interactions with plasma proteins upon intravenous administration. It is expected that under directed ultrasound interrogation the Flu-CPAA-Pep cargo would be released in the region of interest, as a result of the MBs rupture into submicron PLA fragments (SPF). Due to their nanoscale dimension, the SPF will escape from the vasculature and allow a specific binding of the Flu-CPAA-Pep to the suspected malignant tissue. The complex nature of the system requires a multifaceted statistically based experimental design. Here we apply a design of experiment methodology to enable effective screening of key parameters in our experimental setup. It enables the assessment of the role of the different formulation parameters by identifying statistically significant interactions as observed in vitro (cell lines) and in vivo (colon cancer-induced rat model). Particularly important was the identification of the interaction between the fraction (mol%) of the cationic monomer in the Flu-CPAA and (a) the presence of recognition peptide as assessed in the in vitro experiments and (b) the use of a presenting platform (whether MBs or SPF) as assessed in the in vivo experiments. Copyright © 2015 John Wiley & Sons, Ltd.

To increase colonoscopy capability to discriminate benign from malignant polyps, we suggest combining two imaging approaches based on targeted polymeric platforms. Water-soluble cationized polyacrylamide (CPAA) was tagged with the near infrared (NIR) dye IR-783-S-Ph-COOH to form Flu–CPAA. The recognition peptide VRPMPLQ (reported to bind specifically to CRC tissues) was then conjugated with the Flu–CPAA to form Flu–CPAA–Pep which was then incorporated into echogenic microbubbles (MBs) made of polylactic acid (PLA) that are highly responsive to ultrasound. The ultimate design includes intravenous administration combined with local ultrasound and intra-colon inspection at the NIR range. In this proof of principle study PLA MBs were prepared by the double emulsion technique and loaded with several types of Flu–CPAA–Pep polymers. After insonation the submicron PLA fragments (SPF)-containing Flu–CPAA–Pep were examined in vitro for their ability to attach to colon cancer cells and in vivo (DMH induced rat model) for their ability to attach to colon malignant tissues and compared to the specific attachment of the free Flu–CPAA–Pep. The generation of SPF-containing Flu–CPAA–Pep resulted in a tissue attachment similar to that of the free, unloaded Flu–CPAA–Pep. The addition of VRPMPLQ to the polymeric backbone of the Flu–CPAA reduced cytotoxicity and improved the specific binding.

A large group of fluorescent hybridization probes, includes intercalating dyes for example thiazole orange (TO). Usually TO is coupled to nucleic acids post-synthetically which severely limits its use. Here, we have developed a phosphoramidite monomer, 10 , and prepared a 2′-OMe-RNA probe, labeled with 5-( trans - N -hexen-1-yl-)-TO-2′-deoxy-uridine nucleoside, dU TO , (Nucleoside bearing an Inter-Calating moiety, NIC), for selective mRNA detection. We investigated a series of 15-mer 2′-OMe-RNA probes, targeting the cyclin D1 mRNA, containing one or several dU TO at various positions. dU TO -2′-OMe-RNA exhibited up to 7-fold enhancement of TO emission intensity upon hybridization with the complementary RNA versus that of the oligomer alone. This NIC-probe was applied for the specific detection of a very small amount of a breast cancer marker, cyclin D1 mRNA, in total RNA extract from cancerous cells (250 ng/μl). Furthermore, this NIC-probe was found to be superior to our related NIF (Nucleoside with Intrinsic Fluorescence)-probe which could detect cyclin D1 mRNA target only at high concentrations (1840 ng/μl). Additionally, dU T can be used as a monomer in solid-phase oligonucleotide synthesis, thus avoiding the need for post-synthetic modification of oligonucleotide probes. Hence, we propose dU TO oligonucleotides, as hybridization probes for the detection of specific RNA in homogeneous solutions and for the diagnosis of breast cancer.

Rel proteins in bacteria synthesize the signal molecules (p)ppGpp that trigger the Stringent Response, responsible for bacterial survival. Inhibiting the activity of such enzymes prevents the Stringent Response, resulting in the inactivation of long-term bacterial survival strategies, leading to bacterial cell death. Herein, we describe a series of deoxyguanosine-based analogs of the Relacin molecule that inhibit in vitro the synthetic activity of Rel proteins from Gram positive and Gram negative bacteria, providing a deeper insight on the SAR for a better understanding of their potential interactions and inhibitory activity. Among the inhibitors evaluated, compound 2d was found to be more effective and potent than our previously reported Relacin.

Previously, we have described 5-((4-methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6, as a fluorescent uridine analogue exhibiting a 3000-fold higher quantum yield (Φ 0.12) and maximum emission (478 nm) which is 170 nm red-shifted as compared to uridine. Here, we utilized 6 for preparation of labeled oligodeoxynucleotide (ODN) probes based on MS2 and cyclin D1 (a known breast cancer mRNA marker) sequences. Cyclin D1-derived labeled-ssODN showed a 9.5-fold decrease of quantum yield upon duplex formation. On the basis of this finding, we developed the ds-NIF (nucleoside with intrinsic fluorescence)-probe methodology for detection of cyclin D1 mRNA, by which the fluorescent probe is released upon recognition of target mRNA by the relatively dark NIF-duplex-probe. Indeed, we successfully detected, a ss-deoxynucleic acid (DNA) variant of cyclin D1 mRNA using a dark NIF-labeled duplex-probe, and monitoring the recognition process by fluorescence spectroscopy and gel electrophoresis. Furthermore, we successfully detected cyclin D1 mRNA in RNA extracted from cancerous human cells, using ds-NIF methodology.

This manuscript represents a critical review of selected topics relating to the cellular interactions of platinum anticancer drugs. The intent is not to provide a comprehensive summary of all the work described in the literature but to raise questions and cast doubts about selected topics regarding the approaches taken towards trying to elucidate the event that happens in cancer cells that were exposed to platinum complexes. The experimental methods used to study the cellular interactions of platinum complexes are reviewed and the significance of the results obtained from such studies is discussed.

siRNA-based therapeutics possess great potential to treat a wide variety of genetic disorders. However, they suffer from low cellular uptake and short half-lives in blood circulation; issues that remain to be addressed. This work is, to the best of our knowledge, the first to report the production of solid nano-in-nanoparticles, termed double nano carriers (DNCs) by means of the innovative technology of nano spray drying. DNCs (with a median size of 580-770nm) were produced by spraying at low temperatures (50°C) to prevent damage to heat-sensitive biomacromolecules like siRNA. DNCs consisting of Poly (d,l-lactide-co-glycolide) used as a wall material, encapsulating 20% human serum albumin primary nanoparticles (PNPs) loaded with siRNA, were obtained as a dry nanoparticulate powder with smooth spherical surfaces and a unique inner morphology. Incubation of pegylated or non-pegylated DNCs under sink conditions at 37°C, elicited a controlled release profile of the siRNA for up to 12 or 24h, respectively, with a minimal burst effect. Prolonged incubation of pegylated DNCs loaded with active siRNA (anti EGFR) in an A549 epithelial cell culture monolayer did not induce any apparent cytotoxicity. A slow degradation of the internalized DNCs by the cells was also observed resulting in the progressive release of the siRNA for up to 6days, as corroborated by laser confocal microscopy. The structural integrity and silencing activity of the double encapsulated siRNA were fully preserved, as demonstrated by HPLC, gel electrophoresis, and potent RNAi activity of siRNA extracted from DNCs. These results demonstrate the potential use of DNCs as a nano drug delivery system for systemic administration and controlled release of siRNA and potentially other sensitive bioactive macromolecules.

Detection of mRNA alterations is a promising approach for identifying biomarkers as means of differentiating benign from malignant lesions. By choosing the KRAS oncogene as a target gene, two types of molecular beacons (MBs) based on either phosphothioated DNA (PS-DNA-MB) or peptide nucleic acid (TO-PNA-MB, where TO = thiazole orange) were synthesized and compared in vitro and in vivo. Their specificity was examined in wild-type KRAS (HT29) or codon 12 point mutation (Panc-1, SW480) cells. Incubation of both beacons with total RNA extracted from the Panc-1 cell line (fully complementary sequence) showed a fluorescent signal for both beacons. Major differences were observed, however, for single mismatch mRNA transcripts in cell lines HT29 and SW480. PS-DNA-MB weakly discriminated such single mismatches in comparison to TO-PNA-MB, which was profoundly more sensitive. Cell transfection of TO-PNA-MB with the aid of PEI resulted in fluorescence in cells expressing the fully complementary RNA transcript (Panc-1) but undetectable fluorescence in cells expressing the K-ras mRNA that has a single mismatch to the designed TO-PNA-MB (HT29). A weaker fluorescent signal was also detected in SW480 cells; however, these cells express approximately one-fifth of the target mRNA of the designed TO-PNA-MB. In contrast, PS-DNA-MB showed no fluorescence in all cell lines tested post PEI transfection. Based on the fast hybridization kinetics and on the single mismatch discrimination found for TO-PNA-MB we believe that such molecular beacons are promising for in vivo real-time imaging of endogenous mRNA with single nucleotide polymorphism (SNP) resolution.

Triphenyl phosphonium cations (TPPs) are delocalized lipophilic cations that accumulate in the mitochondria of cells. We have explore the effect of increasing the number of TPPs on delivery of a cell-impermeable pro-apoptotic peptide to intact cells.The pro-apoptotic peptide D-(KLAKLAK)(2) (KLA) was extended with 0-3 L-Lysines modified at their ε-amine with TPP. Peptides were studied in HeLa cells to determine their cytotoxic activity and cellular uptake.In HeLa cells, the increased cytotoxicity correlates with the number of TPPs; the peptide with 3 TPP molecules (3-KLA) exerts the highest cytotoxic activity. This FITC-labeled peptide is found to accumulate in intact HeLa cells, whereas peptides with 0-2 TPPs are not detected at the same peptide concentration. Mitochondria-dependent apoptosis of HeLa cells in the presence of 3-KLA was followed by propidium iodide, Annexin-V and DiOC fluorescence by FACS.A facile synthetic methodology has been presented for the delivery of a biologically active peptide into mitochondria of intact cells by attaching multiple TPP moieties to the peptide. This approach was shown to dramatically increase biological activity of the peptide as a pro-apoptotic agent.

Triplex-forming oligonucleotides have been explored in the last 3 decades as highly specific gene-modifying agents. Such agents have been showed to either upregulate or shut down gene expression in vitro, an outcome that depends on the specifically designed biological system. One interesting approach is to tether to the oligonucleotide a photoreactive moiety. After hybridization to the DNA target (typically single- or double-stranded DNA), a site-specific photoinduced reaction may take place at a timely manner. Further, as the light source may be focused at a certain area, one has control on the location at which the phototriggered DNA modification takes place. In this regard, the use of tissue-penetrating photons (typically 630-950 nm) would be most relevant for in vivo applications as photoactivation may lead to site-specific DNA modification at a specific tissue/organ. In this review we highlight the advances made in this field and discuss the hurdles that lay ahead for the realization of phototriggered triplex-forming oligonucleotides as a solid therapeutic approach.

The ability to cleave DNA with the aid of chemical nucleases has been a challenge in the scientific community, particularly in the absence of a redox active metal ion. Inspired by structural characterization of the active site found in Staphylococcal nuclease, we have designed a series of organic molecule comprising cyclic pentapeptides conjugated to a DNA intercalator (e.g., anthraquinone). The cyclic peptide is designed to cleave the phosphodiester backbone, whereas the intercalator is expected to improve binding affinity to the substrate (DNA). Our lead compound (1-AQ), composed of the cyclic peptide cyc-d-Lys-Gly-Arg-Ser-Arg conjugated to anthraquinone, degrades DNA into small fragments at physiologically relevant conditions (i.e., 37 degrees C, pH = 7.4). We find that 1-AQ is highly effective in degrading duplex DNA at micromolar concentrations as corroborated by agarose and polyacrylamide gel electrophoresis. Changing the DNA intercalator to acridine (1-Ac) renders the compound comparable in nuclease activity to 1-AQ. In comparison to control compounds (Lin-1 and 1) that lack either the cyclic scaffold or the DNA intercalator, our lead compound (1-AQ) is found to be significantly more active as a DNA chemical nuclease. We have studied the importance of the triad (Arg-Ser-Arg) as the designed module for DNA cleavage. Changing l-Ser to l-Glu (cyc-d-Lys-Gly-Arg-Glu-Arg, Glu-AQ) results in an inactive compound, whereas the cyclic peptide Gly-AQ (cyc-d-Lys-Gly-Arg-Gly-Arg, where glycine replaces l-serine) has similar DNA nuclease activity to 1-AQ. In addition, changing the stereochemistry from d-lysine to l-lysine results in a cyclic peptide (1-L-AQ) exerting weak DNA nuclease activity, highlighting the importance of the cyclic backbone conformation for efficient DNA nuclease activity. The addition of ROS scavengers does not reduce DNA nuclease activity; an observation that supports a hydrolytic cleavage mechanism. Finally, we have estimated the kinetics of DNA cleavage of a 15-mer duplex DNA substrate by compound 1-AQ. By monitoring DNA duplex degradation by following the change in absorbance (hyperchromicity) at various 1-AQ concentrations, we report a maximal k(obs) value (as an underestimation of k(max)) of 1.62 h(-1) at a 7.5-fold of 1-AQ. We have also compared the other two active peptide conjugates, namely, 1-Ac and Gly-AQ to that of 1-AQ. Both compounds exert similar nuclease activity to that of 1-AQ. To the best of our knowledge, this is the most active metal-free DNA nuclease reported to date that exerts its DNA nuclease activity at biologically relevant conditions.

A variety of diseases are related to mitochondrial dysfunction. Hence, the ability to transport drugs to mitochondria that are otherwise cell impermeable would be of great therapeutic potential. Triphenylphosphonium (TPP) cations have been shown to accumulate in mitochondria when attached to small molecules. Here we report on the consequence of increasing the number of TPP moieties that are covalently linked to a model hydrophilic peptide Hemagglutinin A (HA). By extending the HA peptide with l-lysine amino acids to which the TPP's are covalently linked through the epsilon-amine, we have systematically synthesized the HA peptide with 0-3 TPP's. All peptides were subsequently labeled with FITC at the N-terminus. Cellular uptake and mitochondrial localization of the HA-TPP conjugates in HeLa cells were profoundly augmented with increasing number of TPPs, suggesting that this approach is applicable for the delivery of peptides. Furthermore, confocal microscopy demonstrated that the peptides localize to mitochondria. Importantly, all peptide conjugates did not show apparent toxicity at concentrations that are several orders of magnitude higher than those used for HA peptide delivery.

Selective photoinduced modulation of DNA may provide a powerful therapeutic tool allowing spatial and temporal control of the photochemical reaction. We have explored the photoreactivity of peptide nucleic acid (PNA) conjugates that were conjugated to a highly potent photosensitizer, Rose Bengal (RB). In addition, a short PEGylated peptide (K-PEG8-K) was conjugated to the C-terminus of the PNA to improve its water solubility. A short irradiation (visible light) of PNA conjugates with a synthetic DNA resulted in highly efficient photomodulation of the DNA as evidenced by polyacrylamide gel electrophoresis (PAGE). In addition, a PNA-RB conjugate replacing K-PEG8-K with four l-glutamic acids (E4) was found to be photoinactive. Irradiation of active PNA-RB conjugates with synthetic DNA in D20 augments the photoactivity; supporting the involvement of singlet oxygen. PAGE, HPLC, and MALDI-TOF analyses indicate that PNA-DNA photo-cross-linking is a significant pathway in the observed photoreactivity. Selective photo-cross-linking of such PNA-RB conjugates may be a novel approach to selective photodynamic therapy (sPDT) as such molecules would be sequence-specific, cell-permeable, and photoactivated in the visible region.

Irradiation of plasmid DNA in the presence of Ru(II)-2, a modified tris(2,2'-bipyridyl)Ru(II) complex, in which two hydroxamic acid groups are attached to one of the three bipyridyl ligands, results in total fragmentation of the DNA. The photo-chemical reaction products were analyzed by gel electrophoresis, which revealed complete fragmentation. Further evidence for the complete degradation of the DNA was obtained by imaging the pre- and post-treated plasmid DNA using atomic force microscopy (AFM). A mechanism for the reaction is proposed. It initially involves the photo-chemical generation of Ru(III) ions and superoxide radicals, as corroborated by absorbance difference spectroscopy and electron paramagnetic resonance (EPR). Consequently, Ru(III) preferentially oxidizes guanine, liberating superoxide radicals that yield OH radicals. The OH radicals were identified by observing the spectral change at 532 nm of a 5'-dAdG substrate forming a colored adduct with thiobarbituric acid. These radicals are associated with the major non-specific damage exerted to DNA.

Ruthenium complexes with three bipyridyl ligands, one of which is modified by attaching one or two hydroxamic acids groups (Ru-1 and Ru-2, respectively), were synthesized. Using EPR spectroscopy, we have found that photoexcitation leads to formation of nitroxyl radicals. The nitroxyl radical concentration in Ru-2 increased dramatically in the presence of spin traps DMPO (5,5‘-dimethyl-1-pyrroline-N-oxide) and PBN (N-tert-butyl-α-phenylnitrone) characterized by strong affinity to superoxide radicals. We have attributed this behavior to the formation of a cage complex between Ru-2 and the superoxide radical. This paper concerns the study of cages formed between ruthenium complexes and molecular oxygen and the effect of functional groups attached to modified bipyridyl ligands on cage formation. The complex between Ru-2 and O_2 was formed in the ground state, probably with participation of the hydroxamic acid groups. The equilibrium constant of this complex was determined by EPR as K_(eq) ∼ 3 M^(-1). The formation of the Ru-2−O_2 complex is supported by the temperature-dependent rate of appearance of the EPR signal in the presence of PBN. Additional evidence comes from observation of paramagnetic shifts of the peaks in the 1H NMR spectrum of specific aromatic protons in the substituted bipyridyl ring upon exposure to O_2. Similar shifts were observed in the spectrum of Os-2, with osmium replacing ruthenium. Model compounds with functional groups that replace the hydroxamic acid or compounds without the metal center, but with the two hydroxamic acids, were synthesized. No shifts in the ^1H NMR spectra of these derivatives were observed in the presence of O_2. These results lead to the conclusion that both metal ions, Ru(II) or Os(II), and hydroxamic acid groups are essential components for the formation of the oxygen cage.

The design of Pt(IV) pro-drugs as anticancer agents is predicated on the assumption that they will not undergo substitution reactions before entering the cancer cell. Attempts to improve the cytotoxic properties of Pt(IV) pro-drugs included the use of haloacetato axial ligands. Herein, we demonstrate that Pt(IV) complexes with trifluoroacetato (TFA) or dichloroacetato (DCA) ligands can be unstable under biologically relevant conditions and readily undergo hydrolysis, which results in the loss of the axial TFA or DCA ligands. The half-lives for Pt(IV) complexes with two TFA or DCA ligands at pH 7 and 37 °C range from 6 to 800 min, which is short relative to the duration of cytotoxicity experiments that last 24-96 h. However, complexes with two monochloroacetato (MCA) or acetato axial ligands are stable under biologically relevant conditions. The loss of the axial ligands depends primarily on the electron-withdrawing strength of the axial ligands, but also upon the nature of the equatorial ligands. We were unable to find obvious correlations between the structures of the Pt(IV) complexes and the rates of decay of the parent compounds. The X-ray crystal structures of the bis-DCA and bis-MCA Pt(IV) derivatives of oxaliplatin did not reveal any significant structural differences that could explain the observed differences in stability.

Summary Objective 2-Ethyl-3-methylbutyl-carbamate (EMC) and 2-isopropylpentyl-carbamate (IPC) are among the most potent anticonvulsant carbamate derivatives of valproic acid. EMC and IPC are chiral compounds. Consequently, the aim of the current study was to comparatively evaluate the pharmacokinetic (PK) and pharmacodynamic (PD anticonvulsant activity) profile of EMC and IPC individual enantiomers. Methods The anticonvulsant activity of EMC and IPC individual enantiomers was evaluated in several anticonvulsant rodent models including maximal electroshock (MES), 6 Hz psychomotor, subcutaneous (pentylenetetrazole) (scMet), and the pilocarpine-induced and soman-induced status epilepticus (SE). The PK–PD relationship of EMC and IPC individual enantiomers was evaluated following intraperitoneal administration (50 mg/kg) to rats. Induction of neural tube defects (NTDs) was evaluated in a mouse strain that was highly susceptible to teratogen-induced NTDs. Results In mice and rats, (2S)-EMC exhibited anticonvulsant activity similar to that of racemic EMC in the MES and scMet tests, whereas in the 6 Hz test, racemic EMC was more potent than its two individual enantiomers. Racemic EMC exhibited a potent activity in the soman-induced SE model when administered 5 and 20 min after seizure onset with median effective dose (ED50) values of 33 and 48 mg/kg, respectively. (2R)-IPC and (2S)-IPC exhibited ED50 values similar to those of racemic IPC in the mouse and rat MES and scMet models. (2R)-IPC had similar ED50 values on the 6 Hz tests. Racemic IPC had an ED50 value of 107 mg/kg in the pilocarpine-induced SE model when given 30 min after seizure onset. Racemic EMC and IPC and their enantiomers had similar clearance (3.8–5.5 L/h/kg) and short half-life (

Fluorescent nucleoside analogs replacing natural DNA bases in an oligonucleotide have been widely used for the detection of genetic material. Previously, we have described 2-((4-(trifluoromethyl) phenyl) -trans -vinyl)-2′-deoxy-adenosine, 6 , a nucleoside analog with intrinsic fluorescence (NIF). Analog 6 exhibits a quantum yield 3115-fold higher than that of adenosine ( φ 0.81) and maximum emission which is 120 nm red shifted ( λ em 439 nm). Here, we incorporated this analog in one or several positions of cyclin D1-targeting 15-mer oligonucleotides (ONs). The fluorescence of 6 was quenched upon incorporation into an oligonucleotide (ca. 1.5–22 fold), and was further reduced upon duplex formation. Specifically, ON7 exhibited a fluorescence decrease of ca. 2- or 3-fold upon duplex formation with complementary DNA or RNA strand, respectively. We determined the kinetics of dehybridization/rehybridization process in the presence of ssDNA or ssRNA targets to optimize our probes length and established the probes' selectivity towards a specific target. Furthermore, we proved specificity of our probe to the target vs. singly mismatched targets. Our most promising ds-NIF-probe , ON7 :RNA, was used for the detection of cyclin D1 mRNA marker in cancerous cells total RNA extracts. The ds-probe specifically recognized the target as observed by a 2-fold fluorescence increase within 30 s at RT. These findings illustrate the potential of ds-NIF-probe s for the diagnosis of breast cancer.

A novel ruthenium complex has been synthesized. It is composed of three bipyridyl ligands, one of which is modified and has two hydroxamate groups. Photoexcitation of the complex with blue light (λmax = 477 nm) leads to the formation of a long-lived nitroxyl radical on hydroxamate as was detected and characterized by ESR. In anaerobic conditions, the radical was not formed, suggesting that a reactive oxygen species is required for generating the nitroxyl radical. The quenching of the excited state of ruthenium bipyridyl complexes by molecular oxygen can generate either singlet oxygen via energy transfer or superoxide radical via electron transfer. In this latter case the superoxide radical is confined in a cage complex (vide infra). Singlet oxygen, generated via energy transfer from Ru(II) in its excited state, is the reactive species that is responsible for the oxidation of the hydroxamate group to its corresponding nitroxyl radical. This was confirmed by using a specific quencher (sodium azide) and by f...

Platinum-based drugs are very effective anticancer agents that are used routinely in the clinic, and nearly 50 % of all chemotherapeutic regimens administered to patients include a platinum drug. [1] Cisplatin, carboplatin, and oxaliplatin are square planar d 8 Pt II complexes that trigger cancer cell death by binding to nuclear DNA, distorting its structure. [2] Owing to its reactivity and lack of selectivity most of the cisplatin administered reacts with nucleophiles in the blood, never reaching the tumor. These undesirable interactions limit the bioavailability of the drug and preclude oral administration. [3] One approach to overcome the drawbacks of cisplatin is to use Pt IV complexes as prodrugs. They are prepared by oxidatively adding two axial ligands to a Pt II drug. The design of these prodrugs is predicated on the assumption that the low spin octahedral d 6 Pt IV complexes are inert and will not undergo hydrolysis or ligand substitutions in the blood but will be activated in cells by reductive elimination, releasing the cytotoxic square-planar Pt II drugs (Scheme 1). [4] Yet it was reported that in some of the biotransformation products of ctc-[PtCl2(OAc)2(NH3)(c-hexylamine)] the chlorido ligands were replaced by OH while the axial OAc ligands remained intact. Negligible aquation (< 5 %) was observed for ctc[PtCl2(OAc)2(NH3)2] over 3–4 weeks. [5] Thus, the axial ligands can be used to impart favorable pharmacological properties to the drugs. Many reports describe the use of axial ligands to control the reduction potentials, lipophilicity, charge, selectivity, targeting, and cell uptake of the Pt IV complexes. [6]

Real time detection of biomarkers at the mucosal level is imperative for the prevention and efficient treatment of colorectal cancer. Cationized polyacrylamide (CPAA) with increasing charge densities was prepared by radical polymerization of acrylamide and different mol% ratios of N -acryloyl, N ′-( tert -butyl-carbonyl) diaminoethane. The NIR fluorophore derivative of IR-783, IR-783-S-Ph-COOH, was attached to the CPAA to give CPAA-783. After selecting the optimal IR-783-S-Ph-COOH ratio that avoids quenching, the preferential binding of the polymer was tested in SW-620, SW-480, HT-29, and LS-174T cancer cells. The optimal polymeric product was tested in situ in gut sac preparations of the dimethylhydrazine induced rat model. To increase the detection capabilities of CPAA-783, the FITC-labeled peptide EPPT1, that targets the cell transmembrane underglycosylated MUC-1 (uMUC-1), was conjugated to the polymer to obtain CPAA-783-EPPT1. The dually labeled modified polymer was tested in HT-29 and LS-174T cells (over expressing uMUC-1), followed by an examination in an orthotopic mouse model. CPAA-783 preferentially bound to the cancer cells, depending on CRC staging. The best binding occurred when the fraction of the cationic monomer was 100 mol%, labeled with 0.75 mol% of IR-783-S-Ph-COOH. An increase in the recognition of the dually labeled polymeric product, CPAA-783-EPPT1, towards HT-29 and LS-174T cells occurred in the lowest EPPT1 molar ratio (0.63 mol%) only, probably due to quenching phenomena and steric hindrance. Similar observation was obtained in the orthotopic mice. It is concluded that fluorescently tagged CPAA can be used for the detection of malignant tissues in colorectal cancer after luminal instillation. Dually targeted CPAA with EPPT1is feasible, but requires further optimization.

Summary Background Valproic acid (VPA) is a major antiepileptic drug (AED) that is less potent than other AEDs. 2,2,3,3-Tetramethylcyclopropanecarboxylic acid (TMCA) is an inactive cyclopropyl analogue of VPA that serves as a starting material for the synthesis of CNS-active compounds. Methods New conjugation products between N,N′-dimethylethanolamine to VPA and TMCA to form N,N-dimethylethanolamine valproate (DEVA) and N,N-dimethylethanolamine 2,2,3,3-tetramethylcyclopropionate were synthesized and their anticonvulsant activity was assessed in the maximal electroshock seizure (MES) and subcutaneous metrazol (scMet) seizure tests and the hippocampal kindling model in mice and/or rats. An amide analogue of DEVA (DEVAMIDE) was also synthesized and evaluated. The pharmacokinetics of DEVA and DEVAMIDE was comparatively evaluated in rats. Results In rats DEVA acted as a prodrug of VPA and had ED 50 values of 73mg/kg and 158mg/kg in the MES and the hippocampal kindling models, respectively. At these two anticonvulsant models DEVA was seven-times more potent than VPA. DEVAMIDE was active in the MES test at doses of 100mg/kg (mice) and its rat-MES-ED 50 =38.6mg/kg however, its protective index (PI=TD 50 /ED 50 ) was twice lower than DEVA's PI. The TMCA analogues were inactive at the mice MES and scMet models. DEVA underwent rapid metabolic hydrolysis to VPA and consequently, in its pharmacokinetic analysis only VPA plasma levels were monitored. In contrast, DEVAMIDE was stable in whole blood. Conclusion DEVA acts in rats as a prodrug of VPA yet shows a more potent anticonvulsant activity than VPA. DEVAMIDE acted as the drug on its own and was more potent than DEVA at the rat-MES test.

The bacterium Bacillus subtilis produces the DNA integrity scanning protein (DisA), a checkpoint protein that delays sporulation in response to DNA damage. DisA scans the chromosome and pauses at sites of DNA lesions. Structural analysis showed that DisA synthesizes the small molecule cyclic diadenosine monophosphate (c-di-AMP). Here, we demonstrate that the intracellular concentration of c-di-AMP rises markedly at the onset of sporulation in a DisA-dependent manner. Furthermore, exposing sporulating cells to DNA-damaging agents leads to a global decrease in the level of this molecule. This drop was associated with stalled DisA complexes that halt c-di-AMP production and with increased levels of the c-di-AMP-degrading enzyme YybT. Reduced c-di-AMP levels cause a delay in sporulation that can be reversed by external supplementation of the molecule. Thus, c-di-AMP acts as a secondary messenger, coupling DNA integrity with progression of sporulation.

Early diagnosis of gastric carcinoma is crucial for maximizing medical treatment efficacy. For the purpose of real time diagnosis ("virtual biopsy") of stomach malignancy we developed a polyHEMA platform capable of capturing human alpha1-antitrypsin precursor (A1AT); a model proteinaceous luminal biomarker. Its specific attachment to the polymeric platform was accomplished by immobilized trypsin, which was linked to the surface of the polyHEMA film by a series of PEG-based spacers. Recognition was enabled by adapting an ELISA-like methodology, using rabbit anti-A1AT and HRP-conjugated anti-rabbit IgG as a secondary antibody. Since this A1AT-sensing platform was designed to be detected by endoscopic means such as a video capsule, its physical stability was tested after casting on top of a polycarbonate surface. It was found that, in contrast to classical ELISA analysis performed on polystyrene plates, A1AT detection was possible only when spacer arms were used to immobilize the capturing moiety, trypsin, with a 7-fold increase in the optical signal and a saturation kinetics dependency upon the concentration of the A1AT biomarker.

DNA photocleavage by triplex forming oligonucleotides (TFO) has potential implications in both biotechnology and medicine. We have synthesized a series of homopurine DNA and DNA/LNA 14-mers to which an amino acid (glycine or l-tryptophan) and a cyanine dye are covalently linked. Two cyanine dyes were examined that include a quinolinium ring linked to a benzothiazolium ring through a monomethine (TO1) or trimethine (TO2) linker. The 14-mer sequence was chosen to target mdm2, a ubiquitin ligase (E3) that regulates p53 by promoting its ubiquitylation and proteosomal degradation. Such inhibition has been previously proposed as a therapeutic approach to target wild-type p53-expressing cancers. To examine whether our TFO conjugates photocleave the mdm2 target, we incubated the various conjugates with the mdm2 plasmid and irradiated the samples with visible light. We show that only the TFO with the complementary sequence and with an intervening l-tryptophan leads to the linearization of the plasmid after a short irradiation time (10 min) exciting the dye (lambda(max)(TO1) = 500 nm and lambda(max)(TO2) = 630 nm) with visible light. Furthermore, the photoreactivity is more pronounced for the LNA/DNA conjugate, an observation that is consistent with improved hybridization to the DNA target. Sequence specificity of the photoreaction is further corroborated on a synthetic 44-mer duplex containing the TFO site. Evidence for a ROS-dependent mechanism is also given and discussed.

We report on a rather unknown feature of oligonucleotides, namely, their potent antioxidant activity. Previously, we showed that nucleotides are potent antioxidants in Fe(II)/Cu(I/II)-H(2)O(2) systems. Here, we explored the potential of 2'-deoxyoligonucleotides as inhibitors of the Fe(II)/Cu(I/II)-induced *OH formation from H(2)O(2). The oligonucleotides [d(A)(5,7,20); d(T)(20); (2'-OMe-A)(5)] proved to be highly potent antioxidants with IC(50) values of 5-17 or 48-85 microM in inhibiting Fe(II)/Cu(I)- or Cu(II)-induced H(2)O(2) decomposition, respectively, thus representing a 40-215-fold increase in potency as compared with Trolox, a standard antioxidant. The antioxidant activity is only weakly dependent on the oligonucleotides' length or base identity. We analyzed by matrix-assisted laser desorption/ionization time of flight mass spectrometry and (1)H-NMR spectroscopy the composition of the d(A)(5) solution exposed to the aforementioned oxidative conditions for 4 min or 24 h. We concluded that the primary (rapid) inhibition mechanism by oligonucleotides is metal ion chelation and the secondary (slow) mechanism is radical scavenging. We characterized the Cu(I)-d(A)(5) and Cu(II)-d(A)(7) complexes by (1)H-NMR and (31)P-NMR or frozen-solution ESR spectroscopy, respectively. Cu(I) is probably coordinated to d(A)(5) via N1 and N7 of two adenine residues and possibly also via two phosphate/bridging water molecules. The ESR data suggest Cu(II) chelation through two nitrogen atoms of the adenine bases and two oxygen atoms (phosphates or water molecules). We conclude that oligonucleotides at micromolar concentrations prevent Fe(II)/Cu(I/II)-induced oxidative damage, primarily through metal ion chelation. Furthermore, we propose the use of a short, metabolically stable oligonucleotide, (2'-OMe-A)(5), as a highly potent and relatively long lived (t(1/2) approximately 20 h) antioxidant.

The electrochemistry of DNA films modified with different redox probes linked to DNA through saturated and conjugated tethers was investigated. Experiments feature two redox probes bound to DNA on two surfaces: anthraquinone (AQ)-modified uridines incorporated into thiolated DNA on gold (Au) and 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO)-modified uridines in pyrene-labeled DNA on highly oriented pyrolytic graphite (HOPG). The electrochemistry of these labels when incorporated into DNA has been examined in DNA films containing both well matched and mismatched DNA. DNA-mediated electrochemistry is found to be effective for the TEMPO probe linked with an acetylene linker but not for a saturated TEMPO connected through an ethylenediamine linker. For the AQ probe, DNA-mediated electrochemistry is found with an acetylene linker to uridine but not with an alkyl chain to the 5' terminus of the oligonucleotide. Large electrochemical signals and effective discrimination of intervening base mismatches are achieved for the probes connected through the acetylene linkages, while probes connected through saturated linkages exhibit small electrochemical signals associated only with direct surface to probe charge transfer and poor mismatch discrimination. Thus DNA electrochemistry with these probes is dramatically influenced by the chemical nature of their linkage to DNA. These results highlight the importance of effective coupling into the pi-stack for long-range DNA-mediated electrochemistry.

The [4Fe-4S] cluster is ubiquitous to a class of base excision repair enzymes, in organisms ranging from bacteria to man, and was first considered as a structural element, owing to its redox stability under physiological conditions. When studied bound to DNA, two of these repair proteins (MutY and Endonuclease III from Escherichia coli) display DNA-dependent reversible electron transfer with characteristics typical of high potential iron proteins. These results have inspired a reexamination of the role of the [4Fe-4S] cluster in this class of enzymes. Might the [4Fe-4S] cluster be used as a redox cofactor to search for damaged sites using DNA-mediated charge transport, a process well known to be highly sensitive to lesions and mismatched bases? Described here are experiments demonstrating the utility of DNA-mediated charge transport in characterizing these DNA-binding metalloproteins, as well as efforts to elucidate this new function for DNA as an electronic signaling medium among the proteins.

Despite a low copy number within the cell, base excision repair (BER) enzymes readily detect DNA base lesions and mismatches. These enzymes also contain [Fe 4 S 4 ] clusters, yet a redox role for these iron cofactors had been unclear. Here, we provide evidence that BER proteins may use DNA-mediated redox chemistry as part of a signaling mechanism to detect base lesions. By using chemically modified bases, we show electron trapping on DNA in solution with bound BER enzymes by electron paramagnetic resonance (EPR) spectroscopy. We demonstrate electron transfer from two BER proteins, Endonuclease III (EndoIII) and MutY, to modified bases in DNA containing oxidized nitroxyl radical EPR probes. Electron trapping requires that the modified base is coupled to the DNA π-stack, and trapping efficiency is increased when a noncleavable MutY substrate analogue is located distally to the trap. These results are consistent with DNA binding leading to the activation of the repair proteins toward oxidation. Significantly, these results support a mechanism for DNA repair that involves DNA-mediated charge transport.

Lipophilic Fe(III) chelators were synthesized and shown to protect oligodendrial cells from oxidative damage induced by Fe(III) and hydrogen peroxide.

DNA charge transport (CT) chemistry provides a route to carry out oxidative DNA damage from a distance in a reaction that is sensitive to DNA mismatches and lesions. Here, DNA-mediated CT also leads to oxidation of a DNA-bound base excision repair enzyme, MutY. DNA-bound Ru(III), generated through a flash/quench technique, is found to promote oxidation of the [4Fe-4S] 2+ cluster of MutY to [4Fe-4S] 3+ and its decomposition product [3Fe-4S] 1+ . Flash/quench experiments monitored by EPR spectroscopy reveal spectra with g = 2.08, 2.06, and 2.02, characteristic of the oxidized clusters. Transient absorption spectra of poly(dGC) and [Ru(phen) 2 dppz] 3+ (dppz = dipyridophenazine), generated in situ , show an absorption characteristic of the guanine radical that is depleted in the presence of MutY with formation instead of a long-lived species with an absorption at 405 nm; we attribute this absorption also to formation of the oxidized [4Fe-4S] 3+ and [3Fe-4S] 1+ clusters. In ruthenium-tethered DNA assemblies, oxidative damage to the 5′-G of a 5′-GG-3′ doublet is generated from a distance but this irreversible damage is inhibited by MutY and instead EPR experiments reveal cluster oxidation. With ruthenium-tethered assemblies containing duplex versus single-stranded regions, MutY oxidation is found to be mediated by the DNA duplex, with guanine radical as an intermediate oxidant; guanine radical formation facilitates MutY oxidation. A model is proposed for the redox activation of DNA repair proteins through DNA CT, with guanine radicals, the first product under oxidative stress, in oxidizing the DNA-bound repair proteins, providing the signal to stimulate DNA repair.

Finding bacterial cellular targets for developing novel antibiotics has become a major challenge in fighting resistant pathogenic bacteria. We present a novel compound, Relacin, designed to inhibit (p)ppGpp production by the ubiquitous bacterial enzyme RelA that triggers the Stringent Response. Relacin inhibits RelA in vitro and reduces (p)ppGpp production in vivo. Moreover, Relacin affects entry into stationary phase in Gram positive bacteria, leading to a dramatic reduction in cell viability. When Relacin is added to sporulating Bacillus subtilis cells, it strongly perturbs spore formation regardless of the time of addition. Spore formation is also impeded in the pathogenic bacterium Bacillus anthracis that causes the acute anthrax disease. Finally, the formation of multicellular biofilms is markedly disrupted by Relacin. Thus, we establish that Relacin, a novel ppGpp analogue, interferes with bacterial long term survival strategies, placing it as an attractive new antibacterial agent., Author Summary The development of new antibacterial agents has become the major demand for fighting against pathogenic bacteria. The identification of new unexplored cellular targets in this combat is essential to prevent a possible return to the pre-antibiotic era. Traditional antibiotics target essential cellular components such as ribosomes and cell wall constituents, making them effective mostly during bacterial growth. However, the ability of bacteria to reside in nature at durable stages sets the need to cope with these alternative survival strategies. In this report, we present a novel antibiotic, termed Relacin, which targets the Stringent Response, a process required for the transition into stationary phase, crucial for bacterial survival. Relacin inhibits the abundant bacterial Rel enzymes that synthesize the signaling molecules required to activate the Stringent Response. We found that Relacin perturbs the switch into stationary phase in Gram positive bacteria and leads to cell death. Further, Relacin inhibits sporulation and biofilm formation, additional bacterial long term survival strategies. The ubiquity of Rel enzymes among bacteria, combined with the absence of known homologues in mammalian cells, strengthen the potential of Relacin to turn into a therapeutic antibiotic.

Introduction: Early detection of gastrointestinal malignancies may improve disease-related outcome. In vivo, real time imaging using hybridization of fluorescently-labeled complementary transcripts to intracellular RNA sequences may facilitate early detection of malignant and pre-malignant lesions Methods: Using K-ras oncogene as a model target, and adapting the molecular beacon technology, we performed an hybridization kinetics and hybridization specificity comparison of two types of molecular beacons (MBs) based on either phosphothioated DNA (PS-DNA-MB) or peptide nucleic acid (PNA-TO-MB, where thiazole orange [TO] was used as the fluorescent molecule) both in vitro and in a variety of cell lines. In order to determine the sequence-specificity of MB's at a single base resolution, a codon 12 K-ras oncogene mutation (GGT→GAT) was used as target in different cell lines. Both PS-DNA and PNA-TO MB's were designed to target this specific K-ras point mutation. We studied the hybridization of the two MBs to wild-type K-ras (HT-29 colon cancer cell line) and two cell lines, one harboring this K-ras point mutation (PANC-1) and SW-480 harboring a different (GGT→GTT) mutation. Results: Hybridization kinetics of PNA-TO-MB to target DNA or RNA was faster compared to PS-DNA-MB highlighting the advantage of such probes to be developed into diagnostic kits for the early detection of cancer. However, in solution, using synthetic DNA oligomers as targets, PS-DNA-MB demonstrated higher specificity to its complementary target (3-to 4.6-fold increase in fluorescence in comparison to DNA with a single mismatch) compared to the PNA-TO-MB (only 1.3- to 2.2-fold increase). Yet, incubation of PNA-TO-MB with total RNA (isolated from these cell lines) and with fixed cells, resulted in a significantly higher fluorescent signal (p < 0.001) detected for target (fully complement, PANC-1) compared to single mismatch mRNA transcript in HT29 and SW-480. In contrast, the PS-DNA-MB showed poor discrimination in total RNA and no fluorescent signal with all cell lines after 5 minutes incubation. Conclusions: Based on the fast hybridization kinetics and based on the single mismatch discrimination found for PNA-TO-MB in fixed cells and with total RNA, it is speculated that such PNA-TO-MB's are promising candidates for the early detection of cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3062. doi:10.1158/1538-7445.AM2011-3062