Fluorescence-quenching phenomenon by photoinduced electron transfer between a fluorescent dye and a nucleotide base

Real-time monitoring of the activity and kinetics of T4 polynucleotide kinase by a singly labeled DNA-hairpin smart probe coupled with lambda exonuclease cleavage

We describe a novel method for real-time monitoring of the activity and kinetics of T4 polynucleotide kinase (PNK) by use of a singly fluorophore-labeled DNA-hairpin smart probe (SP) coupled with lambda exonuclease (lambda exo) cleavage. The method was performed in a sealed reaction tube and offered more sensitive, fast, high-throughput, and cost-effective detection. The SP was designed with a fluorophore at the 3'-end, and the fluorescence was quenched by a GGG-triplet at the 5'-end without any other additional quenchers. The 5'-hydroxyl group of the SP was phosphorylated by T4 PNK in the presence of ATP, and the resulting 5'-phosphoryl end product was promptly cleaved by lambda exo, which caused significant enhancement of fluorescence. A fast and accurate method for assaying the kinase activity of T4 PNK was developed with a wide linear detection range from 0.022 to 5.6 nM s(-1). The phosphorylation reaction was monitored at varying substrate concentrations at the molecular level, and K(m), V(max), and K(cat) values were all calculated. Furthermore, the effects of ATP concentration and salts were investigated. The developed method can be easily adapted to the detection of many other nucleic acid enzymes and may find widespread applications.

An emissive C analog distinguishes between G, 8-oxoG, and T

A minimally disruptive fluorescent dC analog provides a rapid and non-destructive method for in vitro detection of G, 8-oxoG, and T, the downstream transverse mutation product.

8-Aza-7-deazaguanine nucleosides and oligonucleotides with octadiynyl side chains: synthesis, functionalization by the azide-alkyne 'click' reaction and nucleobase specific fluorescence quenching of coumarin dye conjugates

Oligonucleotides incorporating 7-(octa-1,7-diynyl) derivatives of 8-aza-7-deaza-2-deoxyguanosine (2d) were prepared by solid-phase synthesis. The side chain of 2d was introduced by the Sonogashira cross coupling reaction and phosphoramidites (3a, 3b) were synthesized. Duplexes containing 2d are more stabilized compared to those incorporating the non-functionalized 8-aza-7-deaza-2-deoxyguanosine (2a) demonstrating that these side chains have steric freedom in duplex DNA. Nucleoside 2d as well as 2d-containing oligonucleotides were conjugated to the non-fluorescent 3-azido-7-hydroxycoumarin 15 by the Huisgen-Meldal-Sharpless click reaction. Pyrazolo[3,4-d]pyrimidine nucleoside conjugate 16 shows a much higher fluorescence intensity than that of the corresponding pyrrolo[2,3-d]pyrimidine derivative 17. The quenching in the dye conjugate 17 was found to be stronger on the stage of monomeric conjugates than in single-stranded or duplex DNA. Nucleobase-dye contact complexes are suggested which are more favourable in the monomeric state than in the DNA chain when the nucleobase is part of the stack. The side chains with the bulky dye conjugates are well accommodated in DNA duplexes thereby forming hybrids which are slightly more stable than canonical DNA.

Nucleobase-specific enhancement of Cy3 fluorescence

We report on the role of dye-nucleobase interactions on the photophysical properties of the indocarbocyanine Cy3. The fluorescence efficiency and lifetime ofCy3 increase in the presence of all four nucleoside monophosphates. This behavior correlates with an increase in the activation energy for photoisomerization and a approximately 4 nm red shift in the fluorescence spectrum. Changes are more dramatic for the purines (dAMP, dGMP) than the pyrimidines(dCMP, dTMP), and for the nonsulfonated cyanine(DiIC2(3)) than the sulfonated dye (Cy3-SE). These results are consistent with a model in which Cy3-nucleoside pi-pi interactions decrease the efficiency of photoisomerization,increasing the efficiency of fluorescence.

Coupling of DNA unwinding to nucleotide hydrolysis in a ring-shaped helicase

The ring-shaped T7 helicase uses the energy of dTTP hydrolysis to perform the mechanical work of translocation and base pair (bp) separation. We have shown that the unwinding rate of T7 helicase decreases with increasing DNA stability. Here, we show that the dTTPase rate also decreases with increasing DNA stability, which indicates close linkage between chemical transition steps and translocation steps of unwinding. We find that the force-producing step during unwinding is not associated with dTTP binding, but dTTP hydrolysis or P(i) release. We determine that T7 helicase extracts approximately 3.7 kcal/mol energy from dTTPase to carry out the work of strand separation. Using this energy, T7 helicase unwinds approximately 4 bp of AT-rich DNA or 1-2 bp of GC-rich DNA. T7 helicase therefore adjusts both its speed and coupling ratio (bp/dTTP) to match the work of DNA unwinding. We discuss the mechanistic implications of the variable bp/dTTP that indicates T7 helicase either undergoes backward movements/futile hydrolysis or unwinds DNA with a variable bp-step size; 'long and fast' steps on AT-rich and 'short and slow' steps on GC-rich DNA.

A highly fluorescent nucleoside analog based on thieno[3,4-d]pyrimidine senses mismatched pairing

A highly emissive nucleobase analog, based on a thieno[3,4-d]pyrimidine core, is enzymatically incorporated into RNA oilgonucleotides that function as base discriminating fluorescent probes.

Tunable blinking kinetics of cy5 for precise DNA quantification and single-nucleotide difference detection

Fluorescence correlation spectroscopy (FCS) can resolve the intrinsic fast-blinking kinetics (FBKs) of fluorescent molecules that occur on the order of microseconds. These FBKs can be heavily influenced by the microenvironments in which the fluorescent molecules are contained. In this work, FCS is used to monitor the dynamics of fluorescence emission from Cy5 labeled on DNA probes. We found that the FBKs of Cy5 can be tuned by having more or less unpaired guanines (upG) and thymines (upT) around the Cy5 dye. The observed FBKs of Cy5 are found to predominantly originate from the isomerization and back-isomerization processes of Cy5, and Cy5-nucleobase interactions are shown to slow down these processes. These findings lead to a more precise quantification of DNA hybridization using FCS analysis, in which the FBKs play a major role rather than the diffusion kinetics. We further show that the alterations of the FBKs of Cy5 on probe hybridization can be used to differentiate DNA targets with single-nucleotide differences. This discrimination relies on the design of a probe-target-probe DNA three-way-junction, whose basepairing configuration can be altered as a consequence of a single-nucleotide substitution on the target. Reconfiguration of the three-way-junction alters the Cy5-upG or Cy5-upT interactions, therefore resulting in a measurable change in Cy5 FBKs. Detection of single-nucleotide variations within a sequence selected from the Kras gene is carried out to validate the concept of this new method.

SNP detection for cytochrome P450 alleles by target-assembled tandem oligonucleotide systems based on exciplexes

We report the first use of exciplex-based split-probes for detection of the wild type and *3 mutant alleles of human cytochrome P450 2C9. A tandem 8-mer split DNA oligonucleotide probe system was designed that allows detection of the complementary target DNA sequence. This exciplex-based fluorescence detector system operates by means of a contiguous hybridization of two oligonucleotide exciplex split-probes to a complementary target nucleic acid target. Each probe oligonucleotide is chemically modified at one of its termini by a potential exciplex-forming partner, each of which is fluorescently silent at the wavelength of detection. Under conditions that ensure correct three-dimensional assembly, the chemical moieties on suitable photoexcitation form an exciplex that fluoresces with a large Stokes shift (in this case 130 nm). Preliminary proof-of-concept studies used two 8-mer probe oligonucleotides, but in order to give better specificity for genomic applications, probe length was extended to give coverage of 24 bases. Eight pairs of tandem 12-mer oligonucleotide probes spanning the 2C9*3 region were designed and tested to find the best set of probes. Target sequences tested were in the form of (i) synthetic oligonucleotides, (ii) embedded in short PCR products (150 bp), or (iii) inserted into plasmid DNA (approximately 3 Kbp). The exciplex system was able to differentiate wild type and human cytochrome P450 2C9 *3 SNP (1075 A-->C) alleles, based on fluorescence emission spectra and DNA melting curves, indicating promise for future applications in genetic testing and molecular diagnostics.

Fluorescence of size-expanded DNA bases: reporting on DNA sequence and structure with an unnatural genetic set

We recently described the synthesis and helix assembly properties of expanded DNA (xDNA), which contains base pairs 2.4 A larger than natural DNA pairs. This designed genetic set is under study with the goals of mimicking the functions of the natural DNA-based genetic system and of developing useful research tools. Here, we study the fluorescence properties of the four expanded bases of xDNA (xA, xC, xG, xT) and evaluate how their emission varies with changes in oligomer length, composition, and hybridization. Experiments were carried out with short oligomers of xDNA nucleosides conjugated to a DNA oligonucleotide, and we investigated the effects of hybridizing these fluorescent oligomers to short complementary DNAs with varied bases opposite the xDNA bases. As monomer nucleosides, the xDNA bases absorb light in two bands: one at approximately 260 nm (similar to DNA) and one at longer wavelength ( approximately 330 nm). All are efficient violet-blue fluorophores with emission maxima at approximately 380-410 nm and quantum yields (Phifl) of 0.30-0.52. Short homo-oligomers of the xDNA bases (length 1-4 monomers) showed moderate self-quenching except xC, which showed enhancement of Phifl with increasing length. Interestingly, multimers of xA emitted at longer wavelengths (520 nm) as an apparent excimer. Hybridization of an oligonucleotide to the DNA adjacent to the xDNA bases (with the xDNA portion overhanging) resulted in no change in fluorescence. However, addition of one, two, or more DNA bases in these duplexes opposite the xDNA portion resulted in a number of significant fluorescence responses, including wavelength shifts, enhancements, or quenching. The strongest responses were the enhancement of (xG)n emission by hybridization of one or more adenines opposite them, and the quenching of (xT)n and (xC)n emission by guanines opposite. The data suggest multiple ways in which the xDNA bases, both alone and in oligomers, may be useful as tools in biophysical analysis and biotechnological applications.

Selective fluorescence detection of 8-oxoguanosine with 8-oxoG-clamp

8-oxoguanosine, which is derived from the oxidation of guanosine (dG), is known to induce transversion mutations (G:C-->T:A) in DNA. The compounds with a small molecular weight for recognizing 8-oxoG were designed on the basis of the structure of the G-clamp, which is reported to have selective affinity toward guanosine. The G-clamp derivatives with the additional binding units toward 8-oxoG were effectively synthesized and named "8-oxoG-clamps." The 8-oxoG-clamp completely discriminated 8-oxoG from other nucleosides by fluorescence quenching.

Calibration-curve-free quantitative PCR: A quantitative method for specific nucleic acid sequences without using calibration curves

We have developed a simple quantitative method for specific nucleic acid sequences without using calibration curves. This method is based on the combined use of competitive polymerase chain reaction (PCR) and fluorescence quenching. We amplified a gene of interest (target) from DNA samples and an internal standard (competitor) with a sequence-specific fluorescent probe using PCR and measured the fluorescence intensities before and after PCR. The fluorescence of the probe is quenched on hybridization with the target by guanine bases, whereas the fluorescence is not quenched on hybridization with the competitor. Therefore, quench rate (i.e., fluorescence intensity after PCR divided by fluorescence intensity before PCR) is always proportional to the ratio of the target to the competitor. Consequently, we can calculate the ratio from quench rate without using a calibration curve and then calculate the initial copy number of the target from the ratio and the initial copy number of the competitor. We successfully quantified the copy number of a recombinant DNA of genetically modified (GM) soybean and estimated the GM soybean contents. This method will be particularly useful for rapid field tests of the specific gene contamination in samples.

Wavelength dependant quenching of 2,5-diphenyloxazole fluorescence by nucleotides

The quenching of 2,5-diphenyloxazole (PPO) fluorescence by nucleotides has been investigated by electronic absorption and steady state fluorescence spectra. Five purine nucleotides AMP, ADP, ATP, GMP and dGMP, one pyrimidine nucleotide UMP and one dinucleotide NAD have been employed in the present study. Electronic absorption studies indicate that there is no ground state complexation between the nucleotides and PPO. The quenching of PPO fluorescence was investigated at two different wavelengths. When excited at 304 nm, the lambda(max) of PPO, the fluorescence spectra of PPO is quenched following Stern-Volmer kinetics. The quenching ability of nucleotides are in the order NAD>AMP>ADP>GMP>dGMP>UMP. The K(SV) and k(q) values obtained indicate that AMP is a better quencher of PPO fluorescence than GMP, which is contrary to commonly observed pattern. The quenching is found to be dynamic in nature. However, when excited at 260 nm, the absorption maximum of the nucleotides, the fluorescence intensity of PPO is reduced with increase in the concentration of the nucleotide. This is attributed to the primary inner filter effect arising due to the absorption of the incident radiation by the nucleotides. Thus the inner filter effect phenomenon can be employed to assay the non-fluorescent molecules by fluorimetry.

Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA

The sulfoindocyanine Cy3 is one of the most commonly used fluorescent dyes in the investigation of the structure and dynamics of nucleic acids by means of fluorescence methods. In this work, we report the fluorescence and photophysical properties of Cy3 attached covalently to single-stranded and duplex DNA. Steady-state and time-resolved fluorescence techniques were used to determine fluorescence quantum yields, emission lifetimes, and fluorescence anisotropy decays. The existence of a transient photoisomer was investigated by means of transient absorption techniques. The fluorescence quantum yield of Cy3 is highest when attached to the 5' terminus of single-stranded DNA (Cy3-5' ssDNA), and decreases by a factor of 2.4 when the complementary strand is annealed to form duplex DNA (Cy3-5' dsDNA). Substantial differences were also observed between the 5'-modified strands and strands modified through an internal amino-modified deoxy uridine. The fluorescence decay of Cy3 became multiexponential upon conjugation to DNA. The longest lifetime was observed for Cy3-5' ssDNA, where about 50% of the decay is dominated by a 2.0-ns lifetime. This value is more than 10 times larger than the fluorescence lifetime of the free dye in solution. These observations are interpreted in terms of a model where the molecule undergoes a trans-cis isomerization reaction from the first excited state. We observed that the activation energy for photoisomerization depends strongly on the microenvironment in which the dye is located. The unusually high activation energy measured for Cy3-5' ssDNA is an indication of dye-ssDNA interactions. In fact, the time-resolved fluorescence anisotropy decay of this sample is dominated by a 2.5-ns rotational correlation time, which evidences the lack of rotational freedom of the dye around the linker that separates it from the terminal 5' phosphate. The remarkable variations in the photophysical properties of Cy3-DNA constructs demonstrate that caution should be used when Cy3 is used in studies employing DNA conjugates.

Fluorescence Measurements of Duplex DNA Oligomers under Conditions Conducive for Forming M−DNA (a Metal−DNA Complex)

M-DNA (a metal complex of DNA with millimolar concentrations of Zn2+, Co2+, or Ni2+ and basic pH) has been proposed to undergo electron transfer over long distances along the helix and has generated interest as a potential building block for nanoelectronics. We show that DNA aggregates form under solvent conditions favorable for M-DNA (millimolar zinc and pH = 8.6) by fluorescence correlation spectroscopy. We have performed steady-state Förster resonance energy transfer (FRET) experiments with DNA oligomers conjugated with 6-carboxyfluorescein and tetramethylrhodamine to the opposite ends of double-stranded DNA (dsDNA) molecules. Enhanced acceptor emission is observed for distances larger than expected for identical DNA molecules with no zinc. To avoid intermolecular FRET, the fluorescently labeled dsDNA is diluted with a 100-fold excess of unlabeled dsDNA. The intramolecular FRET efficiency increases 25-fold for a 30-mer doubly labeled duplex DNA molecule upon addition of millimolar concentrations of zinc ions. Without zinc, this oligomer has less than 1% FRET efficiency. This dramatic increase in the FRET efficiency points to either significant changes in the Förster radius or fraying of the ends of the DNA helices. The latter hypothesis is supported by our experiments with a 9-mer that show dissociation of the duplex by zinc ions.

Technique for quantitative detection of specific DNA sequences using alternately binding quenching probe competitive assay combined with loop-mediated isothermal amplification

We describe a novel technique for a simple, rapid, and reliable quantitative detection of specific DNA sequences using an alternately binding quenching probe (AB-QProbe) that binds to either the gene of interest (target) or an internal standard (competitor) in combination with loop-mediated isothermal amplification (LAMP). The AB-QProbe is a singly labeled oligonucleotide bearing a fluorescent dye at the 5' end. The fluorescence intensity of the AB-QProbe reflects the ratio of the LAMP products from the target and competitor. We amplified the target and competitor by LAMP under isothermal conditions with high specificity, efficiency, and rapidity and calculated the starting quantity of the target from the fluorescence intensities at the beginning and end of LAMP. We call this technique alternately binding quenching probe competitive LAMP (ABC-LAMP). We quantified amoA, which encodes the ammonia-oxidizing enzyme in environmental bacteria, as a model target by ABC-LAMP, real-time PCR, and real-time turbidimetry of LAMP. By comparison, the accuracy of ABC-LAMP was found to be similar to that of real-time PCR. Moreover, ABC-LAMP enables the accurate quantification of DNA in the presence of DNA amplification inhibitors such as humic acid, urea, and Triton X-100 that compromise the values measured by real-time PCR and real-time turbidimetry of LAMP.

Excited-State Dynamics of Donor−Acceptor Bridged Systems Containing a Boron−Dipyrromethene Chromophore: Interplay between Charge Separation and Reorientational Motion

The excited-state dynamics of a series of electron donor-acceptor bridged systems (DABS) consisting of a boron-dipyrromethene chromophore covalently linked to a dinitro-substituted triptycene has been investigated using femtosecond time-resolved spectroscopy. The chromophores differ by the number of bromine atom substituents. The fluorescence lifetime of the DABS without any bromine atom is strongly reduced when going from toluene to polar solvents, this shortening being already present in chloroform. This effect is about 10 times weaker with a single bromine atom and negligible with two bromine atoms on the chromophore. The excited-state lifetime shortening is ascribed to a charge transfer from the excited chromophore to a nitrobenzene moiety, the driving force of this process depending on the number of bromine substituents. The occurrence of this process is further confirmed by the investigation of the excited-state dynamics of the chromophore alone in pure nitrobenzene. Surprisingly, no correlation between the charge separation time constant and the dielectric properties of the solvents could be observed. However, a good correlation between the charge separation time constant and the diffusional reorientation time of the chromophore alone, measured by fluorescence anisotropy, was found. Quantum chemistry calculations suggest that quasi-free rotation about the single bond linking the chromophore to the triptycene moiety permits a sufficient coupling of the donor and the acceptor to ensure efficient charge separation. The charge separation dynamics in these molecules is thus controlled by the reorientational motion of the donor relative to the acceptor.

Multiple Binding Modes for Dicationic Hoechst 33258 to DNA

The binding of dicationic Hoechst 33258 (ligand) to DNA was characterized by means of the fluorescence spectra, fluorescence intensity titration, time-resolved fluorescence decay, light scattering, circular dichroism, and fluorescence thermal denaturation measurements, and two binding modes were distinguished by the experimental results. Type 1 binding has the stoichiometry of one ligand to more than 12 base pairs, and it is defined as quasi-minor groove binding which has the typical prolonged fluorescence lifetime of about 4.4 ns. In type 1 binding, planar conformation of the ligand is favorable. Type 2 binding with phosphate to ligand ratio (P/L) < 2.5 has the stoichiometry of one ligand to two phosphates. It is defined as a highly dense and orderly stacked binding with DNA backbone as the template. Electrostatic interactions between doubly protonated ligands and negatively charged DNA backbone play a predominant role in the type 2 binding mode. The characteristics of this type of binding result in a twisted conformation of the ligand that has a fluorescence lifetime of less than 1 ns. The results also indicate that the binding is in a cooperative manner primarily by stacking of the aromatic rings of the neighboring ligands. Type 1 binding is only observed for double-stranded DNA (dsDNA) with affinity constant of 1.83 x 10(7) M-1. In the type 2 binding mode, the binding affinity constants are 4.9 x 10(6) and 4.3 x 10(6) M-1 for dsDNA and single-stranded DNA (ssDNA), respectively. The type 2 binding is base pair independent while the type 1 binding is base pair related. The experiments described in this paper revealed that the dication bindings are different from the monocation bindings reported by previous study. The dication binding leads to stronger aggregation at low ligand concentration and results in orderly arrangements of the ligands along DNA chains. Furthermore the dication binding is demonstrated to be beneficial for enhancing the DNA's stability.

Fluorescent temporin B derivative and its binding to liposomes

Temporins are short (10-13 amino acids) and linear antimicrobial peptides first isolated from the skin of the European red frog, Rana temporaria, and are effective against Gram-positive bacteria and Candida albicans. Similarly to other antimicrobial peptides, the association of temporins to lipid membranes has been concluded to underlie their antimicrobial effects. Accordingly, a detailed understanding of their interactions with phospholipids is needed. We conjugated a fluorophore (Texas Red) to a Cys containing derivative of temporin B (temB) and investigated its binding to liposomes by fluorescence spectroscopy. Circular dichroic spectra for the Cys-mutant recorded in the absence and in the presence of phospholipids were essentially similar to those for temB. A blue shift in the emission spectra and diminished quenching by ferrocyanide (FCN) of Texas Red labeled temporin B (TRC-temB) were seen in the presence of liposomes. Both of these changes can be attributed to the insertion of the Texas Red into the hydrophobic region of the bilayer. Resonance energy transfer, steady state anisotropy, and fluorescence lifetimes further demonstrate the interaction of TRC-temB with liposomes to be enhanced by negatively charged phospholipids. Instead, cholesterol attenuates the association of TRC-temB with membranes. The interactions between TRC-temB and liposomes of varying negative surface charge are driven by electrostatics as well as hydrophobicity. Similarly to native temporin B also TRC-temB forms amyloid type fibers in the presence of negatively charged liposomes. This property is likely to relate to the cytotoxic activity of this peptide.

Quantitative Method for Specific Nucleic Acid Sequences Using Competitive Polymerase Chain Reaction with an Alternately Binding Probe

We have developed a simple, cost-effective, and accurate method for the quantification of specific nucleic acid sequences by the combined use of competitive PCR and a sequence-specific fluorescent probe that binds to either the gene of interest (target) or internal standard (competitor), referred to as alternately binding probe (ABProbe). In this method, the target and competitor were coamplified with the ABProbe, and then the fluorescence intensity was measured. The ratio of the target to the competitor can be calculated from the fluorescence intensity of the ABProbe using fluorescence quenching and fluorescence resonance energy transfer, that is, the starting quantity of the target is successfully calculated by end-point fluorescence measurement. Therefore, this method eliminates the complex post-PCR steps and expensive devices for real-time fluorescence measurement. We called this method alternately binding probe competitive PCR (ABC-PCR). We quantified amoA as a model target by ABC-PCR and real-time PCR. By comparison, the sensitivity, accuracy, and precision of ABC-PCR were similar to those of real-time PCR. Moreover, ABC-PCR was able to correctly quantify DNA even when PCR was inhibited by humic acid; therefore, this method will enable accurate DNA quantification for biological samples that contain PCR inhibitors.

Novel DNA probes with low background and high hybridization-triggered fluorescence

Novel fluorogenic DNA probes are described. The probes (called Pleiades) have a minor groove binder (MGB) and a fluorophore at the 5′-end and a non-fluorescent quencher at the 3′-end of the DNA sequence. This configuration provides surprisingly low background and high hybridization-triggered fluorescence. Here, we comparatively study the performance of such probes, MGB-Eclipse probes, and molecular beacons. Unlike the other two probe formats, the Pleiades probes have low, temperature-independent background fluorescence and excellent signal-to-background ratios. The probes possess good mismatch discrimination ability and high rates of hybridization. Based on the analysis of fluorescence and absorption spectra we propose a mechanism of action for the Pleiades probes. First, hydrophobic interactions between the quencher and the MGB bring the ends of the probe and, therefore, the fluorophore and the quencher in close proximity. Second, the MGB interacts with the fluorophore and independent of the quencher is able to provide a modest (2–4-fold) quenching effect. Joint action of the MGB and the quencher is the basis for the unique quenching mechanism. The fluorescence is efficiently restored upon binding of the probe to target sequence due to a disruption in the MGB–quencher interaction and concealment of the MGB moiety inside the minor groove.

G quadruplex-based FRET probes with the thrombin-binding aptamer (TBA) sequence designed for the efficient fluorometric detection of the potassium ion

The dual-labeled oligonucleotide derivative, FAT-0, carrying 6- carboxyfluorescein (FAM) and 6-carboxytetramethylrhodamine (TAMRA) labels at the 5' and 3' termini of the thrombin-binding aptamer (TBA) sequence 5'-GGT TGG TGT GGT TGG-3', and its derivatives, FAT-n (n=3, 5, and 7) with a spacer at the 5'-end of a TBA sequence of T(m)A (m=2, 4, and 6) have been designed and synthesized. These fluorescent probes were developed for monitoring K(+) concentrations in living organisms. Circular dichroism, UV-visible absorption, and fluorescence studies revealed that all FAT-n probes could form intramolecular tetraplex structures after binding K(+). Fluorescence resonance energy transfer and quenching results are discussed taking into account dye-dye contact interactions. The relationship between the fluorescence behavior of the probes and the spacer length in FAT-n was studied in detail and is discussed.

Binding of mRNA to the Bacterial Translation Initiation Complex

Translation initiation is a key step for regulating the synthesis of several proteins. In bacteria, translation initiation involves the interaction of the mRNA with the ribosomal small subunit. Additionally, translation initiation factors 1, 2, and 3, and the initiator tRNA, also assemble on the ribosomal small subunit and are essential for efficiently recruiting an mRNA for protein biosynthesis. In the following chapter, we describe fluorescence-based methods for studying the interaction of mRNA with the bacterial initiation complex. Model mRNAs with a covalently attached fluorescent probe showed an increase in fluorescence intensity when bound to the bacterial initiation complex. Utilizing the increase in fluorescence intensity upon mRNA binding to the bacterial initiation complex, we determined the equilibrium binding constants and the association and dissociation rate constants. These methods are important for quantitatively analyzing the effects of mRNA secondary structure and the role of the initiation factors in recruitment of mRNA by the bacterial initiation complex.

Fluorescence energy transfer probes based on the guanine quadruplex formation for the fluorometric detection of potassium ion

Dual-labeled oligonucleotide derivative, FAT-0, carrying 6-carboxyfluorescein (FAM) and 6-carboxy-tetramethylrhodamine (TAMRA) labels at 5'- and 3'-termini of thrombin-binding aptamer (TBA) sequence 5'-GGTTGGTGTGGTTGG-3' and its derivatives, FAT-n (n=3, 5, and 7) were designed and synthesized. FAT-n derivatives contained a T(m)A spacer (m=2, 4, and 6, respectively) at 5'-end of TBA sequence. The probes were developed to estimate the spacer effect on FRET efficiency and to identify the best probe for sensing of K(+). Circular dichroism (CD), UV-vis absorption, and fluorescence studies revealed that all FAT-n probes could form the intramolecular tetraplex structures after binding K(+). Association constants of particular K(+)/FAT-n complexes were determined using different experimental approaches. Suitability of particular probes for sensitive monitoring of K(+) in intra- and extracellular conditions was examined and discussed. Calibration graphs of fluorescence ratio were linear in the K(+) concentration range of 2-10 mM for extracellular conditions showing sensitivity of 1.2% mM(-1) K(+) and for intracellular conditions in the range of 100-200 mM with sensitivity of 0.49% mM(-1) K(+).

Masking oligonucleotides improve sensitivity of mutation detection based on guanine quenching

Guanine quenching of a fluorescence-labeled DNA probe is a powerful tool for detecting a mutation in a targeted site of a DNA strand. However, a different guanine adjacent to a targeted site can interfere with detection of a point mutation, resulting in unsatisfactory sensitivity. In the current study, we developed a simple method to improve sensitivity of the guanine quenching method using a masking DNA oligonucleotide. The simple addition of a masking DNA oligonucleotide was found to mask the interference of a different guanine in a target oligonucleotide on fluorescence and to enhance difference in the quenching ratio between wild-type and mutant oligonucleotides. Based on this strategy, we succeeded in discriminating various mutations from the wild-type YMDD motif of the hepatitis B virus DNA polymerase gene using guanine quenching with a masking oligonucleotide.

Fluorescence anisotropy and FRET studies of G-quadruplex formation in presence of different cations

Results of the steady-state fluorescence, anisotropy and FRET measurements of G-quadruplex formation in the presence of selected cations (Li(+), Na(+), K(+), NEt(4)(+) and Mg(2+)) are reported. Three different fluorescent oligonucleotides with human telomeric sequence labeled with fluorescein (FAM) and tetramethylrhodamine (TAMRA) were investigated: a dual-labeled 21-mer denoted as PSO (Potassium Sensing Oligonucleotide) and two 5'- and 3'- single-labeled probes, FAM-21 and 21-TAMRA, respectively. The fluorescence signal of FAM-21 increased significantly for all systems and the fluorescence enhancement was comparable in magnitude for monovalent cations but it was more pronounced for Mg(2+) cation. This phenomenon was attributed to the protolytic equilibria of FAM affected by the variation in ionic strength. On the other hand, fluorescence of TAMRA was enhanced selectively by Na(I) cation that was explained by the dequenching of TAMRA emission originated from the peculiarity of the basket-type structure of Na(I)-quadruplex. Anisotropy of FAM-21 (but not 21-TAMRA) appeared to be sensitive to the G-quadruplex formation, showing significant increase with an increase in cation concentration and indicating some restrictions in rotational depolarization of FAM. FRET experiments revealed that all tested cations caused quenching of FAM fluorescence in PSO, but only Na(+) and K(+) ions produced sensitized emission of TAMRA acceptor. Higher FRET efficiency observed in the presence of sodium ion was attributed to the specific spectral factor and steric interactions in the basket-type Na(I)-quadruplex.

Electron Transfer in Self-Assembled Orthogonal Structures

Two new molecular dyads, comprising pyrromethene (bodipy) and 2,2':6',2"-terpyridine (terpy) subunits, have been synthesized and fully characterized. Absorption and fluorescence spectral profiles are dominated by contributions from the bodipy unit. Zinc(II) cations bind to the vacant terpy ligand to form both 1:1 and 1:2 (cation:ligand) complexes, as evidenced by X-ray structural data, NMR and spectrophotometric titrations. Attachment of the cations is accompanied by a substantial decrease in fluorescence from the bodipy chromophore due to intramolecular electron transfer across the orthogonal structure. At low temperature, nuclear tunneling occurs and the rate of electron transfer is essentially activationless. However, activated electron transfer is seen at higher temperatures and allows calculation of the corresponding reorganization energy and electronic coupling matrix element. In both cases, charge recombination is faster than charge separation.

Characterization and quantification of ammonia-oxidizing bacteria in eutrophic coastal marine sediments using polyphasic molecular approaches and immunofluorescence staining

Tokyo Bay, a eutrophic bay in Japan, receives nutrients from wastewater plants and other urban diffuse sources via river input. A transect was conducted along a line from the Arakawa River into Tokyo Bay to investigate the ecological relationship between the river outflow and the distribution, abundance and population structure of ammonia-oxidizing bacteria (AOB). Five surficial marine sediments were collected and analysed with polyphasic approaches. Heterogeneity and genetic diversity of beta-AOB populations were examined using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA and amoA genes. A shift of the microbial community was detected in samples along the transect. Both 16S rRNA and amoA genes generated polymorphisms in the restriction profiles that were distinguishable at each sampling site. Two 16S rRNA gene libraries were constructed using the reverse transcription polymerase chain reaction (RT-PCR) method to determine the major ammonia oxidizers maintaining high cellular rRNA content. Two major groups were observed in the Nitrosomonas lineage; no Nitrosospira were detected. The effort to isolate novel AOB was successful; the isolate dominated in the gene libraries. For quantitative analysis, a real-time PCR assay targeting the 16S rRNA gene was developed. The population sizes of beta-AOB ranged from 1.6 x 10(7) to 3.0 x 10(8) cells g(-1) in dry sediments, which corresponded to 0.1-1.1% of the total bacterial population. An immunofluorescence staining using anti-hydroxylamine oxidoreductase (HAO) antibody was also tested to obtain complementary data. The population sizes of ammonia oxidizers ranged between 2.4 x 10(8) and 1.2 x 10(9) cells g(-1) of dry sediments, which corresponded to 1.2-4.3% of the total bacterial fraction. Ammonia-oxidizing bacteria cell numbers deduced by the two methods were correlated (R = 0.79, P < 0.01). In both methods, the number of AOB increased with the distance from the river mouth; ammonia-oxidizing bacteria were most numerous at B30, where the ammonium concentration in the porewater was markedly lower and the nitrite concentration was slightly higher than nearby sites. These results reveal spatial distribution and shifts in the population structure of AOB corresponding to nutrients and organic inputs from the river run-off and phytoplankton bloom.

Fluorescence resonance energy transfer (FRET) for DNA biosensors: FRET pairs and Förster distances for various dye-DNA conjugates

Fluorescence resonance energy transfer (FRET) between the extrinsic dye labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethyl Rhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ), and Iowa Black RQ (IabRQ) has been studied. The Förster distances for these FRET-pairs in single- and double-stranded DNA conjugates have been determined. In particular, it should be noted that the quantum yield of the donors Cy3 and TAMRA varies between single- and double-stranded DNA. While this alters the Förster distance for a donor-acceptor pair, this also allows for detection of thermal denaturation events with a single non-intercalating fluorophore. The utility of FRET in the development of nucleic acid biosensor technology is illustrated by using TAMRA and IabRQ as a FRET pair in selectivity experiments. The differential quenching of TAMRA fluorescence by IabRQ in solution has been used to discriminate between 0 and 3 base pair mismatches at 60 degrees C for a 19 base sequence. At room temperature, the quenching of TAMRA fluorescence was not an effective indicator of the degree of base pair mismatch. There appears to be a threshold of duplex stability at room temperature which occurs beyond two base pair mismatches and reverses the observed trend in TAMRA fluorescence prior to that degree of mismatch. When this experimental system is transferred to a glass surface through covalent coupling and organosilane chemistry, the observed trend in TAMRA fluorescence at room temperature is similar to that obtained in bulk solution, but without a threshold of duplex stability. In addition to quenching of fluorescence by FRET, it is believed that several other quenching mechanisms are occurring at the surface.

Optimization of the Molecular Orbital Energies of Conjugated Polymers for Optical Amplification of Fluorescent Sensors

Cationic water-soluble poly(fluorene-co-phenylene)s with electron withdrawing or donating substituents on the conjugated backbone were designed and synthesized. Fluorescence resonance energy transfer (FRET) experiments between these conjugated polymers and dye-labeled single-stranded DNA (ssDNA-C*) reveal the importance of matching donor and acceptor orbital energy levels to improve the sensitization of C* emission. Quenching of polymer fluorescence with ssDNA-C* and differences in C* emission suggest involvement of photoinduced charge transfer (PCT) as an energy wasting mechanism. The HOMO and LUMO energy levels of the conjugated polymers and C serve as a preliminary basis to understand the competition between FRET and PCT. Dilution of C in polymer/ssDNA-C complexes by addition of ssDNA yields insight into C*...C self-quenching. Under optimized conditions, where there is no probe self-quenching and minimum PCT, efficient signal amplification is demonstrated despite poor spectral overlap between polymer and C.

Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides

rRNA accessibility is a major sensitivity issue limiting the design of working probes for fluorescence in situ hybridization (FISH). Previous studies empirically highlighted the accessibility of target sites on rRNA maps by grouping probes into six classes according to their brightness levels. In this study, a recently proposed mechanistic model of FISH, based on the thermodynamics of secondary nucleic acid interactions, was used to evaluate the accessibility of the 16S rRNA of Escherichia coli to fluorescein-labeled oligonucleotides when thermodynamic and kinetic barriers were eliminated. To cover the entire 16S rRNA, 109 probes were designed with an average thermodynamic affinity (DeltaGo (overall)) of -13.5 kcal/mol. Fluorescence intensity was measured by flow cytometry, and a brightness threshold between classes 3 and 4 was used as the requirement for proof of accessibility. While 46% of the probes were above this threshold with conventional 3-h hybridizations, extending the incubation period to 96 h dramatically increased the fraction of bright probes to 86%. Insufficient thermodynamic affinity and/or fluorophore quenching was demonstrated to cause the low fluorescence intensity of the remaining 14% of the probes. In the end, it was proven that every nucleotide in the 16S rRNA of E. coli could be targeted with a bright probe and, therefore, that there were no truly inaccessible target regions in the 16S rRNA. Based on our findings and mechanistic modeling, a rational design strategy involving DeltaGo(overall), hybridization kinetics, and fluorophore quenching is recommended for the development of bright probes.

Mutation detection in DNA oligonucleotides based on a Guanine quenching method coupled with enzymatic digestion of single-stranded DNA

Fluorescence quenching by guanine allows DNA hybridization to be monitored and any point mutations in oligonucleotides to be detected. However, fluorescence quenching is often affected by untargeted guanine located in a protruding end (single-strand DNA) of the probe-target DNA duplex resulting in an unsatisfactory sensitivity. In the present study, we used enzymatic digestion of the protruding end of a probe-target DNA duplex to avoid interference by untargeted guanine on fluorescence quenching for detection of a nucleobase mutation. Enzymatic digestion of the protruding end of the DNA duplex fully prevented interference by untargeted guanine, and produced a marked difference in the quenching ratios (36% for wild-type, and 0% for mutant).

A Förster-resonance-energy transfer-based method for fluorescence detection of the protein redox state

A method for fluorescence detection of a protein's redox state based on resonance energy transfer from an attached fluorescence label to the prosthetic group of the redox protein is described and tested for proteins containing three types of prosthetic groups: a type-1 copper site (azurin, amicyanin, plastocyanin, and pseudoazurin), a heme group (cytochrome c550), and a flavin mononucleotide (flavodoxin). This method permits one to reliably distinguish between reduced and oxidized proteins and to perform potentiometric titrations at submicromolar concentrations.

Facile conversion of aptamers into sensors using a 2'-ribose-linked fluorophore

In vitro selection can be used to identify nucleic acid receptors, called aptamers, that bind diverse small molecule targets. Aptamers therefore represent an attractive platform for creating sensors. Here, we report a straightforward, semi-rational approach for converting arbitrary aptamers into reagentless, single fluorophore biosensors. The local electrostatic environment at the 2'-ribose position is exquisitely sensitive to whether a nucleotide is conformationally restrained or not. Thus, by tethering an environmentally sensitive fluorescent group at an appropriate 2'-ribose group, we are able to generically detect ligand-induced conformational changes in aptamers. Three aptamers, including one for which no significant structural information can be inferred, were converted into robust small molecule sensors that function well in simple buffers, human urine, and bovine blood serum.

Bias and artifacts in multitemplate polymerase chain reactions (PCR)

Polymerase chain reaction (PCR) is often used for the amplification of a mixture of homologous genes. PCR bias and artifact formation can occur in multitemplate PCR, and provide incorrect information on the abundance and diversity of genes. PCR bias and artifact formation occur at a higher rate during the last few cycles of the reaction, and therefore can be avoided by stopping the PCR earlier.