Congenital Chloride Diarrhea: Diagnosis by Easy-Accessible Chloride Measurement in Feces.

Background. Congenital chloride diarrhea (CCD) is an autosomal recessive disorder caused by mutations in the genes encoding the intestinal Cl(-)/HCO3 (-) exchanger and is clinically characterized by watery, profound diarrhea, electrolyte disturbances, and metabolic alkalosis. The CCD diagnosis is based on the clinical symptoms and measurement of high chloride concentration in feces (>90 mmol/L) and is confirmed by DNA testing. Untreated CCD is lethal, while long-term clinical outcome improves when treated correctly. Case Presentation. A 27-year-old woman had an emergency caesarian due to pain and discomfort in gestational week 36 + 4. The newborn boy had abdominal distension and yellow fluid per rectum. Therapy with intravenous glucose and sodium chloride decreased his stool frequency and improved his clinical condition. A suspicion of congenital chloride diarrhea was strongly supported using blood gas analyzer to measure an increased chloride concentration in the feces; the diagnosis was confirmed by DNA testing. Discussion. Measurement of chloride in feces using an ordinary blood gas analyzer can serve as a preliminary analysis when congenital chloride diarrhea is suspected. This measurement can be easily performed with a watery feces composition. An easy-accessible chloride measurement available will facilitate the diagnostics and support the initial treatment if CCD is suspected.

Label-free and reagentless electrochemical detection of PCR fragments using self-assembled quinone derivative monolayer: application to Mycobacterium tuberculosis.

We report a signal-on, label-free and reagentless electrochemical DNA biosensor, based on a mixed self-assembled monolayer of thiolated hydroxynaphthoquinone and thiolated oligonucleotide. Electrochemical changes resulting from hybridization were evidenced with oligonucleotide targets (as models), as well as with polymerase chain reaction (PCR) products related to different lineages of Mycobacterium tuberculosis strains. With pure oligonucleotides, this system achieves high sensitivity (∼300 pM of DNA target, i.e. 30 fmol in a 100 µL sample) and excellent selectivity, allowing to detect a single mismatch on a sequence of 20 bases. With PCR products, current changes are specific to the bacterial strain from which the PCR fragment is produced. In addition, the sensor response is of the signal-on type, giving a positive signal change upon hybridization, and therefore does not suffer from false positive responses due to non-specific adsorption of DNA.

Label-free DNA electrochemical sensor based on a PNA-functionalized conductive polymer.

An electrochemical hybridization biosensor based on peptide nucleic acid (PNA) probe is presented. PNA were attached covalently onto a quinone-based electroactive polymer. Changes in flexibility of the PNA probe strand upon hybridization generates electrochemical changes at the polymer-solution interface. A reagentless and direct electrochemical detection was obtained by detection of the electrochemical changes using square wave voltammetry (SWV). An increase in the peak current of quinone was observed upon hybridization of probe on the target, whereas no change is observed with non-complementary sequence. In addition, the biosensor is highly selective to effectively discriminate a single mismatch on the target sequence. The sensitivity is also presented and discussed.

The influence of a chiral amino acid on the helical handedness of PNA in solution and in crystals.

The X-ray structure of a self-complementary PNA hexamer (H-CGTACG-L-Lys-NH(2)) has been determined to 2.35 A resolution. The introduction of an L-lysine moiety has previously been shown to induce a preferred left-handedness of the PNA double helices in aqueous solution. However, in the crystal structure an equal amount of interchanging right- and left-handed helices is observed. The lysine moieties are pointing into large solvent channels and no significant interactions between this moiety and the remaining PNA molecule are observed. In contrast, molecular mechanics calculations show a preference for the left-handed helix of this hexameric PNA in aqueous solution as expected. The calculations indicate that the difference in the free energy of solvation between the left-handed and the right-handed helix is the determining factor for the preference of the left-handed helix in aqueous solution.

Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins.

The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex detection. These results indicate that both stable PNA-DNA and DNA-DNA duplexes can be formed with these target hairpins, even when the melting temperatures for the resulting duplexes are up to 50 degrees C lower than that of the hairpin target. Both hairpin/single-stranded and hairpin/hairpin interactions are considered in the scope of these studies. Secondary structures in both target and probe molecules are shown to depress the melting temperatures and free energies of the probe-target duplexes. Kinetic analysis of hybridization yields reaction rates that are up to 160-fold slower than hybridization between two unstructured strands. The thermodynamic and kinetic obstacles to hybridization imposed by both target and probe secondary structure are significant concerns for the continued development of antisense agents and especially diagnostic probes.

Synthesis of a Hoechst 32258 analogue amino acid building block for direct incorporation of a fluorescent, high-affinity DNA binding motif into peptides.

The synthesis of a new versatile "Hoechst 33258-like" Boc-protected amino acid building block for peptide synthesis is described. It is demonstrated that this new ligand is an effective mimic of Hoechst 33258 in terms of DNA affinity and sequence specificity. Furthermore, this minor groove binder was conjugated to a DNA condensing peptide (KSPKKAKK) by continuous solid-phase peptide synthesis, and the conjugate exhibited increased DNA affinity (ca. 10-fold), but similar sequence preference compared to Hoechst 33258 as analyzed by DNaseI footprinting. Finally, the fluorescence quantum yield of the new chromophore is found to increase 30% upon binding to double stranded DNA.

Investigating the kinetics of DNA-DNA and PNA-DNA interactions using surface plasmon resonance-enhanced fluorescence spectroscopy.

Plasmon surface polaritons, resonantly excited in the Kretschmann format, are used to enhance the fluorescence emission of chromophore-labeled oligonucleotides (15mers) binding to surface-attached (via biotin-streptavidin linkages) complement catcher probes. A detailed analysis of the association and dissociation kinetics as well as the affinity constants is given for a mismatch 1 hybrid, emphasizing, in particular, the experimental conditions that are required to allow for an artifact-free determination of rate constants. A first comparison between DNA- and peptide nucleic acid (PNA-) probes shows similar affinities, however, significant deviations from single-exponential kinetics predicted by a simple Langmuir model for the PNA case are found.

Strand displacement recognition of mixed adenine-cytosine sequences in double stranded DNA by thymine-guanine PNA (peptide nucleic acid).

Mixed pyrimidine-purine peptide nucleic acids (PNAs) composed of thymines and guanines are shown to form a PNA(2)-DNA triplex with Watson-Crick complementary adenine-cytosine oligonucleotides and to bind complementary adenine-cytosine targets in double stranded DNA by helix invasion. These results for the first time demonstrate binding of an unmodified PNA oligomer to a mixed pyrimidine-purine target in double stranded DNA and illustrate a novel binding mode of PNA.

Inhibition of promyelocytic leukemia (PML)/retinoic acid receptor-alpha and PML expression in acute promyelocytic leukemia cells by anti-PML peptide nucleic acid.

The fusion protein promyelocytic leukemia (PML)/retinoic acid receptor (RAR)alpha is tightly linked to the pathogenesis of acute promyelocytic leukemia (APL); hence, it represents a tumor-associated, transformation-related molecule. In this study, three anti-PML adamantyl-conjugated peptide nucleic acid (PNA) oligomers previously described as in vitro inhibitors of PML/RARalpha translation were combined and used to block PML/RARalpha synthesis in NB4 cells. Cationic liposomes were used to achieve sufficient delivery of PNAs into the cells. Upon treatment of cells with the liposome/PNA mixture, enhanced cellular uptake of PNA (approximately 5-fold compared with control) was obtained. Concomitantly, a substantial reduction (>90%) of the expression of PML/RARalpha was observed when all of the three PNAs were used together. This resulted in a dramatic effect on the number and viability of NB4 cells in culture after 48 h of treatment. This phenomenon was preceded by induction of apoptosis that could be observed 24 h after treatment. No sign of granulocytic differentiation was observed after treatment. These effects were also noted on other leukemic cell lines that express PML but not the fusion transcript. These results show that it is possible to deliver PNA into hematopoietic cells and obtain specific gene inhibition, and they suggest that a growth inhibitory effect on acute promyelocytic leukemia cells can be obtained through the block of PML/RARalpha and PML expression.

Comparison of electron capture dissociation and collisionally activated dissociation of polycations of peptide nucleic acids.

Electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance mass spectrometry coupled with electrospray ionization enhances the sequence elucidation of peptide nucleic acids compared with conventional low-energy collisionally activated dissociation (CAD). Examples are shown where ECD produced complete or extensive sequence coverage in PNAs six to ten nucleobases long. However, facile base losses from the reduced species and low abundances of backbone ECD fragments presented a significant problem. This was rationalized through the lower degree of charge solvation on the backbone compared to polypeptides. Combination of both CAD and ECD data is advantageous, as these techniques produce cleavages at different sites.

Synthesis of pyrrolidinone PNA: a novel conformationally restricted PNA analogue.

To preorganize PNA for duplex formation, a new cyclic pyrrolidinone PNA analogue has been designed. In this analogue the aminoethylglycine backbone and the methylenecarbonyl linker are connected, introducing two chiral centers compared to PNA. The four stereoisomers of the adenine analogue were synthesized, and the hybridization properties of PNA decamers containing one analogue were measured against complementary DNA, RNA, and PNA strands. The (3S,5R) isomer was shown to have the highest affinity toward RNA, and to recognize RNA and PNA better than DNA. The (3S,5R) isomer was used to prepare a fully modified decamer which bound to rU10 with only a small decrease in Tm (delta Tm/mod = 1 degree C) relative to aminoethylglycine PNA.

Perinatal outcome following fetal single umbilical artery diagnosis.

OBJECTIVE: We report the frequency of associated congenital abnormalities in fetuses with a single umbilical artery as well as the sensitivity, specificity, positive predictive value and negative predictive value of ultrasound for detecting these abnormalities. We also report the pregnancy outcome of fetuses complicated by single umbilical artery, both isolated and with other congenital anomalies. METHODS: All pregnancies complicated by fetal single umbilical artery from 1995 to 1999 were identified. A retrospective chart review was performed on both the prenatal records and the ultrasound records of these pregnancies, determining the nature and incidence of other congenital abnormalities. Delivery data were collected to include gestational age at delivery, Apgar score, birth weight, mode of delivery, fetal gender and any complications. RESULTS: Ninety-two pregnancies were identified with a fetal single umbilical artery, of which outcome data were available for 65. Forty-eight (74%) cases were identified as isolated single umbilical artery. Seventeen (26%) cases had other congenital abnormalities. High-resolution ultrasound had 100% sensitivity and specificity for identifying single umbilical artery and an 85% sensitivity and 98% specificity for detecting other congenital abnormalities. Compared to isolated single umbilical artery, pregnancies complicated by single umbilical artery with other abnormalities had a statistically significantly increased rate of fetal aneuploidy, lower birth weight, preterm delivery and Cesarean delivery. CONCLUSION: Pregnancies complicated by fetal single umbilical artery, especially when associated with other congenital abnormalities, are at increased risk for adverse pregnancy outcome.

Bactericidal antisense effects of peptide-PNA conjugates.

Antisense peptide nucleic acids (PNAs) can specifically inhibit Escherichia coli gene expression and growth and hold promise as anti-infective agents and as tools for microbial functional genomics. Here we demonstrate that chemical modification improves the potency of standard PNAs. We show that 9- to 12-mer PNAs, especially when attached to the cell wall/membrane-active peptide KFFKFFKFFK, provide improvements in antisense potency in E. coli amounting to two orders of magnitude while retaining target specificity. Peptide-PNA conjugates targeted to ribosomal RNA (rRNA) and to messenger RNA (mRNA) encoding the essential fatty acid biosynthesis protein Acp prevented cell growth. The anti-acpP PNA at 2 microM concentration cured HeLa cell cultures noninvasively infected with E. coli K12 without any apparent toxicity to the human cells. These results indicate that peptides can be used to carry antisense PNA agents into bacteria. Such peptide-PNA conjugates open exciting possibilities for anti-infective drug development and provide new tools for microbial genetics.

Targeting double stranded DNA with peptide nucleic acid (PNA).

PNA (peptide nucleic acid) is a DNA mimic with a pseudopeptide (polyamide) backbone which can be used to target double stranded DNA with high sequence specificity. PNA therefore has great potential in the development of biomolecular tools for manipulation of DNA as well as for the development of DNA targeted gene therapeutic drugs. The status of this field is discussed in terms of PNA binding modes and mechanism as well as applications.