Engineering DNAzyme strategies for fluorescent detection of lead ions based on RNA cleavage-propelled signal amplification.

Based on the high recognition ability and flexible programmability of GR5 DNAzyme, two fluorescent biosensors were engineered for amplified detection of Pb2+ via incorporating Ti3C2TX MXenes and embedding 2-aminopurine (2-AP), respectively. The quencher-required approach relied on the DNA affinity and fluorescence quenching ability of Ti3C2TX MXenes. Benefiting from the low background signal modulated by Ti3C2TX MXenes, the sensitive determination of Pb2+ was achieved in the linear range of 0.2-10 ng mL-1 with the limit of detection (LOD) of 0.05 ng mL-1. The quencher-free approach combined the fluorescent trait of 2-AP embedded in DNA structure, and the RNA cleavage-propelled digestion process of Exonuclease I (Exo I) for signal amplification, indicating the sensitive detection of Pb2+ with the LOD as low as 0.02 ng mL-1 in the linear range of 0.1-10 ng mL-1. Both DNAzyme assays exhibited simple procedures, favorable specificity, rapid analysis, and satisfactory application in standard reference materials (lead in drinking water) and spiked water samples. The two fluorescent biosensors established in this work would not only provide theoretic fundament for DNA adsorption of Ti3C2TX MXenes and the design of 2-AP-embedded DNAzyme assays, but also hold a great potential for on-site monitoring of lead pollution in water samples.

LC-MS/MS method for determination of cyclin-dependent kinase inhibitors, BP-14 and BP-20, and its application in pharmacokinetic study in rat.

N2-(4-Amino-cyclohexyl)-9-cyclopentyl-N6-(6-furan-2-yl-pyridine-3-ylmethyl)-9H-purine-2,6-diamine (BP-14) and 2-(5-{[2-(4-amino-cyclohexylamino)-9-cyclopentyl-9H-purine-6-ylamino]-methyl}-pyridine-2-yl)-phenol (BP-20) are novel cyclin-dependent kinase inhibitors, structurally related to roscovitine, with significant biological activity. A simple, selective and sensitive liquid chromatography - tandem mass spectrometry method for determining them in rat plasma, using roscovitine as an internal standard, was developed and validated. Chromatographic separation was performed in reversed phase mode on Acquity BEH C18 column (100 × 2.1 mm, 1.7 µm) by gradient elution with mobile phases composed of 15 mM ammonium formate pH 4.0 and methanol at flow rate 0.25 mL/min at 40 °C. The analytes were detected based on their characteristic multiple reaction monitoring transitions in positive electrospray ionization mode m/z 473.07 > 157.93 for BP-14, m/z 499.62 > 184.2 for BP-20 and m/z 355.5 > 90.86 for internal standard. In plasma the method provided good linearity within the entire concentration range: 1-10,000 nmol/L (r2 = 0.9989) for BP-14 and 10-25,000 nmol/L (r2 = 0.9994) for BP-20; the limit of detection was 0.6 nmol/L for BP-14 and 6.1 nmol/L for BP-20. Validation was also performed in bile and urine. The results of validation fit within the acceptance limits following European Medicines Agency guidelines. The method was applied in a pharmacokinetic study of BP-14 and BP-20 in vivo in rats following intravenous and intraduodenal administration including plasma pharmacokinetics, tissue distribution and excretion (renal and biliary). Both compounds showed low bioavailability after intraduodenal administration (0.630 and 1.58% for BP-14 and BP-20, respectively). Distribution into all the analyzed tissues (brain, lungs, liver, kidney, spleen, muscle, adipose tissue) was observed 3 h after single dose administration, the highest and lowest concentrations being reached in the adipose tissue and brain, respectively. The biliary excretion of the parent BP-14 and BP-20 compounds accounted for 4.81% and 10.6% of the doses, respectively, and renal excretion for <0.5% in both cases. The obtained results represent pilot knowledge for further development of a new generation of compounds with strong anticancer activities.

Shape-selective recognition of DNA abasic sites by metallohelices: inhibition of human AP endonuclease 1.

Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously or under the action of various physical and chemical agents. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of AP sites in synthetic duplexes. We report here on interactions of diastereomerically pure metallo-helical 'flexicate' complexes, bimetallic triple-stranded ferro-helicates [Fe2(NN-NN)3](4+) incorporating the common NN-NN bis(bidentate) helicand, with short DNA duplexes containing AP sites in different sequence contexts. The results show that the flexicates bind to AP sites in DNA duplexes in a shape-selective manner. They preferentially bind to AP sites flanked by purines on both sides and their binding is enhanced when a pyrimidine is placed in opposite orientation to the lesion. Notably, the Λ-enantiomer binds to all tested AP sites with higher affinity than the Δ-enantiomer. In addition, the binding of the flexicates to AP sites inhibits the activity of human AP endonuclease 1, which is as a valid anticancer drug target. Hence, this finding indicates the potential of utilizing well-defined metallo-helical complexes for cancer chemotherapy.

Synthesis and application of a molecularly imprinted polymer for the voltammetric determination of famciclovir.

A molecularly imprinted polymer (MIP) was synthesized and applied as additive within a carbon paste electrode for the cyclic voltammetric determination of famciclovir (FCV). Complementary computational studies were performed to study the intermolecular interactions in the pre-polymerization mixture. Derived from the computational studies, four MIP ratios were synthesized and their performance was evaluated using equilibrium rebinding assays. The MIP with the highest binding capacity was selected. A linear response was obtained in the range of 2.5×10(-6)-1.0×10(-3)M with a limit of detection at 7.5×10(-7)M. Finally, the developed MIP-voltammetry system was successfully applied for the determination of FCV in pure solutions and pharmaceutical preparations.

Dissolution testing and potentiometric determination of famciclovir in pure, dosage forms and biological fluids.

The performance characteristics of two new plastic membrane ion selective electrodes (ISEs) used for the determination of famciclovir (Fcv) based on the ion associate of Fcv with phosphotungstic acid (PTA) or phosphomolybdic acid (PMA) are described. Different experimental conditions as type of plasticizer to be incorporated in the membrane, life span, effect of soaking, pH, temperature, and interferences were studied. Both electrodes showed similar performance under these conditions, exhibiting Nernstian slopes of S (Fcv-PTA)=58.60±0.84 mV/decade and S (Fcv-PMA)=58.77±0.68 mV/decade within a usable concentration range of 10⁻5-10⁻² [Fcv/M] at 298/K. Famciclovir was assayed potentiometrically in its pure solution, pharmaceutical preparations and biological fluids (urine and plasma) using proposed electrodes under batch and flow injection analysis (FIA) conditions with a recovery % ranging between 96.76% and 102.83% having RSD of 0.66%-1.81%. The electrodes were also successfully applied in the determination of the dissolution profile of Fcv tablets and the results came in agreement with the validated results of the HPLC method obtained from the quality control unit of the company producing the tablets.

Stability-indicating methods for the determination of famciclovir in the presence of its alkaline-induced degradation product.

Five sensitive, selective and precise stability-indicating methods are presented for the determination of famciclovir (FCV) in the presence of its alkaline-induced degradation product. Method A utilizes the first derivative spectrophotometry at 321 nm. Method B depends on using the first derivative of the ratio spectrophotometry (DD(1)) by measurement of the amplitude at 256 nm. Method C is based on the reaction of FCV with hydroxylamine to form hydroxamic acid, causing the hydroxamic acid to react with triferric ion to form ferric hydroxamate that is measured at 503 nm. Method D is based on the separation of FCV from its degradation product followed by densitometric measurement of the bands at 304 nm. The separation was carried out on silica gel 60 F(254), using chloroform: methanol (70:30, v/v) as a mobile phase. Method E is based on a high performance liquid chromatographic (HPLC) separation of FCV from its degradation product using an ODS column with a mobile phase consisting of methanol-50 mM dipotassium hydrogen phosphate (25:75, v/v, pH 3.0)with UV detection at 304 nm. Regression analysis showed good correlation in the concentration ranges 16-72 microg/ml, 40-240 microg/ml, 40-240 microg/ml, 0.75-5.25 microg/band and 20-240 microg/ml with percentage recoveries of 99.65 +/- 0.85, 100.27 +/- 0.91, 99.72 +/- 0.84, 100.65 +/- 1.52 and 99.88 +/- 0.50 for methods A, B, C, D and E, respectively. These methods are suitable as stability-indicating methods for the determination of FCV in the presence of its degradation product either in bulk powder or in pharmaceutical formulation. Statistical analysis of the results has been carried out revealing high accuracy and good precision.

Development and validation of a stability-indicating RP-LC method for famciclovir.

A novel stability-indicating gradient reverse phase liquid chromatographic (RP-LC) method was developed for the determination of purity of famciclovir (FCV) in presence of its impurities and degradation products. The method was developed using Inertsil ODS 3 V (250 x 4.6 mm, 5 microm) column with mobile phase containing a gradient mixture of solvent A and B. 0.01 M potassium dihydrogen orthophosphate buffer, pH adjusted to 6.0 with 1% potassium hydroxide was used as buffer. Buffer and methanol in 80:20 (v/v) ratio was used as solvent A and buffer and methanol in 20:80 (v/v) ratio was used as solvent B. The gradient program (T/%B) was set as 0/5, 15/30, 25/50, 45/60, 55/5 and 60/5. The eluted compounds were monitored at 215 nm. FCV was subjected to the stress conditions of oxidative, acid, base, hydrolytic, thermal and photolytic degradation. FCV was found to degrade significantly in oxidative, acid and base degradation conditions and mildly in hydrolytic degradation conditions and stable in thermal and photolytic degradation conditions. The degradation products were well resolved from main peak and its impurities thus proved the stability-indicating power of the method. The developed method was validated as per International Conference on Harmonization (ICH) guidelines with respect to specificity, limit of detection, limit of quantitation, precision, linearity, accuracy, robustness and system suitability. This method is also suitable for the assay of famciclovir which ranged from 99.9% to 100.2%.

T4 DNA ligase is more than an effective trap of cyclized dsDNA.

T4 DNA ligase is used in standard cyclization assays to trap double-stranded DNA (dsDNA) in low-probability, cyclic or highly bent conformations. The cyclization probability, deduced from the relative yield of cyclized product, can be used in conjunction with statistical mechanical models to extract the bending stiffness of dsDNA. By inserting the base analog 2-aminopurine (2-AP) at designated positions in 89 bp and 94 bp dsDNA fragments, we find that T4 DNA ligase can have a previously unknown effect. Specifically, we observe that addition of T4 ligase to dsDNA in proportions comparable to what is used in the cyclization assay leads to a significant increase in fluorescence from 2-AP. This effect is believed to originate from stabilization of local base-pair opening by formation of transient DNA-ligase complexes. Non-specific binding of T4 ligase to dsDNA is also confirmed using fluorescence correlation spectroscopy (FCS) experiments, which reveal a systematic reduction of dsDNA diffusivity in the presence of ligase. ATP competes with regular DNA for non-covalent binding to the T4 ligase and is found to significantly reduce DNA-ligase complexation. For short dsDNA fragments, however, the population of DNA-ligase complexes at typical ATP concentrations used in DNA cyclization studies is determined to be large enough to dominate the cyclization reaction.

Multiphoton excitation of fluorescent DNA base analogs.

Multiphoton excitation was used to investigate properties of the fluorescent DNA base analogs, 2-aminopurine (2AP) and 6-methylisoxanthopterin (6MI). 2-aminopurine, a fluorescent analog of adenine, was excited by three-photon absorption. Fluorescence correlation measurements were attempted to evaluate the feasibility of using three-photon excitation of 2AP for DNA-protein interaction studies. However, high excitation power and long integration times needed to acquire high signal-to-noise fluorescence correlation curves render three-photon excitation FCS of 2AP not very useful for studying DNA base dynamics. The fluorescence properties of 6-methylisoxanthopterin, a guanine analog, were investigated using two-photon excitation. The two-photon absorption cross-section of 6MI was estimated to be about 2.5 x 10(-50) cm(4)s (2.5 GM units) at 700 nm. The two-photon excitation spectrum was measured in the spectral region from 700 to 780 nm; in this region the shape of the two-photon excitation spectrum is very similar to the shape of single-photon excitation spectrum in the near-UV spectral region. Two-photon excitation of 6MI is suitable for fluorescence correlation measurements. Such measurements can be used to study DNA base dynamics and DNA-protein interactions over a broad range of time scales.

Development and validation of liquid chromatographic and UV derivative spectrophotometric methods for the determination of famciclovir in pharmaceutical dosage forms.

A high-performance liquid chromatographic method and a UV derivative spectrophotometric method for the determination of famciclovir, a highly active antiviral agent, in tablets were developed in the present work. The various parameters, such as linearity, precision, accuracy, specificity, robustness, limit of detection and limit of quantitation were studied according to International Conference on Harmonization guidelines. HPLC was carried out by using the reversed-phase technique on an RP-18 column with a mobile phase composed of 50 mM monobasic phosphate buffer and methanol (50 : 50; v/v), adjusted to pH 3.05 with orthophosphoric acid. The mobile phase was pumped at a flow rate of 1 ml/min and detection was made at 242 nm with UV dual absorbance detector. The first derivative UV spectrophotometric method was performed at 226.5 nm. Statistical analysis was done by Student's t-test and F-test, which showed no significant difference between the results obtained by the two methods. The proposed methods are highly sensitive, precise and accurate and therefore can be used for its Intended purpose.

Theoretical investigation of spectral properties and tautomerization mechanism of 2-aminopurine.

In this work the spectral properties and tautomerization mechanism of 2-aminopurine are investigated using quantum chemical calculations. TD-DFT results lead to a conclusion that two tautomers of 2-aminopurine discussed in this work are fluorescent and present the pi-->pi* transition feature of vertical excitation and emission. It is predicted that the tautomerization of 2-aminopurine hardly occurs in a direct isomerization mechanism because of the high barrier. However, the explicit involvement of water molecules into the system reduces the barrier height considerably and hence makes the ground state reaction feasible. An explanation for the almost equal populations of the two tautomers in polar solvent is given through reaction mechanism analysis.

Tautomers and electronic states of jet-cooled 2-aminopurine investigated by double resonance spectroscopy and theory.

We present resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectra of jet-cooled 2-aminopurine (2AP) as well as Fourier transform infrared (FTIR) gas phase spectra. 2AP is a fluorescing isomer of the nucleobase adenine. The results show that there is only one tautomer of 2AP which absorbs in the wavelength range 32,300-34,500 cm(-1). The comparison with the calculated IR spectra of 9H- and 7H-2AP points to 9H-2AP as the dominating tautomer in the gas phase but the spectra are too similar to allow an unambiguous assignment to the respective tautomer. Hence, we determined vertical and adiabatic excitation energies of both tautomers employing combined density functional theory and multi-reference configuration interaction techniques. For the 0-0 band of the first 1pipi* transition of 9H-2AP we obtain a theoretical value of 32,328 cm(-1), in excellent agreement with the band origin of our R2PI spectrum at 32,371 cm(-1). The first singlet pipi* transition of the less stable 7H-2AP tautomer is predicted to be red-shifted by about 1700 cm(-1) with respect to the corresponding transition in 9H-2AP. From the absence of experimental bands in the energy region between 30,300 and 32,350 cm(-1) we conclude that 7H-2AP is not present to an appreciable extent in the molecular beam. Our calculations yield nearly equal energies for the 1npi* and 1pipi* minima of isolated 2AP, similar to the situation in adenine. The hitherto existing argument that the energetic order of states is responsible for the different spectroscopic properties of these isomers therefore does not hold. Rather, vibronic levels close to the origin of the 1pipi* transition cannot access the conical intersection between the 1pipi* and S(0) states along a puckering coordinate of the six-membered ring, in contrast to the situation in electronically excited 9H-adenine. As a consequence, a rich vibrational structure can be observed in the R2PI spectrum of 2AP whereas the spectrum of 9H-adenine breaks off at low energies.

Ultraviolet surface plasmon-coupled emission using thin aluminum films.

Surface plasmon-coupled emission (SPCE) is the directional radiation of light into a substrate due to excited fluorophores above a thin metal film. To date, SPCE has only been observed with visible wavelengths using silver or gold films. We now show that SPCE can be observed in the ultraviolet region of the spectrum using thin (20 nm) aluminum films. We observed directional emission in a quartz substrate from the DNA base analogue 2-aminopurine (2-AP). The SPCE radiation occurs within a narrow angle at 59 degrees from the normal to the hemicylindrical prism. The excitation conditions precluded the creation of surface plasmons by the incident light. The directional emission at 59 degrees is almost completely p-polarized, consistent with its origin from surface plasmons due to coupling of excited 2-AP with the aluminum. The emission spectra and lifetimes of the SPCE are those characteristic of 2-AP. Different emission wavelengths radiate at slightly different angles on the prism providing intrinsic spectral resolution from the aluminum film. These results indicate that SPCE can be used with numerous UV-absorbing fluorophores, suggesting biochemical applications with simultaneous surface plasmon resonance and SPCE binding assays.

Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin.

The parallel (recombination) 'R-triplex' can accommodate any nucleotide sequence with the two identical DNA strands in parallel orientation. We have studied oligonucleotides able to fold back into such a recombination-like structure. We show that the fluorescent base analogs 2-aminopurine (2AP) and 6-methylisoxanthopterin (6MI) can be used as structural probes for monitoring the integrity of the triple-stranded conformation and for deriving the thermodynamic characteristics of these structures. A single adenine or guanine base in the third strand of the triplex-forming and the control oligonucleotides, as well as in the double-stranded (ds) and single-stranded (ss) reference molecules, was substituted with 2AP or 6MI. The 2AP*(T.A) and 6MI*(C.G) triplets were monitored by their fluorescence emission and the thermal denaturation curves were analyzed with a quasi-two-state model. The fluorescence of 2AP introduced into an oligonucleotide sequence unable to form a triplex served as a negative control. We observed a remarkable similarity between the thermodynamic parameters derived from melting of the secondary structures monitored through absorption of all bases at 260 nm or from fluorescence of the single base analog. The similarity suggests that fluorescence of the 2AP and 6MI base analogs may be used to monitor the structural disposition of the third strand. We consider the data in the light of alternative 'branch migration' and 'strand exchange' structures and discuss why these are less likely than the R-type triplex.

Spectroscopic determination of open complex formation at promoters for Escherichia coli RNA polymerase.

A considerable amount of effort has been expended studying the kinetics of association of Escherichia coli RNA polymerase with promoter DNA in forming the open complex. Strand separation occurs over about 12 base pairs and includes the transcription start site. However, these efforts have been significantly hampered by the lack of a sensitive, real time method by which formation of an open complex could be assayed. Here, we employ short (86 bp) synthetic promoters with 2-aminopurine (2-AP) substitutions in the region that becomes single-stranded to spectroscopically monitor open complex formation. We demonstrate that promoters bearing the substitutions behave in a manner similar to that of those containing only the four common bases with respect to both the region of strand separation and start site selection. Open complex formation was found to yield an increased fluorescence signal with an emission maximum characteristic of 2-aminopurine. This spectroscopic assay for open complex formation was found to be well-suited to the investigation of a strong promoter, allowing open complex formation to be followed over a time scale of seconds with a stopped flow apparatus. The introduction of two additional nonconsensus base pairs in the -35 region resulted in a promoter for which open complex formation was 100-fold slower. The same substrates were also used to monitor the promoter re-annealing that ensues upon initiation of RNA synthesis. Similar rates for this process were observed for the two promoter variants employed in this study.

Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine.

The base analog 2-aminopurine (AP) strongly promotes A.T to G.C and G.C to A.T transitions in bacteria and bacteriophage. During DNA replication, the primary mutagenic event involves formation of a heteroduplex with an AP.C site at a much higher frequency than formation of the corresponding heteroduplex with an A.C site. It is not known if AP-induced mutagenesis correlates with differences in the thermodynamic properties of an AP.C versus an A.C site, or whether interactions involving DNA polymerases are controlling. To address this specific question, and more generally to characterize AP-containing duplexes, we have used a combination of spectroscopic and calorimetric techniques to determine the thermodynamic properties of six 11-mer duplexes. The sequences of these duplexes are identical except for the identity of the variable central base pair which can be either A.T, A.C, AP.T, AP.C, AP.A, or AP.G, and which we use to designate each duplex. Analyses and interpretation of the optically and calorimetrically derived thermal and thermodynamic data on these six duplexes reveal the relative stabilizing influence of the central base pairs to be A.T > AP.T > AP.C > AP.A > AP.G > A.C, with the AP.C-containing duplex being significantly more stable than the A.C-containing duplex. In the aggregate, our results suggest that during incorporation, base pair discrimination by DNA polymerases is influenced, in part, by differences in the thermodynamic stabilities of the newly formed base pairs.

[Intensification of genomic dactyloscopy by means of hybridization with modified oligonucleotides, forming duplexes with increased stability]. / Intensifikatsiia genomnoi daktiloskopii putem gibridizatsii s modifitsirovannymi oligonukleotidami, obrazuiushchimi dupleksy s povyshennoi stabil'nostiu.

The modified oligodeoxyribonucleotide (m5C-n2A-m5C)5 containing 5-methylcytosine and 2-aminoadenine instead of cytosine and adenine residues, respectively has been used as a hybridisation probe in DNA fingerprinting. The oligonucleotide, due to the substitutions forms more stable duplexes with complementary sequence in DNA than the corresponding nonmodified pentadecanucleotide. The comparison with its natural counterpart displays considerably increased intensity of bands in patterns obtained with modified analog. The use of such analogues can increase sensitivity and shorten time of DNA fingerprinting.

On the molecular basis of transition mutations. Frequency of forming 2-aminopurine-cytosine base mispairs in the G X C----A X T mutational pathway by T4 DNA polymerase in vitro.

An in vitro model system including wild-type T4 DNA polymerase, the mutagenic nucleotide analogue 2-aminopurine deoxyribonucleoside triphosphate, and poly[d(A,C)] X oligo(dT) poly(dC) X oligo(dG) template-primers is used to measure the frequency of 2-aminopurine X cytosine base mispairs formed in the G X C----A X T mutational pathway. Incorporation and turnover of the analogue into DNA is dependent on the presence of cytosine on the template strand and is reduced significantly in the presence of dGTP. 2-Aminopurine X cytosine mispairs are observed to occur at a 2-3 order of magnitude greater frequency than adenine X cytosine mispairs. The frequency of inserting 2-aminopurine deoxyribonucleoside monophosphate in place of dGMP opposite template cytosine sites is about 3-6% when either strong or weak base-stacking partners are present on the primer strand. However, enzymatic proofreading of the mispair strongly depends on base-stacking partners. Greater than 85% of misinserted 2-aminopurine deoxynucleotides are excised whenever the mispairs are formed next to 5'-primer thymine sites. A 5-fold reduction in proofreading frequency occurs when the mispair is formed with 2-aminopurine deoxynucleoside monophosphate stacked adjacent to a 5'-primer guanine. The frequency of 2-aminopurine X cytosine base mispair formation in the G X C----A X T pathway is similar to that found previously in the A X T----G X C pathway (Watanabe, S. M., and Goodman, M.F. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 2864-2868). We propose a criterion for base selection by DNA polymerase to account for the unexpected similarity in base mispairing rates in the two transition pathways.