Joseph Sperling

Measurement of the conductance of single conjugated molecules

Electrical conduction through molecules depends critically on the delocalization of the molecular electronic orbitals and their connection to the metallic contacts. Thiolated (- SH) conjugated organic molecules are therefore considered good candidates for molecular conductors: in such molecules, the orbitals are delocalized throughout the molecular backbone, with substantial weight on the sulphur–metal bonds. However, their relatively small size, typically ∼1 nm, calls for innovative approaches to realize a functioning single-molecule device. Here we report an approach for contacting a single molecule, and use it to study the effect of localizing groups within a conjugated molecule on the electrical conduction. Our method is based on synthesizing a dimer structure, consisting of two colloidal gold particles connected by a dithiolated short organic molecule, and electrostatically trapping it between two metal electrodes. We study the electrical conduction through three short organic molecules: 4,4′-biphenyldithiol (BPD), a fully conjugated molecule; bis-(4-mercaptophenyl)-ether (BPE), in which the conjugation is broken at the centre by an oxygen atom; and 1,4-benzenedimethanethiol (BDMT), in which the conjugation is broken near the contacts by a methylene group. We find that the oxygen in BPE and the methylene groups in BDMT both suppress the electrical conduction relative to that in BPD.

Protein kinase CK2 and protein kinase D are associated with the COP9 signalosome

The COP9 signalosome (CSN) purified from human erythrocytes possesses kinase activity that phosphoryl ates proteins such as c‐Jun and p53 with consequence for their ubiquitin (Ub)‐dependent degradation. Here we show that protein kinase CK2 (CK2) and protein kinase D (PKD) co‐purify with CSN. Immunoprecipi tation and far‐western blots reveal that CK2 and PKD are in fact associated with CSN. As indicated by electron microscopy with gold‐labeled ATP, at least 10% of CSN particles are associated with kinases. Kinase activity, most likely due to CK2 and PKD, co‐immuno precipitates with CSN from HeLa cells. CK2 binds to ΔCSN3(111–403) and CSN7, whereas PKD interacts with full‐length CSN3. CK2 phosphorylates CSN2 and CSN7, and PKD modifies CSN7. Both CK2 and PKD phosphorylate c‐Jun as well as p53. CK2 phosphoryl ates Thr155, which targets p53 to degradation by the Ub system. Curcumin, emodin, DRB and resveratrol block CSN‐associated kinases and induce degradation of c‐Jun in HeLa cells. Curcumin treatment results in elevated amounts of c‐Jun–Ub conjugates. We conclude that CK2 and PKD are recruited by CSN in order to regulate Ub conjugate formation.

Plasmonic Control of the Shape of the Raman Spectrum of a Single Molecule in a Silver Nanoparticle Dimer

We study surface-enhanced Raman scattering (SERS) of individual organic molecules embedded in dimers of two metal nanoparticles. The good control of the dimer preparation process, based on the usage of bifunctional molecules, enables us to study quantitatively the effect of the nanoparticle size on the SERS intensity and spectrum at the single molecule level. We find that as the nanoparticle size increases the total Raman intensity increases and the lower energy Raman modes become dominant. We perform an electromagnetic calculation of the Raman enhancement and show that this behavior can be understood in terms of the overlap between the plasmonic modes of the dimer structure and the Raman spectrum. As the nanoparticle size increases, the plasmonic dipolar mode shifts to longer wavelength and thereby its overlap with the Raman spectrum changes. This suggests that the dimer structure can provide an external control of the emission properties of a single molecule. Indeed, clear and systematic differences are observed between Raman spectra of individual molecules adsorbed on small versus large particles.

RNA editing activity is associated with splicing factors in lnRNP particles: The nuclear pre-mRNA processing machinery

Multiple members of the ADAR (adenosine deaminases acting on RNA) gene family are involved in A-to-I RNA editing. It has been speculated that they may form a large multicomponent protein complex. Possible candidates for such complexes are large nuclear ribonucleoprotein (lnRNP) particles. The lnRNP particles consist mainly of four spliceosomal subunits that assemble together with the pre-mRNA to form a large particle and thus are viewed as the naturally assembled pre-mRNA processing machinery. Here we investigated the presence of ADARs in lnRNP particles by Western blot analysis using anti-ADAR antibodies and by indirect immunoprecipitation. Both ADAR1 and ADAR2 were found associated with the spliceosomal components Sm and SR proteins within the lnRNP particles. The two ADARs, associated with lnRNP particles, were enzymatically active in site-selective A-to-I RNA editing. We demonstrate the association of ADAR RNA editing enzymes with physiological supramolecular complexes, the lnRNP particles.

Exciton–Plasmon Interactions in Quantum Dot–Gold Nanoparticle Structures

We present a self-assembly method to construct CdSe/ZnS quantum dot-gold nanoparticle complexes. This method allows us to form complexes with relatively good control of the composition and structure that can be used for detailed study of the exciton-plasmon interactions. We determine the contribution of the polarization-dependent near-field enhancement, which may enhance the absorption by nearly two orders of magnitude and that of the exciton coupling to plasmon modes, which modifies the exciton decay rate.

Structure and Function of the Pre-mRNA Splicing Machine

Most eukaryotic pre-mRNAs contain non-coding sequences (introns) that must be removed in order to accurately place the coding sequences (exons) in the correct reading frame. This critical regulatory pre-mRNA splicing event is fundamental in development and cancer. It occurs within a mega-Dalton multicomponent machine composed of RNA and proteins, which undergoes dynamic changes in RNA-RNA, RNA-protein, and protein-protein interactions during the splicing reaction. Recent years have seen progress in functional and structural analyses of the splicing machine and its subcomponents, and this review is focused on structural aspects of the pre-mRNA splicing machine and their mechanistic implications on the splicing of multi-intronic pre-mRNAs. It brings together, in a comparative manner, structural information on spliceosomes and their intermediates in the stepwise assembly process in vitro, and on the preformed supraspliceosomes, which are isolated from living cell nuclei, with a view of portraying a consistent picture.

PACT: cloning and characterization of a cellular p53 binding protein that interacts with Rb

Cellular functions of tumor suppressor proteins can be mediated by protein-protein interactions. Using p53 as a probe to screen an expression library, a cDNA encoding a 250 kDa protein was isolated. Recombinant forms of this protein, designated PACT, bind to wild type p53 while two different mutations abolish this interaction. PACT protein can also interfere with p53 specific DNA binding. PACT contains a serine/arginine (SR) rich region and a C′ terminal lysine rich domain. The 250 kDa PACT protein can be precipitated from cell lysates by a method specific for SR proteins. snRNPs can be co-immunoprecipitated from cells with anti-PACT antibodies. These antibodies stain cell nuclei in a speckled pattern reminiscent of the distribution of known splicing factors. Recently, RBQ1, a truncated human homologue of PACT was identified by virtue of Rb binding. We show that RBQ1 is truncated as a result of a possible mutational event. PACT can interact with both cellular Rb and p53.

Heterogeneous Nuclear Ribonucleoprotein G Regulates Splice Site Selection by Binding to CC(A/C)-rich Regions in Pre-mRNA

Almost every protein-coding gene undergoes pre-mRNA splicing, and the majority of these pre-mRNAs are alternatively spliced. Alternative exon usage is regulated by the transient formation of protein complexes on the pre-mRNA that typically contain heterogeneous nuclear ribonucleoproteins (hnRNPs). Here we characterize hnRNP G, a member of the hnRNP class of proteins. We show that hnRNP G is a nuclear protein that is expressed in different concentrations in various tissues and that interacts with other splicing regulatory proteins. hnRNP G is part of the supraspliceosome, where it regulates alternative splice site selection in a concentration-dependent manner. Its action on alternative exons can occur without a functional RNA-recognition motif by binding to other splicing regulatory proteins. The RNA-recognition motif of hnRNP G binds to a loose consensus sequence containing a CC(A/C) motif, and hnRNP G preferentially regulates alternative exons where this motif is clustered in close proximity. The X-chromosomally encoded hnRNP G regulates different RNAs than its Y-chromosomal paralogue RNA-binding motif protein, Y-linked (RBMY), suggesting that differences in alternative splicing, evoked by the sex-specific expression of hnRNP G and RBMY, could contribute to molecular sex differences in mammals.

Fabrication of nanoscale gaps in integrated circuits

Nanosize objects such as metal clusters present an ideal system for the study of quantum phenomena and for the construction of practical quantum devices. Integrating these small objects in a macroscopic circuit is, however, a difficult task. So far, nanoparticles have been contacted and addressed by highly sophisticated techniques not suitable for large-scale integration in macroscopic circuits. We present an optical lithography method that allows for the fabrication of a network of electrodes separated by gaps of controlled nanometer size. The main idea is to control the gap size with subnanometer precision using a structure grown by molecular-beam epitaxy.

Stop codons affect 5′ splice site selection by surveillance of splicing

Pre-mRNA splicing involves recognition of a consensus sequence at the 5′ splice site (SS). However, only some of the many potential sites that conform to the consensus are true ones, whereas the majority remain silent and are not normally used for splicing. We noticed that in most cases the utilization of such a latent intronic 5′ SS for splicing would introduce an in-frame stop codon into the resultant mRNA. This finding suggested a link between SS selection and maintenance of an ORF within the mRNA. Here we tested this idea by analyzing the splicing of pre-mRNAs in which in-frame stop codons upstream of a latent 5′ SS were mutated. We found that splicing with the latent site is indeed activated by such mutations. Our findings predict the existence of a checking mechanism, as a component of the nuclear pre-mRNA splicing machine, to ensure the maintenance of an ORF. This notion is highly important for accurate gene expression, as perturbations that would lead to splicing at these latent sites are expected to introduce in-frame stop codons into the majority of mRNAs.