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At least 505 records · Page 28Linked to original sources
PubMed1993

High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). Novel intermolecular base-paired G*(G.C) triplets.

The DNA decamer d(CCCGGCCGGG) crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 24.88, b = 44.60 and c = 46.97 A containing a duplex in the asymmetric unit. The structure was solved by molecular replacement and refined to an R factor of 18.5% using 6033 reflections at 1.65 A resolution. The decamer duplex adopts an A-DNA conformation. The abrupt dislocation of the duplex at the fourth base-pair G(4).C(17) by an abutting symmetry related molecule results in distortion of the backbone bonds of the fifth residue G(5), P-O(5')(alpha) and C(4')-C(5')(gamma), to the trans conformations from their favored gauche- and gauche+ conformations, respectively. In this close encounter the terminal G(10).C(11) base-pair of the symmetry related molecule hydrogen bonds to the G(4).C(17) base-pair forming a novel base-paired G(4)*(G10).C(11)) triplet, where G(4) is hydrogen bonded to both G(10) and C(11). To facilitate this hydrogen bonding the G(4).C(17) base-pair slides into the minor groove, causing a toll on the backbone conformation of the adjacent residue G(5). A similar triplet base-pairing interaction with somewhat weaker hydrogen bonds occurs at the pseudo dyad related C(7).G(14) base-pair with G(20) of another symmetry related duplex. This pseudo triplet interaction (C(7).G(14))*G(20), does not perturb the backgone alpha and gamma torsions of G(15). Both the novel base triplets are non-planar. The abrupt dislocation/bend at the G(4).C(17) base-pair jolts the global helical base-pair parameters, inclination, tilt, roll, tip, etc. quite markedly. Therefore a better description of the helix parameters is obtained by splitting the duplex and calculating the local helix axis for the top half consisting of the first three base-pairs, and the lower half consisting of the last six base-pairs, omitting the fourth base-pair. The two half duplexes are bent by only 10 degrees. This structure further demonstrates that crystal packing interactions, which can also be governed by base sequence, play a dominant role in determining DNA conformation.

Base Composition↗
PubMed1996

Relationship between Escherichia coli growth and deletions of CTG.CAG triplet repeats in plasmids.

Instabilities that are intrinsic to natural repetitive DNA sequences produce high frequencies of length changes in vivo. Triplet repeats cloned in plasmids in Escherichia coli undergo expansions and deletions, and this instability is affected by multiple factors. We show that CTG-CAG repeats in plasmids can influence the growth of E. coli, which affects the observed stabilities. At extended growth periods, the observed frequencies of deletions were dramatically increased if the cells passed through stationary phase before subculturing. Deletions were particularly pronounced for a plasmid containing the longest repeat, 525 bp in total, with the CTG sequence as the lagging strand template for replication. Measurements of cell growth showed that the lag phase associated with E. coli growth was increased for cultures containing plasmids with long CTG-CAG repeats, particularly when the CTG-containing strand was the lagging template. High frequencies of deletions were observed because of a growth advantage of cells containing plasmids with deleted triplet repeats. Incubation conditions that reduced the bacterial growth-rate produced a decreased extent of deletions, presumably because they alleviated the growth advantage of cells harboring plasmids with deleted triplet repeats. The experimental observations were simulated by a model in which shorter triplet repeats provided a growth advantage due to a shorter lag phase. We demonstrate that the accumulation of deletions within repeating sequences during growth of E. coli can be prevented, and discuss these findings in relation to the studies of repetitive DNA sequences. These are the first observations to show a direct influence between a plasmid-based DNA sequence or structure and factors controlling bacterial growth.

Base Sequence↗
PubMed2001

An intramolecular quadruplex of (GGA)(4) triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction.

The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K(+) conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer versus intermolecular quadruplex for 7-mer; heptad versus hexad in the quadruplex; and three sheared G:A base-pairs versus two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.

Base Pairing↗
PubMed2001

Determination of relative triplet sublevel populating rates during optical pumping using ODMR.

A method is introduced, based on optical detection of triplet state magnetic resonance (ODMR), to determine the relative populating rates of photoexcited triplet state sublevels during optical pumping. Phosphorescence transients induced by microwave rapid passage during optical pumping are analyzed globally utilizing kinetic parameters obtained from separate microwave-induced delayed phosphorescence measurements to obtain relative sublevel populating rates. Results are unaffected by phosphorescence from triplet populations that do not yield an ODMR response. The method is applied to the triplet state of the indole chromophore in various environments to reveal the effects of local interactions on the pattern of intersystem crossing. Enhanced spin--orbit coupling effects are attributed to interactions that reduce the planar symmetry of the indole chromophore.

Capsid↗
PubMed2000

The Mechanism of Magnetically Tuned Singlet-Triplet Avoided Crossings in the Ã(1)A(2)-&Xtilde;(1)A(1) 4(1)(0) Band of Thioformaldehyde H(2)C&dbond;S.

Magnetically tuned singlet-triplet perturbations in the 4(1)Ã(1)A(2)-2(1)3(1)ã(3)A(2) system of thioformaldehyde, found in ortho-rotational states (I = 1, the two hydrogen spins parallel) have been identified as being caused by vibronic spin-orbit coupling. This perturbation mechanism has been confirmed in several avoided crossings observed in this work for para states (I = 0, hydrogen spins antiparallel) which are much stronger. Parametrization of the theory has led to a quantitative understanding of the experimental frequency-field relations, and to an accurate prediction of the rovibrational energies of the triplet state. This in turn permitted the detection of about 100 Doppler-limited 2(1)3(1)ã(3)A(2)-0(0) &Xtilde;(1)A(1) rovibronic transitions which led into fine structure states. The combined data was then used to determine a set of rotational, fine, and hyperfine triplet-state parameters, the term value T(0)(2(1)3(1)ã(3)A(2)) = (16 685.385 +/- 0.002) cm(-1), and the spin-orbit vibronic singlet-triplet coupling constant, W(ST) = (0.0691 +/- 0.0016) cm(-1). A large number of frequency perturbations observed in the crossings, ranging from 2 to 300 MHz, can be explained with this single parameter. Copyright 2000 Academic Press.

Journal Article↗
PubMed1997

Computer simulation of expansions of DNA triplet repeats in the fragile X syndrome and Huntington's disease.

The expansion of DNA triplet repeats has been shown to be responsible for about a dozen hereditary diseases. In this paper we are concerned with a computer model of such expansion, applied to the fragile X syndrome and Huntington's disease, for which enough quantitative data have been collected. The nucleotide sequence associated with the fragile X consists of CGG repeats and is located inside the FMR1 gene. In normal individuals there is a variable number of triplet repeats less than 60; in asymptomatic carriers the number of repeats is 60-200 (premutation). From the premutation range, the number of triplet repeats can increase within one generation to more than 200 producing affected individuals. In Huntington's disease the CAG repeats are located inside the HD gene. In normal individuals the number of repeats varies from around 11, up to 34. In the intermediate range (34-37 repeats), the mutability is increased, frequently leading to alleles of more than 37 repeats, and the disease phenotype. The rapid increase of the number of triplet repeats in affected individuals has been proposed to be due to the formation of folded DNA structures (hairpins) and their repair or misrepair. In order to determine if this proposed mechanism is adequate to account for the rapid increase of repeats and the large number of repeats in affected individuals we developed a mathematical model that includes the known mechanisms of hairpin formation, and strand synthesis and repair. Simulations based on the model using realistic probabilities of hairpin formation produced results that corresponded with the observed range of repeats and transition probabilities from normal to affected individuals. Similar modelling has been published for the Huntington's disease data. However, in this paper we demonstrate that a uniform approach works for fragile X and Huntington's disease, although the detailed assumptions of the model have to be different. These difference provide insight into the mechanisms of expansion in both cases. Among these insights is that an apparent threshold in the number of repeats for rapid expansion, and the preference for expansion over contraction, may be accounted for by relative probabilities of hairpin formation, replication, slippage and repair.

Computer Simulation↗
PubMed1975

Triplet state population study in relation to the aggregation of proflavine in frozen solutions.

The evolution of the proflavine triplet state population with the extent of aggregation is examines, by ESRmeasurements, as a function of organic solvents and mineral salts, well known for their ability to influence the aggregation process. The intensity of the triplet state population has also been investigated as a function of pH. The insertion of aromatic molecules like DNA's nucleotides between dye molecules is shown to increase the intensity of the triplet state. It is put forward that the observed triplet state is characteristic of the singly protonated proflavine which seems to be the active species in in vivo experiments.

Acridines↗
PubMed2006

Comparative expression profiling in meristems of inbred-hybrid triplets of maize based on morphological investigations of heterosis for plant height.

Heterosis, the superior performance of hybrids as compared to their parental mean is an agronomically important phenomenon well-described morphologically. However, little is known about its molecular basis. We investigated four genetically unrelated maize (Zea mays L.) inbred lines and their F(1) crosses both at the phenotype and transcriptome level, focusing on plant height (PHT) component traits. Substantial mid-parent heterosis (MPH) was found for all parent-hybrid triplets for PHT in the range of 37.9-56.4% in the field and 11.1-39.5% under controlled greenhouse conditions. Analyses of heterosis for number and length of internodes showed two to three times higher MPH in the field as compared to the greenhouse. All three traits exhibited high heritabilities, highest for PHT 95-98%. Two methods for gene expression quantification were applied. High-density cDNA uni-gene microarrays containing 11,827 ESTs were utilized for the selection of differentially expressed genes related to heterosis for PHT. For the four triplets with eight possible parent-hybrid comparisons we identified 434 consistently differentially expressed genes with a p < or = 0.05. Microarray results were used to verify the dominance/overdominance hypothesis. In our study, more than 50% genes showed overdominance, 26% partial dominance, 12.6% complete dominance and 10.2% additive gene action. Moreover, more consistently differentially expressed genes were detected in related triplets, sharing one parent, than in unrelated triplets. Quantitative RT-PCR was applied in order to validate microarray results. The role of the differentially expressed genes in relation to heterosis for PHT is discussed.

Gene Expression Profiling↗
PubMed2005

A fluorescence detected magnetic resonance investigation of the carotenoid triplet states associated with photosystem II of isolated spinach thylakoid membranes.

The carotenoid triplet populations associated with the fluorescence emission chlorophyll forms of Photosystem II have been investigated in isolated spinach thylakoid membranes by means of fluorescence detected magnetic resonance in zero field (FDMR). The spectra collected in the 680-690 nm emission range, have been fitted by a global analysis procedure. At least five different carotenoid triplet states coupled to the terminal emitting chlorophyll forms of PS II, peaking at 682 nm, 687 nm and 692 nm, have been characterised. The triplets associated with the outer antenna emission forms, at 682 nm, have zero field splitting parameters |D| = 0.0385 cm-1, |E| = 0.00367 cm-1; |D| = 0.0404 cm-1, |E| = 0.00379 cm-1 and |D| = 0.0386 cm-1, |E| = 0.00406 cm-1 which are very similar to those previously reported for the xanthophylls of the isolated LHC II complex. Therefore the FDMR spectra recorded in this work provide insights into the organisation of the LHC II complex in the unperturbed environment represented by thylakoid membranes. The additional carotenoid triplet populations, detected by monitoring the chlorophyll emission at 687 and 692 nm, are assigned to carotenoids bound to inner antenna complexes and hence attributed to beta-carotene molecules.

Carotenoids↗
PubMed2006

Triplet state spectra and dynamics of geometric isomers of carotenoids.

The observation of preferential binding of cis-carotenoids in purple bacterial photosynthetic reaction centers versus trans-isomers in antenna pigment protein complexes has led to the hypothesis that the natural selection of stereoisomers has physiological significance. In order to test this hypothesis, we have undertaken a systematic series of investigations comparing the optical spectroscopic properties and excited state dynamics of cis and trans isomers of carotenoids. The present work compares the triplet state spectra, lifetimes, and energy transfer rates of all-trans-spheroidene and 13,14-locked-cis-spheroidene, the latter of which is incapable of isomerizing to the all-trans configuration, and therefore provides a unique opportunity to examine the triplet state properties of a structurally stable cis molecule. The data reveal only small differences in spectra, decay dynamics, and transfer times and suggest there is little intrinsic advantage in either triplet energy transfer or triplet state decay arising from the inherently different isomeric forms of cis compared to trans carotenoids.

Carotenoids↗
PubMed1975

Carotenoid triplet states in reaction centers from Rhodopseudomonas sphaeroides and Rhodospirillum rubrum.

Purified photochemical reaction centers from three strains of Rhodopseudomonas sphaeroides and two of Rhodospirillium rubrum were reduced with Na2S2O4 so as to block their photochemical electron transfer reactions. They then were excited with flashes lasting 5-30 ns. In all cases, absorbance measurements showed that the flash caused the immediate formation of a transient state (PF) which had been detected previously in reaction centers from Rps. sphaeroides strain R26. Previous work has shown that state PF is an intermediate in the photochemical electron transfer reaction in the reaction centers of that particular strain, and the present work generalizes that conclusion. In the reaction centers from two strains that lack carotenoids (Rps. sphaeroides R26 and R. rubrum G9), the decay of PF yields a longer-lived state (PR) which is probably a triplet state of the bacteriochlorophyll of the reaction center. In the R26 preparation, the decay of PF was found to have a half-time of 10 +/- 2 ns. The decay kinetics rule out the identification of PF as the fluorescent excited singlet state of the reaction center. In the reaction centers from three strains that contain carotenoids (Rps sphaeroides 2.4.1 and Ga, and R. rubrum S1), state PR was not detected, and the decay of PF generated triplet states of carotenoids. The efficiency of the coupling between the decay of PF and the formation of the carotenoid triplet appeared to be close to 100% at room temperature, but somewhat lower at 77 degrees K. Taken with previous results, this suggests that the coupling is direct and does not require the intermediate formation of state PR. This conclusion would be consistent with the view that PF is a biradical which can be triplet in character.

Carotenoids↗
PubMed1978

Electron spin resonance in zero magnetic field of the reaction center triplet of photosynthetic bacteria.

The decay rates kx, ky, kz of the individual spin levels of the light-induced triplet state have been accurately measured by the zero-field resonance technique under conditions of very low light intensity and a microwave sweep rate of 2.5 MHz/microseconds, which is in excess of that commonly used in optical detection magnetic resonance experiments. The rates ku found correspond well with those previously determined under somewhat different conditions (Hoff, A.J. (1976) Biochim. Biophys. Acta 440, 765--771) and with those inferred from the decay at 4.2 degrees K of the triplet-triplet absorption after picosecond excitation (Parson, W.W. and Monger, T.G. (1977) Brookhaven Symp. Biology 28, 195--212). Thus there seems no reason to doubt that PR corresponds to the triplet state detected by ESR. In a recent publication Clarke and Connors (Clarke, R.H. and Conners, R.E. (1976) Chem. Phys. Lett. 42, 69--72) published values of the rates ku which differ substantially from ours and which lead to a mean lifetime in excess of that of PR. We show that erroneous rates are obtained when the microwave sweep rate is not made fast relative to the decay of the individual spin levels. Zero-field splitting parameters for a member of photosynthetic bacteria have been measured with an accuracy of better than 0.4% for D and 1% for E. The enhanced precision as compared to conventional ESR allows one to discriminate between species of one family. Deuteration reduces the ku values by a factor of about 2, with little spin selectivity. This effect is much larger than previously observed for chlorophyll a. The present results explain the decrease in fluorescence intensity observed on microwave saturation in zero-field optical detection magnetic resonance experiments, and they also show that the simple exciton model is inadequate to derive the geometry of the reaction center dimer from the observed zerofield splitting and decay rates.

Electron Spin Resonance Spectroscopy↗
PubMed1979

Orientation of the bacteriochlorophyll triplet and the primary ubiquinone acceptor of Rhodospirillum rubrum in membrane multilayers determined by ESR spectroscopy (I).

Chromatophores from Rhodospirillum rubrum were oriented as multilayers on quartz slides under reducing conditions. Irradiation of these multilayers in the resonance cavity of an ESR spectrometer at 6 K yielded the spectrum of the bacteriochlorophyll dimer triplet. The relative intesities of the main six lines of the triplet were dependent on the angle subtended by the direction of the external magnetic field with plane of the multilayers. The angular dependence of the intensities of these transitions can best be interpreted in terms of one of the principal axes of the triplet lying along the plane of the membrane while the other two axes are titled 10--20 degrees away from the parallel to and normal to the membrane directions. If we assume the porphyrin planes of the dimer to be parallel and the largest splitting of the triplet transitions to correspond to those transitions in a direction normal to this plane, then these data imply that the dimer planes are nearly perpendicular to the membrane plane. Purified iron-depleted phototrap complexes were similarly oriented in reconstituted phosphatidylcholine multilayers and the angular dependence of the light-induced spectrum recorded at room temperature. A computer analysis of this angular dependence suggests that the plane of the primary ubiquinone acceptor molecule is parallel to the plane of the membrane and therefore perpendicular to the donor.

Bacterial Chromatophores↗
PubMed1979

A laser flash photolysis study of the reactivities of the triplet states of 8-methoxypsoralen and 4,5',8-trimethylpsoralen with nucleic acid bases in solution.

The extinction coefficients, quantum yields and reactivities of the triplet states of 8-methoxypsoralen and 4,5',8-trimethylpsoralen in methanolic solution have been determined using laser flash photolysis techniques. The second-order rate constants for the quenching of these triplet states by pyrimidine and purine bases were found to be several orders of magnitude lower than those found for other furocoumarin derivatives. This may suggest, therefore, that the skin photosensitising ability of such compounds does not necessarily correlate with in vitro triplet state reactivity. Preliminary experiments on the reactivity of the psoralen triplet state with DNA itself indicate that no transient absorptions due to psoralen excited states can be observed when a photon is absorbed by the psoralen-DNA complex.

Carotenoids↗
PubMed1983

A conformational rationale for the wobble behaviour of the first base of the anticodon triplet in tRNA.

We present a conformational rationale for wobble behaviour of the first base in the anticodon triplet of tRNA and hence for the well-known degeneracy of the genetic code. The U-turn hydrogen bond plays an important role in the structure of the anticodon arm and particularly for the anticodon triplet to be in a geometry suitable for the process of recognition in the adaptor-mediated synthesis of proteins. This hydrogen bond in turn precludes a hydrogen bond between the first two sugars of the anticodon triplet, allowing the first base to wobble, while it facilitates one between the second and third sugars of the triplet, positioning these bases for the standard base-pairing with the codon. This neatly explains why there is a degeneracy in the code and why a RNA happens to be the adaptor for protein synthesis. Relevent conformational calculations are presented in support of the theory.

Anticodon↗
PubMed1990

Outcome of triplet pregnancies resulting from IVF at Bourn Hallam 1984-1987.

43 consecutive sets of triplet pregnancies progressing beyond 16 weeks and conceived following in vitro fertilisation at the Bourn Hallam Centre between 1984-1987 were included in the study. Follow-up information was available in the 31 sets born to United Kingdom residents. 91 live births resulted at an average gestation of 33 weeks and 2 days (range 26-38 weeks). All but one of the deliveries was by Caesarean section. The average birth weight was 1.85 kg and was significantly higher in the first-born triplet than in the third (1.93 kg versus 1.74 kg, respectively). The perinatal mortality rate amongst the triplets was 32.26 per thousand births, and the neonatal death rate was 21.98 per thousand live births. This compares favourably with the latest published data on perinatal mortality rates in triplets.

Adult↗
PubMed1986

Enols of aldehydes in the peroxidase/oxidase-promoted generation of excited triplet species.

General (acid and base) or specific (fluoride ion) catalysis generates the enol of isobutanal and propanal from the corresponding trimethylsilyl enol ethers. The enols are directly rapidly oxidized by peroxidase (acting as an oxidase) to triplet acetone or triplet acetaldehyde, respectively, and formic acid. Due to the faster rate of reaction and the absence of quenching by excess aldehyde, the excited carbonyl emits more strongly than when the aldehyde itself is the substrate. With both enols the emission is pure phosphorescence. Both triplet acetone and triplet acetaldehyde are generated within the enzyme, as shown by the different quenching by D- and L-tryptophan, and are somewhat protected from oxygen quenching, as attested by the very fact that phosphorescence is observed. The use of enol precursors as substrates opens wide possibilities for photochemical investigations in the absence of light over a much broader range of experimental conditions.

Acetone↗
PubMed1994

Genes with triplet repeats: a new class of mutations causing neurological diseases.

Microsatellites, simple tamdem repeats of 2 to 4 nucleotide sequences, are widely distributed throughout the genome. Trinucleotide repeats are found every 300 to 500 kb. Recently, a new type of mutation was described involving a specific expansion of triplets within or in close proximity to a gene. Expanded triplets have been found in the genes causing six different neurological disorders: fragile X syndrome (FRAXA), spinal and bulbar muscular atrophy (SBMA), myotonic dystrophy (DM), Huntington's disease (HD), spinocerebellar ataxia type 1 (SCA1), and dentato-rubra-pallidoluysian atrophy (DRPLA). These neurological disorders have in common a variable age of onset and clinical severity, as well as a decrease in the age of onset over generations, known as anticipation. These unusual characteristics are related to the observation that expanded repeats are unstable both in meioses and mitoses. A younger age of onset and an increase in severity correlate with a higher number of repeats. Interestingly, particular haplotypes are in disequilibrium with the mutation for FRAXA, DM and HD, suggesting instability for selected chromosomes. How expanded triplets affect the expression and the function of genes is still unknown. Since neurodegenerative disorders are often variable in age of onset and clinical severity, the list of expanding triplet mutations should increase in the very near future.

DNA↗