Molecular packing-dependent exciton dynamics in functionalized anthradithiophene derivatives: From solutions to crystals.

Understanding the impact of inter-molecular orientation on the optical properties of organic semiconductors is important for designing next-generation organic (opto)electronic and photonic devices. However, fundamental aspects of how various features of molecular packing in crystalline systems determine the nature and dynamics of excitons have been a subject of debate. Toward this end, we present a systematic study of how various molecular crystal packing motifs affect the optical properties of a class of high-performance organic semiconductors: functionalized derivatives of fluorinated anthradithiophene. The absorptive and emissive species present in three such derivatives (exhibiting "brickwork," "twisted-columnar," and "sandwich-herringbone" motifs, controlled by the side group R) were analyzed both in solution and in single crystals, using various modalities of optical and photoluminescence spectroscopy, revealing the nature of these excited states. In solution, in the emission band, two states were identified: a Franck-Condon state present at all concentrations and an excimer that emerged at higher concentrations. In single crystal systems, together with ab initio calculations, it was found in the absorptive band that Frenkel and Charge Transfer (CT) excitons mixed due to nonvanishing CT integrals in all derivatives, but the amount of admixture and exciton delocalization depended on the packing, with the "sandwich-herringbone" packing motif least conducive to delocalization. Three emissive species in the crystal phase were also identified: Frenkel excitons, entangled triplet pairs 1(TT) (which are precursors to forming free triplet states via singlet fission), and self-trapped excitons (STEs, similar in origin to excimers present in concentrated solution). The "twisted-columnar" packing motif was most conducive to the formation of Frenkel excitons delocalized over 4-7 molecules depending on the temperature. These delocalized Frenkel states were dominant across the full temperature range (78 K-293 K), though at lower temperatures, the entangled triplet states and STEs were present. In the derivative with the "brickwork" packing, all three emissive species were observed across the full temperature range and, most notably, the 1(TT) state was present at room temperature. Finally, the derivative with the "sandwich-herringbone" packing exhibited localized Frenkel excitons and had a strong propensity for self-trapped exciton formation even at higher temperatures. In this derivative, no formation of the 1(TT) state was observed. The temperature-dependent dynamics of these emissive states are reported, as well as their origin in fundamental inter-molecular interactions.

Escherichia coli host strains SURE and SRB fail to preserve a palindrome cloned in lambda phage: improved alternate host strains.

We have attempted to produce Escherichia coli strains with the optimal combination of host mutations required for the construction of genomic libraries in lambda and cosmid vectors. For lambda vectors, we defined this as a strain that combined high efficiency of phage plating with optimal tolerance to DNA methylation and the ability to propagate recombinants containing regions of potential secondary structure. To optimize this latter property, we have tested a series of strains for the ability to propagate a lambda phage containing a palindromic sequence. These included an mcr- derivative of a strain shown by Ishiura et al. [J. Bacteriol. 171 (1989) 1068-1074] to allow optimal stability of inserts in cosmid clones. All the sbcC strains allowed plaque formation of the palindrome-containing lambda phage. However, while the palindrome-containing phage plated with reasonable efficiency on SURE (recB sbcC recJ umuC uvrC) and SRB (sbcC recJ umuC uvrC), the majority of phage recovered from these strains no longer required an sbcC host for subsequent plating. These two strains also gave poorer titres with a low-yielding phage clone from the human Prader-Willi chromosome region. Optimal phage hosts appear to be those that are mcrA delta(mcrBC-hsd-mrr) combined with mutations in sbcC plus recBC or recD and without mutations in additional recombination functions such as recJ or recJ umuC uvrC (all of our E. coli strains are available on request).

Effects of mcr restriction of methylated CpG islands of the L1 transposons during packaging and plating stages of mammalian genomic library construction.

The use of optimally methylation-tolerant mcrA- mcrB- strains has been shown to produce an over tenfold increase in the plating efficiencies of mammalian genomic libraries, compared to a superior conventional phage host strain LE392 which is mcrB+. However, there is an even more significant effect of mcr restriction. Amongst the recombinants recovered with an mcrB+ host, we have found that there is an additional 30-fold reduction in the frequencies of clones containing the heavily methylated 5'-CpG island sequences of both the human and rat L1 repetitive elements. The mcrA product was also found to restrict clones of these methylated genomic segments, but not as strongly as mcrB. However, the use of packaging extracts made from mcrA+ lysogens did not result in convincing reductions in the recoveries of these dispersed methylated elements. The magnitude of mcr restriction during plating due to methylated dispersed elements is sufficient to make a significant proportion of mammalian genomes unclonable from genomic libraries constructed previously using conventional mcr+ hosts.

Exciton dynamics in semiconducting carbon nanotubes.

We report a femtosecond transient absorption spectroscopic study on the (6, 5) single-walled carbon nanotubes and the (7, 5) inner tubes of a dominant double-walled carbon nanotube species. We found that the dynamics of exciton relaxation probed at the first transition-allowed state (E(11)) of a given tube type exhibits a markedly slower decay when the second transition-allowed state (E(22)) is excited than that measured by exciting its first transition-allowed state (E(11)). A linear intensity dependence of the maximal amplitude of the transient absorption signal is found for the E(22) excitation, whereas the corresponding amplitude scales linearly with the square root of the E(11) excitation intensity. Theoretical modeling of these experimental findings was performed by developing a continuum model and a stochastic model with explicit consideration of the annihilation of coherent excitons. Our detailed numerical simulations show that both models can reproduce reasonably well the initial portion of decay kinetics measured upon the E(22) and E(11) excitation of the chosen tube species, but the stochastic model gives qualitatively better agreement with the intensity dependence observed experimentally than those obtained with the continuum model.

Adenine methylation at dam sites increases transient gene expression in plant cells.

Escherichia coli encodes two major DNA methylation systems: dam, which produces 6-methyladenine; and dcm, which produces 5-methylcytosine. About 1-2% of adenine and cytosine residues in plasmid DNAs prepared in E. coli are methylated by these systems. Since DNA methylation profoundly influences gene expression in eukaryotes, we were interested in determining whether these bacterially encoded modifications might also effect plant gene expression in experimental systems. We therefore examined the influence of dam and dcm methylation on gene expression from four GUS fusion constructs in transient assays in protoplasts and microprojectile-bombarded whole tissues. In these constructs, GUS expression was driven by promoter regions derived from the Arabidopsis alcohol dehydrogenase (Adh1), maize ubiquitin (Ubi1), rice actin (Act1) and CaMV 35S genes. We show that methyladenine produced by dam methylation increased gene expression from constructs based on the Adh1, Ubi1 and Act1 genes. The increase in gene expression ranged from three-fold for Ubi1 and Adh1 in protoplasts to 50-fold for Act1 in bombarded wheat tissues. Expression of a 35S.GUS construct was, however, insensitive to dam methylation. dcm methylation had little if any effect on transient gene expression for any of these constructs. We provide indirect evidence that the critical sites of adenine methylation lie within sequences from the promoter regions, suggesting that dam methylation increases transcription rate. These results have important experimental implications and also raise the intriguing possibility that methyladenine might play a role in the regulation of gene expression in vivo.

Expression patterns of vascular-specific promoters RolC and Sh in transgenic potatoes and their use in engineering PLRV-resistant plants.

The expression patterns of GUS fusion constructs driven by the Agrobacterium rhizogenes RolC and the maize Sh (Shrunken; sucrose synthase-1) promoters were examined in transgenic potatoes (cv. Atlantic). RolC drove high-level gene expression in phloem tissue, bundle sheath cells and vascular parenchyma, but not in xylem or non-vascular tissues. Sh expression was exclusively confined to phloem tissue. Potato leafroll luteovirus (PLRV) replicates only in phloem tissues, and we show that when RolC is used to drive expression of the PLRV coat protein gene, virus-resistant lines can be obtained. In contrast, no significant resistance was observed when the Sh promoter was used.

Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA.

Many examples of extreme virus resistance and posttranscriptional gene silencing of endogenous or reporter genes have been described in transgenic plants containing sense or antisense transgenes. In these cases of either cosuppression or antisense suppression, there appears to be induction of a surveillance system within the plant that specifically degrades both the transgene and target RNAs. We show that transforming plants with virus or reporter gene constructs that produce RNAs capable of duplex formation confer virus immunity or gene silencing on the plants. This was accomplished by using transcripts from one sense gene and one antisense gene colocated in the plant genome, a single transcript that has self-complementarity, or sense and antisense transcripts from genes brought together by crossing. A model is presented that is consistent with our data and those of other workers, describing the processes of induction and execution of posttranscriptional gene silencing.

Comparison of the coat protein, movement protein and RNA polymerase gene sequences of Australian, Chinese, and American isolates of barely yellow dwarf virus transmitted by Rhopalosiphum padi.

Barely yellow dwarf luteovirus-GPV (BYDV-GPV) is a common problem in Chinese wheat crops but is unrecorded elsewhere. A defining characteristic of GPV is its capacity to be transmitted efficiently by both Schizaphis graminum and Rhopaloshiphum padi. This dual aphid species transmission contrasts with those of BYDV-RPV and BYDV-SGV, globally distributed viruses, which are efficiently transmitted only by Rhopaloshiphum padi and Schizaphis graminum respectively. The viral RNA sequences encoding the coat protein (22K) gene, the movement protein (17K) gene, the region surrounding the conserved GDD motif of the polymerase gene and the intergenic sequences between these genes were determined for GPV and an Australian isolate of BYDV-RPV (RPVa). In all three genes, the sequences of GPV and RPVa were more similar to those of an American isolate of BYDV-RPV (RPVu) than to any other luteovirus for which there is data available. RPVa and RPVu were very similar, especially their coat proteins which had 97% identity at the amino acid level. The coat protein of GPV had 76% and 78% amino acid identity with RPVa and RPVu respectively. The data suggest that RPVu and RPVa are correctly named as strains of the same serotype and that GPV is sufficiently different from either RPV strain to be considered a distinct BYDV type. The coat protein and movement protein genes of GPV are very dissimilar to SGV. The polymerase sequences of RPVu, RPVa and GPV show close affinities with those of the sobemo-like luteoviruses and little similarity with those of the carmo-like luteoviruses. The sequences of the coat proteins, movement proteins and the polymerase segments of BYDV serotypes, other than RPV and GPV, form a cluster that is separate from their counterpart sequences from dicot-infecting luteoviruses. The RPV and GPV isolates consistently fall within a dicot-infecting cluster. This suggests that RPV and GPV evolved from within this group of viruses. Since these other viruses all infect dicots it seems likely that their common ancestor infected a dicot and that RPV and GPV evolved from a virus that switched hosts from a dicot to a monocot.

Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants.

Many strains of E. coli K12 restrict DNA containing cytosine methylation such as that present in plant and animal genomes. Such restriction can severely inhibit the efficiency of cloning genomic DNAs. We have quantitatively evaluated a total of 39 E. coli strains for their tolerance to cytosine methylation in phage and plasmid cloning systems. Quantitative estimations of relative tolerance to methylation for these strains are presented, together with the evaluation of the most promising strains in practical recombinant cloning situations. Host strains are recommended for different recombinant cloning requirements. These data also provide a rational basis for future construction of 'ideal' hosts combining optimal methylation tolerance with additional advantageous mutations.

A promoter from sugarcane bacilliform badnavirus drives transgene expression in banana and other monocot and dicot plants.

A 1369 bp DNA fragment (Sc) was isolated from a full-length clone of sugarcane bacilliform badnavirus (ScBV) and was shown to have promoter activity in transient expression assays using monocot (banana, maize, millet and sorghum) and dicot plant species (tobacco, sunflower, canola and Nicotiana benthamiana). This promoter was also tested for stable expression in transgenic banana and tobacco plants. These experiments showed that this promoter could drive high-level expression of the beta-glucuronidase (GUS) reporter gene in most plant cells. The expression level was comparable to the maize ubiquitin promoter in standardised transient assays in maize. In transgenic banana plants the expression levels were variable for different transgenic lines but was generally comparable with the activities of both the maize ubiquitin promoter and the enhanced cauliflower mosaic virus (CaMV) 35S promoter. The Sc promoter appears to express in a near-constitutive manner in transgenic banana and tobacco plants. The promoter from sugarcane bacilliform virus represents a useful tool for the high-level expression of foreign genes in both monocot and dicot transgenic plants that could be used similarly to the CaMV 35S or maize polyubiquitin promoter.