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PubMed2006

Reactivity of halides with triplets of 6-chloro and 6-bromopicolinic acids: contrasting effects of bromide and chloride.

The reactivity of Br(-) and Cl(-) with triplet of anionic 6-chloropicolinic acid (pH = 5.4) and with triplets of 6-chloro and 6-bromopicolinic acids in zwitterionic forms (pH = 0.9) was studied by laser flash photolysis and steady-state irradiation. Br(-) was found to trap the three triplets. Triplet lifetime measurements gave quenching rate constants of 8 x 10(8) mol(-1) dm(3) s(-1) for the zwitterion of 6-chloropicolinic acid and of 3.4 x 10(5) mol(-1) dm(3) s(-1) for the anionic counterpart. No secondary transient species were observed indicating that the charge transfer intermediates are subject to dissipative processes. Cl(-) trapped triplet of zwitterions only, and reactions were found to be associated with a high quantum yield of radicals. The photolysis of 6-bromopicolinic acid photolysis was drastically enhanced by Cl(-), 6-chloropicolinic acid being produced with a chemical yield of about 90%. The 6-bromo-2-carboxypyridinyl radical could be characterized (lambda(max)/nm = 318 with shoulder at 370 nm and epsilon/mol(-1) dm(3) cm(-1) = 8100).

Journal Article↗
PubMed2006

The inter-relationship between triplet energies and spin chemistry.

Triplet energies play a considerable role in optical spectroscopy, and can be determined from phosphorescence or the quenching thereof. Their role in spin chemistry may not be as obvious, but the triplet state has always had an important function or utility, namely of reaction intermediates such as radical pairs, their precursors, of carbenes, and of the final products. In situ NMR spectroscopy represents a useful tool to explore certain properties of the triplet state, especially in cases with no phosphorescence. The 'phase' of CIDNP resonances, i.e., emission or enhanced absorption, reflects the spin selectivity of electron transfer reactions. In radical ion pairs the spin selectivity is determined by the relation between the change of the standard free enthalpy DeltaG degrees during the electron back transfer and the triplet energies (E(T)) of the products. If triplet recombination is energetically feasible (DeltaG degrees > E(T)), it is typically the more efficient process in agreement with the Marcus theory.

Journal Article↗
PubMed2004

Photophysics of protoporphyrin ions in vacuo: triplet-state lifetimes and quantum yields.

Lifetimes of triplet-state molecules and triplet quantum yields are important parameters in photobiology as they determine the generation of singlet-oxygen upon irradiation with visible light. Here we report lifetimes of protoporphyrin IX (pp) in vacuo measured in an ion storage ring. We find that after 532 nm photon absorption, pp(-) (free base and negatively charged carboxylate) and pp(+) (single protonation of ring nitrogen) have triplet-state lifetimes of 12 and 6 ms, respectively. After 415 or 390 nm absorption the lifetime of the anion is shorter (1.5 and 0.6 ms) as expected from the increase in temperature. Triplet quantum yields of pp(-) and pp(+) are similar, 0.6-0.7, close to values reported for the free base and monocation in solution. The other channel, direct decay to the electronic ground state and subsequent dissociation of vibrationally excited ions, is much faster than triplet-singlet intersystem crossing. We measured lifetimes of 63 micros, 96 micros, and 0.3 ms after 390, 415, and 532 nm excitation, respectively. A fit of a statistical model to the pp(-) decay results in an Arrhenius activation energy of 0.5+/-0.2 eV for CO(2) loss and a low preexponential factor (10(6)-10(10) s(-1)), indicative of an entropic barrier.

Absorption↗
PubMed2004

Triplet build in and decay of isolated polyspirobifluorene chains in dilute solution.

The triplet kinetics of a conjugated polymer, polyspirobifluorene, have been studied using time resolved photoinduced absorption spectroscopy and gated emission delayed fluorescence. Working on isolated polymer chains in dilute solution, we pay particular attention to the buildup and decay of the triplet states following intersystem crossing from the excited singlet state. Confirmation of intersystem crossing as a monomolecular cold process has been made. At high excitation powers an initial fast decay of the triplet has been observed; this is attributed to intrachain triplet-triplet annihilation. From this observation we estimate the lower bound of the intersystem crossing yield as 1.2%. We also calculate the intrachain annihilation constant to be (2.9+/-0.1)x 10(8) cm(3) s(-1).

Journal Article↗
PubMed1978

Flash photolysis of human serum albumin: characterization of the indole triplet absorption spectrum and decay at ambient temperature.

The method of flash photolysis was used to identify the transient absorption spectrum and to characterize the decay kinetics of the indole triplet of human serum albumin. This protein was studied because it contains a single indole side chain which is deeply buried in an expandable oily region and because the phosphorescence of the homologous indole in bovine serum albumin could not be detected at ambient temperatures. The transient was identified on the following basis: (i) its triplet-triplet absorption spectrum was similar to those previously reported for indole and tryptophan; (ii) it was quenched by small quantities of oxygen; and (iii) it was photobleached by 370- to 700-nm light. In a nitrogen-saturated solution at room temperature, the indole triplet decays exponentially for more than a factor of 10 with a lifetime of 0.5 msec. These observations suggest that, because of its exponential decay and relatively long lifetime, the triplet will be more valuable than the indole singlet as an intrinsic reporter group for the study of the structure and dynamics of proteins in solution.

Humans↗
PubMed2000

Base stacking and even/odd behavior of hairpin loops in DNA triplet repeat slippage and expansion with DNA polymerase.

Repetitions of CAG or CTG triplets in DNA can form intrastrand hairpin loops with combinations of normal and mismatched base pairs that easily rearrange. Such loops may promote primer-template slippage in DNA replication or repair to give triplet-repeat expansions like those associated with neurodegenerative diseases. Using self-priming sequences (e.g. (CAG)(16)(CTG)(4)), we resolve all hairpin loops formed and measure their slippage and expansion rates with DNA polymerase at 37 degrees C. Comparing CAG/CTG loop structures with GAC/GTC structures, having similar hydrogen bonding but different base stacking, we find that CAG, CTG, and GTC triplets predominantly form even-membered loops that slip in steps of two triplets, whereas GAC triplets favor odd-numbered loops. Slippage rates decline as hairpin stability increases, supporting the idea that slippage initiates more easily in less stable regions. Loop stabilities (in low salt) increase in the order GTC < CAG < GAC < CTG, while slippage rates decrease in the order GTC > CAG approximately GAC > CTG. Loops of GTC compared with CTG melt 9 degrees C lower and slip 6-fold faster. We interpret results in terms of base stacking, by relating melting temperature to standard enthalpy changes for doublets of base pairs and mispairs, considering enthalpy-entropy compensation.

DNA↗
PubMed2002

Weak strand displacement activity enables human DNA polymerase beta to expand CAG/CTG triplet repeats at strand breaks.

Using synthetic DNA constructs in vitro, we find that human DNA polymerase beta effectively catalyzes CAG/CTG triplet repeat expansions by slippage initiated at nicks or 1-base gaps within short (14 triplet) repeat tracts in DNA duplexes under physiological conditions. In the same constructs, Escherichia coli DNA polymerase I Klenow Fragment exo(-) is much less effective in expanding repeats, because its much stronger strand displacement activity inhibits slippage by enabling rapid extension through two downstream repeats into flanking non-repeat sequence. Polymerase beta expansions of CAG/CTG repeats, observed over a 32-min period at rates of approximately 1 triplet added per min, reveal significant effects of break type (nick versus gap), strand composition (CTG versus CAG), and dNTP substrate concentration, on repeat expansions at strand breaks. At physiological substrate concentrations (1-10 microm of each dNTP), polymerase beta expands triplet repeats with the help of weak strand displacement limited to the two downstream triplet repeats in our constructs. Such weak strand displacement activity in DNA repair at strand breaks may enable short tracts of repeats to be converted into longer, increasingly mutable ones associated with neurological diseases.

Catalysis↗
PubMed1998

The GAA triplet-repeat expansion in Friedreich ataxia interferes with transcription and may be associated with an unusual DNA structure.

Friedreich ataxia (FRDA), an autosomal recessive, neurodegenerative disease is the most common inherited ataxia. The vast majority of patients are homozygous for an abnormal expansion of a polymorphic GAA triplet repeat in the first intron of the X25 gene, which encodes a mitochondrial protein, frataxin. Cellular degeneration in FRDA may be caused by mitochondrial dysfunction, possibly due to abnormal iron accumulation, as observed in yeast cells deficient for a frataxin homologue. Using RNase protection assays, we have shown that patients homozygous for the expansion have a marked deficiency of mature X25 mRNA. The mechanism(s) by which the intronic GAA triplet expansion results in this reduction of X25 mRNA is presently unknown. No evidence was found for abnormal splicing of the expanded intron 1. Using cloned repeat sequences from FRDA patients, we show that the GAA repeat per se interferes with in vitro transcription in a length-dependent manner, with both prokaryotic and eukaryotic enzymes. This interference was most pronounced in the physiological orientation of transcription, when synthesis of the GAA-rich transcript was attempted. These results are consistent with the observed negative correlation between triplet-repeat length and the age at onset of disease. Using in vitro chemical probing strategies, we also show that the GAA triplet repeat adopts an unusual DNA structure, demonstrated by hyperreactivity to osmium tetroxide, hydroxylamine, and diethyl pyrocarbonate. These results raise the possibility that the GAA triplet-repeat expansion may result in an unusual yet stable DNA structure that interferes with transcription, ultimately leading to a cellular deficiency of frataxin.

Antisense Elements (Genetics)↗
PubMed1999

Structural basis for triplet repeat disorders: a computational analysis.

MOTIVATION: Over a dozen major degenerative disorders, including myotonic distrophy, Huntington's disease and fragile X syndrome, result from unstable expansions of particular trinucleotides. Remarkably, only some of all the possible triplets, namely CAG/CTG, CGG/CCG and GAA/TTC, have been associated with the known pathological expansions. This raises some basic questions at the DNA level. Why do particular triplets seem to be singled out? What is the mechanism for their expansion and how does it depend on the triplet itself? Could other triplets or longer repeats be involved in other diseases? RESULTS: Using several different computational models of DNA structure, we show that the triplets involved in the pathological repeats generally fall into extreme classes. Thus, CAG/CTG repeats are particularly flexible, whereas GCC, CGG and GAA repeats appear to display both flexible and rigid (but curved) characteristics depending on the method of analysis. The fact that (1) trinucleotide repeats often become increasingly unstable when they exceed a length of approximately 50 repeats, and (2) repeated 12-mers display a similar increase in instability above 13 repeats, together suggest that approximately 150 bp is a general threshold length for repeat instability. Since this is about the length of DNA wrapped up in a single nucleosome core particle, we speculate that chromatin structure may play an important role in the expansion mechanism. We furthermore suggest that expansion of a dodecamer repeat, which we predict to have very high flexibility, may play a role in the pathogenesis of the neurodegenerative disorder multiple system atrophy (MSA). CONTACT: pfbaldi@ics.uci.edu, yves@netid.com, brunak@cbs.dtu.dk, gorm@cbs.dtu.dk.

Anticipation, Genetic↗
PubMed1995

The synthesis of blocked triplet-phosphoramidites and their use in mutagenesis.

A general approach for the synthesis of oligonucleotide-triplet phosphoramidites and the synthesis of four such blocks are described. A strategy was devised to minimize the number of dimer precursors needed for synthesis of a complete set of triplet-amidite blocks encoding all 20 amino acids. Whereas synthesis of 20 triplet-amidite blocks consisting of codon sequences requires 16 dimer blocks, just seven dimer blocks are required to synthesize all required antisense sequences. The antisense sequences are then converted to codons in template mediated replication. Using a mixture of four triplet-amidites and conventional automated solid-phase DNA synthesis, short (6mer) and medium length (30mer) oligonucleotide mixtures were synthesized and analyzed. The latter was replicated in vitro and used as a mutagenic cassette to produce four mutants of Asp 221 in the enzyme thymidylate synthase. The method establishes the direction and utility for the production and use of triplet-amidite blocks in DNA synthesis.

Amides↗
PubMed2004

Replication-mediated instability of the GAA triplet repeat mutation in Friedreich ataxia.

Friedreich ataxia is caused by the expansion of a polymorphic and unstable GAA triplet repeat in the FRDA gene, but the mechanisms for its instability are poorly understood. Replication of (GAA*TTC)n sequences (9-105 triplets) in plasmids propagated in Escherichia coli displayed length- and orientation-dependent instability. There were small length variations upon replication in both orientations, but large contractions were frequently observed when GAA was the lagging strand template. DNA replication was also significantly slower in this orientation. To evaluate the physiological relevance of our findings, we analyzed peripheral leukocytes from human subjects carrying repeats of similar length (8-107 triplets). Analysis of 9400 somatic FRDA molecules using small-pool PCR revealed a similar mutational spectrum, including large contractions. The threshold length for the initiation of somatic instability in vivo was between 40 and 44 triplets, corresponding to the length of a eukaryotic Okazaki fragment. Consistent with the stabilization of premutation alleles during germline transmission, we also found that instability of somatic cells in vivo and repeats propagated in E.coli were abrogated by (GAGGAA)n hexanucleotide interruptions. Our data demonstrate that the GAA triplet repeat mutation in Friedreich ataxia is destabilized, frequently undergoing large contractions, during DNA replication.

DNA↗
PubMed2005

Characterization of the triplet repeats in the central domain of the gamma134.5 protein of herpes simplex virus 1.

The gamma134.5 protein of herpes simplex virus 1 (HSV-1) consists of an amino-terminal domain, a central domain with triplet repeats (Ala-Thr-Pro) and a carboxyl-terminal domain. The triplet repeats are a unique feature of the gamma134.5 protein encoded by HSV-1, but the number of repeats varies among different strains. Notably, the central domain containing the triplet repeats is implicated in neuroinvasion. In this report, it has been shown that partial or full deletion of triplet repeats, i.e. from ten to either three or zero, in the gamma134.5 protein has no effect on the virus response to interferon. The triplet deletion mutants replicate efficiently in CV-1 and mouse 10T1/2 cells. However, in mouse 3T6 cells, these mutants grow with delayed growth kinetics. This decrease in growth, compared with wild-type HSV-1(F), does not result from failure of the virus to suppress the RNA-dependent protein kinase response, but rather from a delay in virus release or egress. Accordingly, these mutant viruses are predominantly present within infected cells. These results indicate that deletions in the central domain of the gamma134.5 protein impair virus egress, but not virus response to interferon.

Animals↗
PubMedDate not supplied

Parenting stress, infant emotion regulation, maternal sensitivity, and the cognitive development of triplets: a model for parent and child influences in a unique ecology.

To examine the development of triplets, 23 sets of triplets were matched with 23 sets of twins and 23 singletons (N=138). Maternal sensitivity was observed at newborn, 3, 6, and 12 months, and infants' cognitive and symbolic skills at 1 year. Triplets received lower maternal sensitivity across infancy and exhibited poorer cognitive competencies compared with singletons and twins. The most medically compromised triplet showed the lowest regulation, received lower maternal sensitivity, and demonstrated the weakest outcomes compared with siblings. Structural modeling charted three levels of influence on cognitive outcomes: direct, indirect, and contextual. The triplet ecology provides a context for assessing the relations among infant inborn dispositions, the rearing environment, and the role of exclusive parenting in development.

Adult↗
PubMed1990

Triplet yield of merocyanine 540 in water is wavelength dependent.

Monomers and aggregates of Merocyanine 540 (MC540) in water are able to photoisomerize. The shape of the photoisomer absorption spectrum is very similar to that of the ground state. Triplet state of MC540 in water has been produced by energy transfer from triplet anthracene and displays a broad absorption spectrum between 600 and 700 nm. The triplet state may also be produced by direct excitation of MC540 with UV light. However, when the dye is excited by visible light, no triplet state absorbance in the red could be detected so that the triplet yield of MC540 in water seems to be excitation wavelength dependent.

Kinetics↗
PubMed1990

Determination of triplet excitation energies of cyclic enones by time-resolved photoacoustic calorimetry.

Energies and lifetimes of triplet states of a series of 2-cyclohexenones have been measured in solution under ambient conditions by time-resolved photoacoustic calorimetry (PAC). The PAC triplet lifetimes are in excellent agreement with lifetimes measured by kinetic absorption spectrophotometry (KAS) using nanosecond flash techniques, indicating that the present data indeed pertain to the enone triplets previously studied using KAS. The data demonstrate that, as previously proposed, the pi pi triplet energies in these systems are indeed correlated with triplet lifetimes, and vary sensibly with the anticipated extent of conformational flexibility of the C = C bond. No evidence supporting formation of metastable trans-cyclohexenones was obtained. The data also demonstrate greater precision and, for lifetimes, greater accuracy than has hitherto been claimed for the PAC technique for study of transients with lifetimes in the 25 ns range.

Calorimetry↗
PubMed2004

Progressive multiple alignment using sequence triplet optimizations and three-residue exchange costs.

In this paper we demonstrate a practical approach to construct progressive multiple alignments using sequence triplet optimizations rather than a conventional pairwise approach. Using the sequence triplet alignments progressively provides a scope for the synthesis of a three-residue exchange amino acid substitution matrix. We develop such a 20 x 20 x 20 matrix for the first time and demonstrate how its use in optimal sequence triplet alignments increases the sensitivity of building multiple alignments. Various comparisons were made between alignments generated using the progressive triplet methods and the conventional progressive pairwise procedure. The assessment of these data reveal that, in general, the triplet based approaches generate more accurate sequence alignments than the traditional pairwise based procedures, especially between more divergent sets of sequences.

Algorithms↗
PubMed2002

One-radius triplets.

The one-radius triplet is an optical system that consists of three lenses. Either the radii of curvature of the lenses have the same absolute value or one radius of curvature has an infinitely large value. The advantage of such optical systems is that their production cost is less than that of systems with ordinary triplets. Here a theory of one-radius triplets is described and tables of parameters for their modification are provided. Residual aberrations are given for several selected triplets. One-radius triplets are suitable for use in laser technology and metrology.

Journal Article↗
PubMed2000

Studies on the radiolytically produced transients of neutral red: triplet and reduced radicals.

The spectral and kinetic properties of reduced radicals and the triplet state of neutral red (NR), a phenazine-based dye, have been investigated using pulse radiolysis technique. A mixed water-isopropanol-acetone solvent has been used to study the reduced radicals of NR for a wide pH range of about 1-13, due to limitation of solubility of the dye in aqueous solutions particularly above pH 8. From pH-dependent absorption studies it has been established that the reduced radicals of NR can exist in four different prototropic forms in solution. Three pKa values for the corresponding prototropic equilibria have been estimated. The formation and decay rate constants of reduced radicals have also been measured. The triplet state characteristics of the dye have been investigated in neat benzene solutions, both in the presence and in the absence of triplet sensitizers. The T1-->Tn absorption spectrum and decay kinetics of the triplet state have been measured. The triplet state energy (ET) of NR in benzene have been estimated to be within 36-42 kcal mol-1, using an energy transfer method.

Free Radicals↗