Out-of-focus spatial map imaging of magnetically deflected sodium ammonia clusters.

This paper introduces out-of-focus spatial map imaging (SMI) as a detection method for magnetic deflection of molecular/cluster beams, using Nam(NH3)n to illustrate its capabilities. This method enables imaging of the complete spatial distribution, simplifying measurements and allowing for cluster-size-resolved analysis by shifting away from traditional in-focus SMI conditions. Incorporating out-of-focus SMI with TOF-MS and velocity map imaging into a single setup allows for direct assessment of clusters' magnetic moments without needing to pre-select velocities. Key findings include a slower relaxation for Na(NH3)4 compared to Na(NH3)3 and Na(NH3)5, unexpectedly high deflection for larger clusters up to Na(NH3)9, hinting at changes in cluster dynamics as the first solvation shell closes. The study also covers the first measurements of Na2(NH3)1 and Na3(NH3)n, showing distinct deflection behaviors and underscoring the improved capabilities of the new detection method.

Magnetic deflection of neutral sodium-doped ammonia clusters.

We describe the setup and the performance of a new pulsed Stern-Gerlach deflector and present results for small sodium-doped ammonia clusters Na(NH3)n (n = 1-4) in a molecular beam. NaNH3 shows the expected deflection of a spin ½ system, while all lager clusters show much smaller deflections. Experimental deflection ratios are compared with the values calculated from molecular dynamics simulations. The comparison reveals that intracluster spin relaxation in NaNH3 takes place on a time scale significantly longer than 200 µs. Assuming that intracluster relaxation is the cause of the reduced deflection, relaxation times seem to be on the order of 200 µs for all larger clusters Na(NH3)n (n = 2-4). Our work is a first attempt to understand the magnetic properties of isolated, weakly-bound clusters with relevance to the variety of diamagnetic and paramagnetic species expected in solvated electron systems.

Requirement of proliferating cell nuclear antigen in RAD6-dependent postreplicational DNA repair.

The proliferating cell nuclear antigen (PCNA) acts as a processivity factor for replicative DNA polymerases and is essential for DNA replication. In vitro studies have suggested a role for PCNA-in the repair synthesis step of nucleotide excision repair, and PCNA interacts with the cyclin-dependent kinase inhibitor p21. However, because of the lack of genetic evidence, it is not clear which of the DNA repair processes are in fact affected by PCNA in vivo. Here, we describe a PCNA mutation, pol30-46, that confers ultraviolet (UV) sensitivity but has no effect on growth or cell cycle progression, and the mutant pcna interacts normally with DNA polymerase delta and epsilon. Genetic studies indicate that the pol30-46 mutation is specifically defective in RAD6-dependent postreplicational repair of UV damaged DNA, and this mutation impairs the error-free mode of bypass repair. These results implicate a role for PCNA as an intermediary between DNA replication and postreplicational DNA repair.

A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair.

The saccharomyces cerevisiae proliferating cell nuclear antigen (PCNA), encoded by the POL30 gene, is essential for DNA replication and DNA repair processes. Twenty-one site-directed mutations were constructed in the POL30 gene, each mutation changing two adjacently located charged amino acids to alanines. Although none of the mutant strains containing these double-alanine mutations as the sole source of PCNA were temperature sensitive or cold sensitive for growth, about a third of the mutants showed sensitivity to UV light. Some of those UV-sensitive mutants had elevated spontaneous mutation rates. In addition, several mutants suppressed a cold-sensitive mutation in the CDC44 gene, which encodes the large subunit of replication factor C. A cold-sensitive mutant, which was isolated by random mutagenesis, showed a terminal phenotype at the restrictive temperature consistent with a defect in DNA replication. Several mutant PCNAs were expressed and purified from Escherichia coli, and their in vitro properties were determined. The cold-sensitive mutant (pol30-52, S115P) was a monomer, rather than a trimer, in solution. This mutant was deficient for DNA synthesis in vitro. Partial restoration of DNA polymerase delta holoenzyme activity was achieved at 37 degrees C but not at 14 degrees C by inclusion of the macromolecular crowding agent polyethylene glycol in the assay. The only other mutant (pol30-6, DD41,42AA) that showed a growth defect was partially defective for interaction with replication factor C and DNA polymerase delta but completely defective for interaction with DNA polymerase epsilon. Two other mutants sensitive to DNA damage showed no defect in vitro. These results indicate that the latter mutants are specifically impaired in one or more DNA repair processes whereas pol30-6 and pol30-52 mutants show their primary defects in the basic DNA replication machinery with probable associated defects in DNA repair. Therefore, DNA repair requires interactions between repair-specific protein(s) and PCNA, which are distinct from those required for DNA replication.

ATP-independent loading of the proliferating cell nuclear antigen requires DNA ends.

The proliferating cell nuclear antigen (PCNA) is a processivity subunit for eukaryotic DNA polymerase delta. We present biochemical evidence that yeast PCNA likely adopts a toroidal structure containing an inside cavity through which double-stranded DNA slides. A comparative study of DNA replication reactions on circular versus linear model substrates shows that PCNA can only interact productively with DNA polymerase delta if the substrate is linear. This combined with the observation that a large molar excess of PCNA is required for maximal stimulatory activity is consistent with a model in which PCNA slips onto the end of the DNA in an ATP-independent manner.

A Saccharomyces cerevisiae DNA helicase associated with replication factor C.

A novel DNA helicase has been isolated from Saccharomyces cerevisiae. This DNA helicase co-purified with replication factor C (RF-C) during chromatography on S-Sepharose, DEAE-silica gel high performance liquid chromatography (HPLC), Affi-Gel Blue-agarose, heparin-agarose, single-stranded DNA-cellulose, fast protein liquid chromatography MonoS, and hydroxyapatite HPLC. Surprisingly, the helicase could be separated from RF-C by sedimentation on a glycerol gradient in the presence of 200 mM NaCl. The helicase is probably a homodimer of a 60-kDa polypeptide, which by UV cross-linking has been shown to bind ATP. It has a single-stranded DNA-dependent ATPase activity, with a Km for ATP of 60 microM. The DNA helicase activity depends on the hydrolysis of NTP (dNTP), with ATP and dATP the most efficient cofactors, followed by CTP and dCTP. The DNA helicase has a 5' to 3' directionality and is only marginally stimulated by coating the single-stranded DNA with the yeast single-stranded DNA-binding protein RF-A.

Three new DNA helicases from Saccharomyces cerevisiae.

At least six DNA helicases have been identified during fractionation of extracts from the yeast Saccharomyces cerevisiae. Three of those, DNA helicases B, C, and D, have been further purified and characterized. DNA helicases B and C co-purified with DNA polymerase delta through several chromatographic steps, but were separated from the polymerase by hydrophobic chromatography. DNA helicase D co-purified with Replication Factor C over seven chromatographic steps, and was only separated from it by glycerol gradient centrifugation in the presence of 0.2 M NaCl. All three helicases are DNA dependent ATPases with Km values for ATP of 190 microM, 325 microM, and 60 microM for DNA helicases B, C, and D, respectively. Their DNA helicase activities are comparable. They are 5'-3' helicases and have pH optima of 6.5-7 and Mg2+ optima of 1-2 mM. However, they differ in the nucleotide requirement for helicase action. Whereas all three helicases preferred ATP, dATP, UTP, CTP, and dCTP as cofactors, DNA helicase C also used GTP, but not dTTP. On the other hand, DNA helicase D used dTTP, but not GTP, and DNA helicase B used neither nucleotide as cofactor. These studies allowed us to conclude that DNA helicases B, C, and D are not only distinct enzymes, but also different from two previously identified yeast DNA helicases, the RAD3 protein and ATPase III.

Saccharomyces cerevisiae replication factor C. I. Purification and characterization of its ATPase activity.

Saccharomyces cerevisiae replication factor C (RF-C) was purified 25,000-fold from a protease-deficient strain of yeast. RF-C is a complex of 6 subunits of 130, 86, 41, 40, 37, and 27 kDa. None of the subunits are related through proteolysis or differential phosphorylation. The assay for RF-C used as a substrate single-stranded DNA binding protein-coated singly primed single-stranded mp 18 DNA. This DNA was poorly replicated by yeast DNA polymerase delta with or without its cofactor proliferating cell nuclear antigen (PCNA). In the presence of RF-C, however, replication of the template proceeded efficiently when both ATP and PCNA were present as well. Formation of this replication-proficient complex of DNA polymerase delta required an input of one to two molecules of PCNA per replicated DNA molecule. DNA polymerase epsilon also formed an ATP-dependent complex with PCNA and RF-C. RF-C has a DNA-dependent ATPase activity, equally active on single-stranded and primed single-stranded mp18 DNA. Addition of PCNA stimulated the ATPase of RF-C on primed but not on unprimed DNA, indicating that the increase in ATPase was due to PCNA-enhanced binding of RF-C to the primer terminus. Calf thymus PCNA also stimulated the ATPase activity of yeast RF-C and participated in holoenzyme formation with DNA polymerase delta. These results attest to the structural and functional homology between yeast and mammalian cells for these components of the replication machinery.

Microtest procedure for isolation of Chlamydia trachomatis.

Management of patients potentially infected with Chlamydia trachomatis has been hampered by the cost and time required to perform Chlamydia cultures. To isolate C. trachomatis, we developed a microtiter method that exhibited equal sensitivity but less frequent contamination than our previously used vial-cover slip culture system. In addition, costs and technician time were substantially reduced with the microtest method. Subsequent studies showed that cycloheximide-treated cells were superior to 5-iodo-2-deoxyuridine-treated cells in the microtest method and that a subpassage significantly enhanced the sensitivity of the method. The microtest method appears to be a sensitive, rapid, and economical method for isolating C. trachomatis.