TLR5-Derived, TIR-Interacting Decoy Peptides to Inhibit TLR Signaling.

TLR5, which is activated by flagellin, plays an important role in initiating immune response to a broad spectrum of motile bacterial pathogens. TLRs induce intracellular signaling via dimerization of their TIR domains followed by adapter recruitment through multiple interactions of receptor and adapter TIRs. Here, a library of cell-permeable decoy peptides derived from the TLR5 TIR was screened for TLR5 signaling inhibition in the HEK-Blue-mTLR5 reporter cell line. The peptide demonstrating the strongest inhibition, 5R667, corresponded to the second helix of the region between the third and fourth ß-strands (helix C″). In addition to the TLR5-induced cytokine expression, 5R667 inhibited cytokine expression elicited by TLR4, TLR2, and TLR9. 5R667 also suppressed the systemic cytokine induction elicited by LPS administration in mice. 5R667 binding specificity was studied by time-resolved fluorescence spectroscopy in a cell-based assay. 5R667 demonstrated a multispecific binding pattern with respect to TIR domains: It bound TIRs of TLR adapters of the MyD88-dependent pathway, Toll/interleukin-1 receptor domain-containing adapter protein/MyD88 adapter-like (TIRAP) and MyD88, and also the TIR of TLR5. TR667, the peptide derived from the TIRAP region, which is structurally homologous to 5R667, demonstrated binding and inhibitory properties similar to that of 5R667. The surface-exposed residues within TIR regions represented by 5R667 and TR667 form motifs, which are nearly 90% conserved in vertebrate evolution and are distinctive of TLR5 and TIRAP TIR domains. Thus, we have identified an evolutionary conserved adapter recruitment motif within TLR5 TIR, the function of which can be inhibited by selective cell-permeable decoy peptides, which can serve as pan-specific TLR inhibitors.

Two-Photon Excited Fluorescence Lifetime Imaging of Tetracycline-Labeled Retinal Calcification.

Deposition of calcium-containing minerals such as hydroxyapatite and whitlockite in the subretinal pigment epithelial (sub-RPE) space of the retina is linked to the development of and progression to the end-stage of age-related macular degeneration (AMD). AMD is the most common eye disease causing blindness amongst the elderly in developed countries; early diagnosis is desirable, particularly to begin treatment where available. Calcification in the sub-RPE space is also directly linked to other diseases such as Pseudoxanthoma elasticum (PXE). We found that these mineral deposits could be imaged by fluorescence using tetracycline antibiotics as specific stains. Binding of tetracyclines to the minerals was accompanied by increases in fluorescence intensity and fluorescence lifetime. The lifetimes for tetracyclines differed substantially from the known background lifetime of the existing natural retinal fluorophores, suggesting that calcification could be visualized by lifetime imaging. However, the excitation wavelengths used to excite these lifetime changes were generally shorter than those approved for retinal imaging. Here, we show that tetracycline-stained drusen in post mortem human retinas may be imaged by fluorescence lifetime contrast using multiphoton (infrared) excitation. For this pilot study, ten eyes from six anonymous deceased donors (3 female, 3 male, mean age 83.7 years, range 79-97 years) were obtained with informed consent from the Maryland State Anatomy Board with ethical oversight and approval by the Institutional Review Board.

Fluorescence Lifetime Imaging of Human Sub-RPE Calcification In Vitro Following Chlortetracycline Infusion.

We have shown that all sub-retinal pigment epithelial (sub-RPE) deposits examined contain calcium phosphate minerals: hydroxyapatite (HAP), whitlockite (Wht), or both. These typically take the form of ca. 1 µm diameter spherules or >10 µm nodules and appear to be involved in the development and progression of age-related macular degeneration (AMD). Thus, these minerals may serve as useful biomarkers the for early detection and monitoring of sub-RPE changes in AMD. We demonstrated that HAP deposits could be imaged in vitro by fluorescence lifetime imaging microscopy (FLIM) in flat-mounted retinas using legacy tetracycline antibiotics as selective sensors for HAP. As the contrast on a FLIM image is based on the difference in fluorescence lifetime and not intensity of the tetracycline-stained HAP, distinguishing tissue autofluorescence from the background is significantly improved. The focus of the present pilot study was to assess whether vascular perfusion of the well tolerated and characterized chlortetracycline (widely used as an orally bioavailable antibiotic) can fluorescently label retinal HAP using human cadavers. We found that the tetracycline delivered through the peripheral circulation can indeed selectively label sub-RPE deposits opening the possibility for its use for ophthalmic monitoring of a range of diseases in which deposit formation is reported, such as AMD and Alzheimer disease (AD).

Sulforaphane covalently interacts with the transglutaminase 2 cancer maintenance protein to alter its structure and suppress its activity.

Type 2 transglutaminase (TG2) functions as an important cancer cell survival protein in a range of cancers including epidermal squamous cell carcinoma. TG2 exists in open and closed conformations each of which has a distinct and mutually exclusive activity. The closed conformation has GTP-binding/GTPase activity while the open conformation functions as a transamidase to catalyze protein-protein crosslinking. GTP-binding/GTPase activity is required for TG2 maintenance of the aggressive cancer phenotype. Thus, identifying agents that convert TG2 from the closed to the open GTP-binding/GTPase inactive conformation is an important cancer prevention/treatment strategy. Sulforaphane (SFN) is an important diet-derived cancer prevention agent that is known to possess a reactive isothiocyanate group and has potent anticancer activity. Using a biotin-tagged SFN analog (Biotin-ITC) and kinetic analysis we show that SFN covalently and irreversibly binds to recombinant TG2 to inhibit transamidase activity and shift TG2 to an open/extended conformation, leading to a partial inhibition of GTP binding. We also show that incubation of cancer cells or cancer cell extract with Biotin-ITC results in formation of a TG2/Biotin-ITC complex and that SFN treatment of cancer cells inhibits TG2 transamidase activity and shifts TG2 to an open/extended conformation. These findings identify TG2 as a direct SFN anticancer target in epidermal squamous cell carcinoma.

Sodium-Sensitive Contact Lens for Diagnostics of Ocular Pathologies.

The ability to measure all the electrolyte concentrations in tears would be valuable in ophthalmology for research and diagnosis of dry eye disease (DED) and other ocular pathologies. However, tear samples are difficult to collect and analyze because the total volume is small and the chemical composition changes rapidly. Measurements of electrolytes in tears is challenging because typical clinical assays for proteins and other biomarkers cannot be used to detect ion concentrations tears. Here, we report the contact lens which is sensitive to sodium ion (Na+), one of the dominant electrolytes in tears. The Na ions in tears is diagnostic for DED. Three sodium-sensitive fluorophores (SG-C16, SG-LPE and SG-PL) were synthesized by derivatizing the sodium green with 1-hexadecyl amine, 1-oleoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine or poly-L-lysine, respectively. These probes were bound to modern silicone hydrogel (SiHG) contact lens, Biofinity from Cooper Vision. Doped lenses were tested for sodium ion dependent spectral properties of probes within the contact lens. The probes displayed changes in intensity and lifetime in response to Na+ concentration, were completely reversible, no significant probe wash-out from the lenses, were not affected by proteins in tears and were not removed after repeated washing. These results are the first step to our long-term goal, which is a lens sensitive to all the electrolytes in tears. We presented design, synthesis and implementation of three new sodium sensitive probes within a silicon hydrogel lens. Contact lenses to measure the other electrolytes in tears can be developed using the same approach by synthesis and testing of new ion-sensitive fluorophores.

Fluorescent contact lens for continuous non-invasive measurements of sodium and chloride ion concentrations in tears.

Rapid and non-invasive measurement of hydration status is medically important because even mild levels of dehydration can have a significant impact on physical and cognitive performance. Despite the potential value of determining whole-body hydration based on the electrolytes found in tears, very few tests are available. An area of intense interest is the development of a contact lens which could measure ion concentrations in tears, specifically that of sodium (Na+) and chloride (Cl-) ions, the dominant electrolytes in blood plasma and tears. Here, we describe a method to make fluorescent contact lenses which allow determination of Na+ and Cl- ion concentrations in tears. Fluorophores known to be sensitive to Na+ and Cl- were derivatized to bind non-covalently to two commercially-available silicone hydrogel (SiHG) contact lenses-the Biofinity (Comfilcon A) or MyDay (Stenfilcon A) lenses. The sodium- and chloride-sensitive fluorophores displayed spectral changes in the physiological range for Na+ and Cl- ions in tears. The lenses for both Na+ and Cl- ions were completely reversible. The sodium responses were not sensitive to protein interference including human lysozyme, human serum albumin and mucin type 2. The chloride sensitivity was similar with both lenses, but the sodium-sensitive range was different in the Biofinity and MyDay lenses. We also fabricated a lens with both the Na+ and Cl- probes in a single MyDay lens resulting in a contact lens that independently measured Na+ and Cl- concentrations without physical separation of the fluorophores. Our findings indicated that a sodium and chloride-sensitive contact lens (NaCl-lens) could be used for rapid non-invasive detection of whole-body hydration, as well as associated diseases or other infections.

Blocking TIR Domain Interactions in TLR9 Signaling.

Interaction of TLR9 with ligands activates NF-κB, leading to proinflammatory cytokine production. Excessive TLR activation is a pathogenic factor for inflammatory diseases. This study has examined cell-permeating decoy peptides (CPDPs) derived from the TLR9 Toll/IL-1R resistance (TIR) domain. CPDP 9R34, which included AB loop, ß-strand B, and N-terminal BB loop residues, inhibited TLR9 signaling most potently. CPDPs derived from α-helices C, D, and E (i.e., 9R6, 9R9, and 9R11) also inhibited TLR9-induced cytokines but were less potent than 9R34. 9R34 did not inhibit TLR2/1, TLR4, or TLR7 signaling. The N-terminal deletion modification of 9R34, 9R34-ΔN, inhibited TLR9 as potently as the full length 9R34. Binding of 9R34-ΔN to TIR domains was studied using cell-based Förster resonance energy transfer/fluorescence lifetime imaging approach. Cy3-labeled 9R34-ΔN dose-dependently decreased fluorescence lifetime of TLR9 TIR-Cerulean (Cer) fusion protein. Cy3-9R34-ΔN also bound TIRAP TIR, albeit with a lesser affinity, but not MyD88 TIR, whereas CPDP from the opposite TIR surface, 9R11, bound both adapters and TLR9. i.p. administration of 9R34-ΔN suppressed oligonucleotide-induced systemic cytokines and lethality in mice. This study identifies a potent, TLR9-specific CPDP that targets both receptor dimerization and adapter recruitment. Location of TIR segments that represent inhibitory CPDPs suggests that TIR domains of TLRs and TLR adapters interact through structurally homologous surfaces within primary receptor complex, leading to formation of a double-stranded, filamentous structure. In the presence of TIRAP and MyD88, primary complex can elongate bidirectionally, from two opposite ends, whereas in TIRAP-deficient cells, elongation is unidirectional, only through the αE side.

Unexpected complex formation between coralyne and cyclic diadenosine monophosphate providing a simple fluorescent turn-on assay to detect this bacterial second messenger.

Cyclic diadenosine monophosphate (c-di-AMP) has emerged as an important dinucleotide that is involved in several processes in bacteria, including cell wall remodeling (and therefore resistance to antibiotics that target bacterial cell wall). Small molecules that target c-di-AMP metabolism enzymes have the potential to be used as antibiotics. Coralyne is known to form strong complexes with polyadenine containing eight or more adenine stretches but not with short polyadenine oligonucleotides. Using a panel of techniques (UV, both steady state fluorescence and fluorescence lifetime measurements, circular dichroism (CD), NMR, and Job plots), we demonstrate that c-di-AMP, which contains only two adenine bases is an exception to this rule and that it can form complexes with coralyne, even at low micromolar concentrations. Interestingly, pApA (the linear analog of c-di-AMP that also contains two adenines) or cyclic diguanylate (c-di-GMP, another nucleotide second messenger in bacteria) did not form any complex with coralyne. Unlike polyadenine, which forms a 2:1 complex with coralyne, c-di-AMP forms a higher order complex with coralyne (≥6:1). Additionally, whereas polyadenine reduces the fluorescence of coralyne when bound, c-di-AMP enhances the fluorescence of coralyne. We use the quenching property of halides to selectively quench the fluorescence of unbound coralyne but not that of coralyne bound to c-di-AMP. Using this simple selective quenching strategy, the assay could be used to monitor the synthesis of c-di-AMP by DisA or the degradation of c-di-AMP by YybT. Apart from the practical utility of this assay for c-di-AMP research, this work also demonstrates that, when administered to cells, intercalators might not only associate with polynucleotides, such as DNA or RNA, but also could associate with cyclic dinucleotides to disrupt or modulate signal transduction processes mediated by these nucleotides.

Sometimes it takes two to tango: contributions of dimerization to functions of human α-defensin HNP1 peptide.

Human myeloid α-defensins called HNPs play multiple roles in innate host defense. The Trp-26 residue of HNP1 was previously shown to contribute importantly to its ability to kill S. aureus, inhibit anthrax lethal factor (LF), bind gp120 of HIV-1, dimerize, and undergo further self-association. To gain additional insights into the functional significance of dimerization, we compared wild type HNP1 to dimerization-impaired, N-methylated HNP1 monomers and to disulfide-tethered obligate HNP1 dimers. The structural effects of these modifications were confirmed by x-ray crystallographic analyses. Like the previously studied W26A mutation, N-methylation of Ile-20 dramatically reduced the ability of HNP1 to kill Staphylococcus aureus, inhibit LF, and bind gp120. Importantly, this modification had minimal effect on the ability of HNP1 to kill Escherichia coli. The W26A and MeIle-20 mutations impaired defensin activity synergistically. N-terminal covalent tethering rescued the ability of W26A-HNP1 to inhibit LF but failed to restore its defective killing of S. aureus. Surface plasmon resonance studies revealed that Trp-26 mediated the association of monomers and canonical dimers of HNP1 to immobilized HNP1, LF, and gp120, and also indicated a possible mode of tetramerization of HNP1 mediated by Ile-20 and Leu-25. This study demonstrates that dimerization contributes to some but not all of the many and varied activities of HNP1.

Targeting TLR4 signaling by TLR4 Toll/IL-1 receptor domain-derived decoy peptides: identification of the TLR4 Toll/IL-1 receptor domain dimerization interface.

Agonist-induced dimerization of TLR4 Toll/IL-1R (TIR) domains initiates intracellular signaling. Therefore, identification of the TLR4-TIR dimerization interface is one key to the rational design of therapeutics that block TLR4 signaling. A library of cell-permeating decoy peptides, each of which represents a nonfragmented patch of the TLR4 TIR surface, was designed such that the peptides entirely encompass the TLR4 TIR surface. Each peptide was synthesized in tandem with a cell-permeating Antennapedia homeodomain sequence and tested for the ability to inhibit early cytokine mRNA expression and MAPK activation in LPS-stimulated primary murine macrophages. Five peptides--4R1, 4R3, 4BB, 4R9, and 4αE--potently inhibited all manifestations of TLR4, but not TLR2 signaling. When tested for their ability to bind directly to TLR4 TIR by Förster resonance energy transfer using time-resolved fluorescence spectroscopy, Bodipy-TMR-X-labeled 4R1, 4BB, and 4αE quenched fluorescence of TLR4-Cerulean expressed in HeLa or HEK293T cells, whereas 4R3 was partially active, and 4R9 was least active. These findings suggest that the area between the BB loop of TLR4 and its fifth helical region mediates TLR4 TIR dimerization. Moreover, our data provide direct evidence for the utility of the decoy peptide approach, in which peptides representing various surface-exposed segments of a protein are initially probed for the ability to inhibit protein function, and then their specific targets are identified by Förster resonance energy transfer to define recognition sites in signaling proteins that may be targeted therapeutically to disrupt functional transient protein interactions.

BfpL is essential for type IV bundle-forming pilus biogenesis and interacts with the periplasmic face of BfpC.

Enteropathogenic Escherichia coli (EPEC) causes diarrhoea among infants in developing countries. The bundle-forming pilus (BFP), a type IV pilus found on the surface of EPEC, is essential for full virulence of typical EPEC strains. The machinery for BFP assembly and function is encoded by an operon of 14 genes. Here we investigate the role in pilus biogenesis of BfpL, a small protein with a single N-terminal predicted transmembrane domain reminiscent of pilin-like proteins. We confirmed that a bfpL mutant lacks BFP, and associated auto-aggregation and localized adherence phenotypes. Furthermore, we found that a double mutant unable to express both the putative retraction ATPase BfpF and BfpL also lacks BFP and associated phenotypes, distinguishing BfpL from pilin-like proteins. Western blots of sheared pilus preparations did not suggest that BfpL is a component of BFP. Topology studies using C-terminal truncations and a dual reporter revealed that most of the BfpL protein resides in the periplasm. Further, we demonstrated through yeast two-hybrid assays and confirmed by fluorescence anisotropy that BfpL interacts with the periplasmic face of BfpC. Thus, BfpL has a function distinct from those of pilin-like proteins and is instead part of an inner-membrane subassembly complex that is believed to extract bundlin, the main pilus subunit, from the inner membrane to be incorporated into BFP.

Frontline Science: Targeting the TLR7 signalosome assembly.

TLRs sense a broad range of microbial molecules and initiate antimicrobial immune response. The members of the TLR family use cytoplasmic Toll/interleukin-1R homology (TIR) domain to initiate intracellular signaling. The activated TLRs dimerize their TIRs and recruit adapter proteins to the dimer, through multiple interactions of receptor and adapter TIR domains. Although TLRs play an essential role in innate immunity, the aberrant TLR signaling may cause pathogenic inflammation. This study has screened a library of cell-permeable decoy peptides (CPDPs) derived from the TLR7 TIR for interference with TLR7 signaling and identified new CPDPs that target the TLR7 signalosome assembly. Peptides 7R1, 7R6, 7R9, and 7R11 inhibited the TLR7-induced signaling in murine and human macrophages. The most potent inhibitory peptide of the four, 7R11, significantly reduced the systemic cytokine levels elicited by administration of a TLR7 agonist to mice. TLR7 TIR surface regions that correspond to inhibitory peptides generally corresponded to four TIR sites that mediate signalosome assembly for other TLRs. The cell-based Förster resonance energy transfer/fluorescence lifetime imaging confirmed that 7R9 and 7R11 interact with adapter TIRs. These findings clarify the molecular mechanisms that trigger the adapter recruitment to activated TLR7 and suggest that 7R9 and 7R11 have a significant translational potential as candidate or lead therapeutics for treatment of TLR7-related inflammatory diseases.

Imaging hydroxyapatite in sub-retinal pigment epithelial deposits by fluorescence lifetime imaging microscopy with tetracycline staining.

SIGNIFICANCE: Recent evidence suggests that hydroxyapatite (HAP) in sub-retinal pigment epithelial (sub-RPE) deposits in aged human eyes may act to nucleate and contribute to their growth to clinically detectable size. Sub-RPE deposits such as drusen are clinical hallmarks of age-related macular degeneration (AMD), therefore enhanced and earlier detection is a clinical need. We found that tetracycline-family antibiotics, long known to stain HAP in teeth and bones, can also label the HAP in sub-RPE deposits. However, HAP-bound tetracycline fluorescence excitation and emission spectra overlap with the well-known autofluorescence of outer retinal tissues, making them difficult to resolve. AIM: In this initial study, we sought to determine if the HAP-bound tetracyclines also exhibit enhanced fluorescence lifetimes, providing a useful difference in lifetime compared with the short lifetimes observed in vivo in the human retina by the pioneering work of Schweitzer, Zinkernagel, Hammer, and their colleagues, and thus a large enough effect size to resolve the HAP from background by fluorescence lifetime imaging. APPROACH: We stained authentic HAP with tetracyclines and measured the lifetime(s) by phase fluorometry, and stained aged, fixed human cadaver retinas with drusen with selected tetracyclines and imaged them by fluorescence lifetime imaging microscopy (FLIM). RESULTS: We found that chlortetracycline and doxycycline exhibited substantial increase in fluorescence lifetime compared to the free antibiotics and the retinal background, and the drusen were easily resolvable from the retinal background in these specimens by FLIM. CONCLUSIONS: These findings suggest that FLIM imaging of tetracycline (and potentially other molecules) binding to HAP could become a diagnostic tool for the development and progression of AMD.

Enhanced fluorescence of proteins and label-free bioassays using aluminum nanostructures.

We report the enhanced intrinsic fluorescence from several proteins in proximity to aluminum nanostructured surfaces. Intrinsic fluorescence in proteins is dominated by the tryptophan residues. Intensities and lifetimes of several proteins with different numbers of tryptophan residues assembled on the surfaces of quartz or aluminum nanostructured films were measured. Immobilized protein molecules on the surface of an aluminum nanostructured film resulted in a significant fluorescence intensity enhancement (up to 14-fold) and lifetime decrease (up to 6-fold) compared to the quartz substrates. These large spectroscopic changes allow design of label-free bioassays where detection of binding interactions between proteins can be observed in the presence of a bulk sample solution. Binding of streptavidin to the biotinylated aluminum surface was demonstrated in the presence of 100 microg/mL bovine serum albumin in the sample solution by measurements of tryptophan intensity and lifetime changes.

Metal-enhanced fluorescence of tryptophan residues in proteins: application toward label-free bioassays.

The detection of submonolayers of proteins based on native fluorescence is a potentially valuable approach for label-free detection. We have examined the possibility of using silver nanostructures to increase the emission of tryptophan residues in proteins. Fluorescence spectra, intensities, and lifetimes of multilayers and submonolayers of proteins deposited on the surfaces of silver island films were measured. Increased fluorescence intensities from two- to three-fold and similar decreases in lifetimes were observed in the presence of the silver nanoparticles compared with the proteins on the surface of the bare quartz. The observed spectral effects of silver nanoparticles on tryptophan fluorescence indicates the possibility for the design of analytical tools for the detection of proteins without traditional labeling by extrinsic fluorophores.

Depolarization of surface-enhanced fluorescence: an approach to fluorescence polarization assays.

Localized surface plasmons of metallic particles of subwavelength sizes strongly modify the spectral properties of nearby fluorophores. The enhanced radiative decay rate leads to high fluorescence efficiencies and decreased fluorescence lifetimes. In this report we show that metal-enhanced fluorescence generated by the presence of the silver islands on the glass substrate displays high depolarization. Intensities, lifetimes, and emission anisotropies of several fluorophore protein conjugates have been studied in the absence and presence of metallic nanostructures. Despite highly decreased lifetimes of about 10-fold and immobilization of conjugates on the solid substrate, the observed emission anisotropies for all fluorophores on the metal-enhanced substrate decreased 300-500% compared to that in solution. This observation implies a new generation of fluorescence polarization immunoassays with broad applications because of no restrictions to the lifetime of the probe and the size of labeled biomolecules. The changes in polarization are due to binding that occur on the bioactive surface localized near the metal particles.

A novel method for monitoring monoclonal antibody production during cell culture.

We describe a new format for surface-based fluoroimmunoassays that allows detection of biomolecule interactions without separation steps. The bioactive layer was immobilized on the surface of a glass substrate covered with silver islands that provide optical amplification of the distinctive fluorescence signal from bound probes when compared to unbound probes. The technique used was phase-modulation fluorometry that allows sensitive detection of bound probes with a very short lifetime in the presence of excess free probes in solution. The new method was applied to assay monoclonal antibody production during cell culture. Excellent agreement was found between the new method and ELISA analysis of hybridoma cell culture samples. It is predicted that the near real time monitoring of protein products during bioprocessing will be possible with the described technology.

Plasmon-controlled fluorescence: a new paradigm in fluorescence spectroscopy.

Fluorescence spectroscopy is widely used in biological research. Until recently, essentially all fluorescence experiments were performed using optical energy which has radiated to the far-field. By far-field we mean at least several wavelengths from the fluorophore, but propagating far-field radiation is usually detected at larger macroscopic distances from the sample. In recent years there has been a growing interest in the interactions of fluorophores with metallic surfaces or particles. Near-field interactions are those occurring within a wavelength distance of an excited fluorophore. The spectral properties of fluorophores can be dramatically altered by near-field interactions with the electron clouds present in metals. These interactions modify the emission in ways not seen in classical fluorescence experiments. In this review we provide an intuitive description of the complex physics of plasmons and near-field interactions. Additionally, we summarize the recent work on metal-fluorophore interactions and suggest how these effects will result in new classes of experimental procedures, novel probes, bioassays and devices.

Correlation between scattering properties of silver particle arrays and fluorescence enhancement.

We report on the nanofabrication of patterned silver particle arrays using electron-beam lithography and the evaluation of their optical properties using backscattering and fluorescence spectroscopy. The silver particles varied in size from 100 to 250 nm and were in the shape of circles, squares, and triangles. Three inter-particle separations, 40, 65, and 90 nm as measured from the side of one particle to the side of the next particle, were used. We observed distinctive patterns of backscattering and fluorescence intensity depending on the particle size, inter-particle spacing, and excitation/emission wavelength used. Our approach allows for a study of the correlation between the backscattering intensities and fluorescence enhancement of silver particle arrays, which can be used to optimize the arrays for multi-fluorophore configuration for advanced sensing designs.

Supramolecular polymer formation by cyclic dinucleotides and intercalators affects dinucleotide enzymatic processing.

BACKGROUND: Cyclic dinucleotides form supramolecular aggregates with intercalators, and this property could be utilized in nanotechnology and medicine. METHODS & RESULTS: Atomic force microscopy and electrophoretic mobility shift assays were used to show that cyclic diguanylic acid (c-di-GMP) forms G-wires in the presence of intercalators. The average fluorescence lifetime of thiazole orange, when bound to c-di-GMP was greater than when bound to DNA G-quadruplexes or dsDNA. The stability of c-di-GMP supramolecular polymers is dependent on both the nature of the cation present and the intercalator. C-di-GMP or cyclic diadenylic acid/intercalator complexes are more resistant to cleavage by YybT, a phosphodiesterase, than the uncomplexed nucleotides. CONCLUSION: Cleavage of bacterial cyclic dinucleotides could be slowed down via complexation with small molecules and that this could be utilized for diverse applications in nanotechnology and medicine.