Total wash elimination for solid phase peptide synthesis.

We present a process for solid phase peptide synthesis (SPPS) that completely eliminates all solvent intensive washing steps during each amino acid addition cycle. A key breakthrough is the removal of a volatile Fmoc deprotection base through bulk evaporation at elevated temperature while preventing condensation on the vessel surfaces with a directed headspace gas flushing. This process was demonstrated at both research and production scales without any impact on product quality and when applied to a variety of challenging sequences (up to 89 amino acids in length). The overall result is an extremely fast, high purity, scalable process with a massive waste reduction (up to 95%) while only requiring 10-15% of the standard amount of base used. This transformation of SPPS represents a step-change in peptide manufacturing process efficiency, and should encourage expanded access to peptide-based therapeutics.

Evidence for reduced BRCA2 functional activity in Homo sapiens after divergence from the chimpanzee-human last common ancestor.

We performed a comparative analysis of human and 12 non-human primates to identify sequence variations in known cancer genes. We identified 395 human-specific fixed non-silent substitutions that emerged during evolution of human. Using bioinformatics analyses for functional consequences, we identified a number of substitutions that are predicted to alter protein function; one of these mutations is located at the most evolutionarily conserved domain of human BRCA2.

Analysis of epigenetic features characteristic of L1 loci expressed in human cells.

Only a select few L1 loci in the human genome are expressed in any given cell line or organ, likely to minimize damage done to the genome. The epigenetic features and requirements of expressed L1 loci are currently unknown. Using human cells and comprehensive epigenetic analysis of individual expressed and unexpressed L1 loci, we determined that endogenous L1 transcription depends on a combination of epigenetic factors, including open chromatin, activating histone modifications, and hypomethylation at the L1 promoter. We demonstrate that the L1 promoter seems to require interaction with enhancer elements for optimal function. We utilize epigenetic context to predict the expression status of L1Hs loci that are poorly mappable with RNA-Seq. Our analysis identified a population of 'transitional' L1 loci that likely have greater potential to be activated during the epigenetic dysregulation seen in tumors and during aging because they are the most responsive to targeted CRISPR-mediated delivery of trans-activating domains. We demonstrate that an engineered increase in endogenous L1 mRNA expression increases Alu mobilization. Overall, our findings present the first global and comprehensive analysis of epigenetic status of individual L1 loci based on their expression status and demonstrate the importance of epigenetic context for L1 expression heterogeneity.

Distinct pathways of homologous recombination controlled by the SWS1-SWSAP1-SPIDR complex.

Homology-directed repair (HDR), a critical DNA repair pathway in mammalian cells, is complex, leading to multiple outcomes with different impacts on genomic integrity. However, the factors that control these different outcomes are often not well understood. Here we show that SWS1-SWSAP1-SPIDR controls distinct types of HDR. Despite their requirement for stable assembly of RAD51 recombinase at DNA damage sites, these proteins are not essential for intra-chromosomal HDR, providing insight into why patients and mice with mutations are viable. However, SWS1-SWSAP1-SPIDR is critical for inter-homolog HDR, the first mitotic factor identified specifically for this function. Furthermore, SWS1-SWSAP1-SPIDR drives the high level of sister-chromatid exchange, promotes long-range loss of heterozygosity often involved with cancer initiation, and impels the poor growth of BLM helicase-deficient cells. The relevance of these genetic interactions is evident as SWSAP1 loss prolongs Blm-mutant embryo survival, suggesting a possible druggable target for the treatment of Bloom syndrome.

Altered DNA repair creates novel Alu/Alu repeat-mediated deletions.

Alu elements are the most abundant source of nonallelic homology that influences genetic instability in the human genome. When there is a DNA double-stranded break, the Alu element's high copy number, moderate length and distance and mismatch between elements uniquely influence recombination processes. We utilize a reporter-gene assay to show the complex influence of Alu mismatches on Alu-related repeat-mediated deletions (RMDs). The Alu/Alu heteroduplex intermediate can result in a nonallelic homologous recombination (HR). Alternatively, the heteroduplex can result in various DNA breaks around the Alu elements caused by competing nucleases. These breaks can undergo Alt-nonhomologous end joining to cause deletions focused around the Alu elements. Formation of these heteroduplex intermediates is largely RAD52 dependent. Cells with low ERCC1 levels utilize more of these alternatives resolutions, while cells with MSH2 defects tend to have more RMDs with a specific increase in the HR events. Therefore, Alu elements are expected to create different forms of deletions in various cancers depending on a number of these DNA repair defects.

Interhomolog Homologous Recombination in Mouse Embryonic Stem Cells.

Homologous recombination is a critical mechanism for the repair of DNA double-strand breaks (DSBs). It occurs predominantly between identical sister chromatids and at lower frequency can also occur between homologs. Interhomolog homologous recombination (IH-HR) has the potential lead to substantial loss of genetic information, i.e., loss of heterozygosity (LOH), when it is accompanied by crossing over. In this chapter, we describe a system to study IH-HR induced by a defined DSB in mouse embryonic stem cells derived from F1 hybrid mice. This system is based on the placement of mutant selectable marker genes, one of which contains an I-SceI endonuclease cleavage site, on the two homologs such that repair of the I-SceI-generated DSB from the homolog leads to drug resistance. Loss of heterozygosity arising during IH-HR is analyzed using a PCR-based approach. Finally, we present a strategy to analyze the role of BLM helicase in this system.

Enhanced photoreduction of water catalyzed by a cucurbit[8]uril-secured platinum dimer.

A cucurbit[8]uril (CB[8])-secured platinum terpyridyl chloride dimer was used as a photosensitizer and hydrogen-evolving catalyst for the photoreduction of water. Volumes of produced hydrogen were up to 25 and 6 times larger than those obtained with the corresponding free and cucurbit[7]uril-bound platinum monomer, respectively, at equal Pt concentration. The thermodynamics of the proton-coupled electron transfer from the Pt(ii)-Pt(ii) dimer to the corresponding Pt(ii)-Pt(iii)-H hydride key intermediate, as quantified by density functional theory, suggest that CB[8] secures the Pt(ii)-Pt(ii) dimer in a particularly reactive conformation that promotes hydrogen formation.

Exosome Isolation: Cyclical Electrical Field Flow Fractionation in Low-Ionic-Strength Fluids.

The influence of buffer substitution and dilution effects on exosome size and electrophoretic mobility were shown for the first time. Cyclical electrical field flow fractionation (Cy-El-FFF) in various substituted fluids was applied to exosomes and other particles. Tested carrier fluids of deionized (DI) water, 1× phosphate buffered saline (PBS), 0.308 M trehalose, and 2% isopropyl alcohol (IPA) influenced Cy-El-FFF-mediated isolation of A375 melanoma exosomes. All fractograms revealed a crescent-shaped trend in retention times with increasing voltage with the maximum retention time at ∼1.3 V AC. A375 melanoma exosome recovery was approximately 70-80% after each buffer substitution, and recovery was independent of whether the sample was substituted into 1× PBS or DI water. Exosome dilution in deionized water produced a U-shaped dependence on electrophoretic mobility. The effect of dilution using 1× PBS buffer revealed a very gradual change in electrophoretic mobility of exosomes from ∼-1.6 to -0.1 µm cm/s V, as exosome concentration was decreased. This differed from the use of DI water, where a large change from ∼-5.5 to -0.1 µm cm/s V over the same dilution range was observed. Fractograms of separated A375 melanoma exosomes in two substituted low-ionic-strength buffers were compared with synthetic particle fractograms. Overall, the ability of Cy-El-FFF to separate exosomes based on their size and charge is a highly promising, label-free approach to initially catalogue and purify exosome subtypes for biobanking as well as to enable further exosome subtype interrogations.

Detection of Neutral CO Lost During Ionic Dissociation Using Atmospheric Pressure Thermal Dissociation Mass Spectrometry (APTD-MS).

Elucidation of ion dissociation patterns is particularly important to structural analysis by mass spectrometry (MS). However, typically, only the charged fragments from an ion dissociation event are detected in tandem MS experiments; neutrals are not identified. In recent years, we have developed an atmospheric pressure thermal dissociation (APTD) technique that can be applied to dissociate ions at atmosphere pressure and thus provide one way to characterize neutral fragments. In this paper, we focus on the detection of neutral CO resulting from amino acid and peptide ion dissociation. In the first set of experiments, several protonated amino acids (e.g., + 1 ion of phenylalanine) were found to undergo loss of a neutral (s) of total mass 46 Da, a process leading to iminium ion formation. We successfully detected the neutral species CO by using a CO sensor, UV-Vis and MS analysis following selective CO trapping with a rhodium complex. The capture of CO from dissociation of protonated amino acids supports the assignment of the loss of 46 Da to neutral losses of CO and H2O, rather than loss of formaldehyde or dihydroxycarbene, other possible fragmentation pathways that have been subject of debate for a long time. In a second experiment, we used the APTD method in combination with the CO detection technique, to demonstrate the formation of CO in the conversion of b ions to a ions during peptide ion dissociations. These results showed the potential of APTD in the elucidation of ion dissociation mechanisms, using simple home-built apparatus. Graphical Abstract ᅟ.

Visible-Light-Driven Photosystems Using Heteroleptic Cu(I) Photosensitizers and Rh(III) Catalysts To Produce H2.

The synthesis of two new heteroleptic Cu(I) photosensitizers (PS), [Cu(Xantphos)(NN)]PF6 (NN = biq = 2,2'-biquinoline, dmebiq = 2,2'-biquinoline-4,4'-dimethyl ester; Xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene), along with the associated structural, photophysical, and electrochemical properties, are described. The biquinoline diimine ligand extends the PS light absorbing properties into the visible with a maximum absorption at 455 and 505 nm for NN = biq and dmebiq, respectively, in CH2Cl2 solvent. Following photoexcitation, both Cu(I) PS are emissive at low energy, albeit displaying stark differences in their excited state lifetimes (τMLCT = 410 ± 5 (biq) and 44 ± 4 ns (dmebiq)). Cyclic voltammetry indicates a Cu-based HOMO and NN-based LUMO for both complexes, whereby the methyl ester substituents stabilize the LUMO within [Cu(Xantphos)(dmebiq)]+ by ∼0.37 V compared to the unsubstituted analogue. When combined with H2O, N,N-dimethylaniline (DMA) electron donor, and cis-[Rh(NN)2Cl2]PF6 (NN = Me2bpy = 4,4'-dimethyl-2,2'-bipyridine, bpy = 2,2'-bipyridine, dmebpy = 2,2'-bipyridine-4,4'-dimethyl ester) water reduction catalysts (WRC), photocatalytic H2 evolution is only observed using the [Cu(Xantphos)(biq)]+ PS. Furthermore, the choice of cis-[Rh(NN)2Cl2]+ WRC strongly affects the catalytic activity with turnover numbers (TONRh = mol H2 per mol Rh catalyst) of 25 ± 3, 22 ± 1, and 43 ± 3 for NN = Me2bpy, bpy, and dmebpy, respectively. This work illustrates how ligand modification to carefully tune the PS light absorbing, excited state, and redox-active properties, along with the WRC redox potentials, can have a profound impact on the photoinduced intermolecular electron transfer between components and the subsequent catalytic activity.

Social Media Based STEM Enrichment Curriculum Positively Impacts Rural Adolescent Health Measures.

Some STEM outreach programs connect students to real-world problems and challenge them to work towards solutions. Research shows one-third of children between ages 5-17 in the U.S. are overweight. Socioeconomic status, race, and parental educational attainment all influence this issue as well as living in a rural or urban area. A rural high school STEM outreach program used a social media curriculum focused on healthy lifestyles and measured impact on the health of adolescents from these backgrounds. Health screenings and college mentors were provided to 134 adolescents from 26 counties in WV. The social media intervention lasted seven months with participants using near-peer and mentor support to achieve personal health goals set at the initial health screening. The results of pre- and post-intervention health screenings were compared for any changes in health measures by student goal and participation. BMI decreased significantly in the group of participants who selected a weight loss goal, while those choosing to improve their nutrition significantly increased healthy cholesterol levels. A positive impact was seen on adolescent health outcomes through linking a high school STEM outreach program with a higher education institution to deliver STEM enrichment curriculum through social media.

New Ligand Design Provides Delocalization and Promotes Strong Absorption throughout the Visible Region in a Ru(II) Complex.

The new Ru(II)-anthraquinone complex [Ru(bpy)2(qdpq)](PF6)2 (Ru-qdpq; bpy = 2,2'-bipyridine; qdpq = 2,3-di(2-pyridyl)naphtho[2,3-f]quinoxaline-7,12-quinone) possesses a strong 1MLCT Ru → qdpq absorption with a maximum at 546 nm that tails into the near-IR and is significantly red-shifted relative to that of the related complex [Ru(bpy)2(qdppz)](PF6)2 (Ru-qdppz; qdppz = naphtho[2,3-a]dipyrido[3,2-h:2',3'-f]phenazine-5,18-dione), with λmax = 450 nm. Ru-qdppz possesses electronically isolated proximal and distal qdppz-based excited states; the former is initially generated and decays to the latter, which repopulates the ground state with τ = 362 ps. In contrast, excitation of Ru-qdpq results in the population of a relatively long-lived (τ = 19 ns) Ru(dπ) → qdpq(π*) 3MLCT excited state where the promoted electron is delocalized throughout the qdpq ligand. Ultrafast spectroscopy, used together with steady-state absorption, electrochemistry, and DFT calculations, indicates that the unique coordination modes of the qdpq and qdppz ligands impart substantially different electronic communication throughout the quinone-containing ligand, affecting the excited state and electron transfer properties of these molecules. These observations create a pathway to synthesize complexes with red-shifted absorptions that possess long-lived, redox-active excited states that are useful for various applications, including solar energy conversion and photochemotherapy.

Evaluating different DNA binding domains to modulate L1 ORF2p-driven site-specific retrotransposition events in human cells.

DNA binding domains (DBDs) have been used with great success to impart targeting capabilities to a variety of proteins creating highly useful genomic tools. We evaluated the ability of five types of DBDs and strategies (AAV Rep proteins, Cre, TAL effectors, zinc finger proteins, and Cas9/gRNA system) to target the L1 ORF2 protein to drive retrotransposition of Alu inserts to specific sequences in the human genome. First, we find that the L1 ORF2 protein tolerates the addition of protein domains both at the amino- and carboxy-terminus. Although in some instances retrotransposition efficiencies slightly diminished, all fusion proteins containing an intact ORF2 were capable of driving retrotransposition. Second, the stability of individual ORF2 fusion proteins varies and difficult to predict. Third, DBDs that require the formation of multimers for target recognition are unlikely to modify targeting of ORF2p-driven insertions. Fourth, the more components needed to assemble into a complex to drive targeted retrotransposition, the less likely the strategy will increase targeted insertions. Fifth, abundance of target sequences present in the genome will likely dictate the effectiveness and efficiency of targeted insertions. Lastly, the cleavage capabilities of Cas9 (or a Cas9 nickase variant) are unable to substitute for the L1 ORF2 endonuclease domain functions, suggestive that the endonuclease domain has alternate functions needed for retrotransposition. From these studies, we conclude that the most critical component for the modification of the human L1 ORF2 protein to drive targeted insertions is the selection of the DBD due to the varying functional requirements and impacts on protein stability.

New Rh2(II,II) Complexes for Solar Energy Applications: Panchromatic Absorption and Excited-State Reactivity.

The new heteroleptic paddlewheel complexes cis-[Rh2(µ-form)2(µ-np)2][BF4]2, where form = p-ditolylformamidinate (DTolF) or p-difluorobenzylformamidinate (F-form) and np = 1,8-napthyridyine, and cis-Rh2(µ-form)2(µ-npCOO)2 (npCOO- = 1,8-naphthyridine-2-carboxylate), were synthesized and characterized. The complexes absorb strongly throughout the ultraviolet (λmax = 300 nm, ε = 20 300 M-1 cm-1) and visible regions (λmax = 640 nm ε = 3500 M-1 cm-1), making them potentially useful new dyes with panchromatic light absorption for solar energy conversion applications. Ultrafast and nanosecond transient absorption and time-resolved infrared spectroscopies were used to characterize the identity and dynamics of the excited states, where singlet and triplet Rh2/form-to-naphthyridine, metal/ligand-to-ligand charge-transfer (ML-LCT) excited states were observed in all four complexes. The npCOO- complexes exhibit red-shifted absorption profiles extending into the near-IR and undergo photoinitiated electron transfer to generate reduced methyl viologen, a species that persists in the presence of a sacrificial donor. The energy of the triplet excited state of each complex was estimated from energy-transfer quenching experiments using a series of organic triplet donors (E(3ππ*) from 1.83 to 0.78 eV). The singlet reduction (+0.6 V vs Ag/AgCl) potentials, and singlet and triplet oxidation potentials (-1.1 and -0.5 V vs Ag/AgCl, respectively) were determined. Based on the excited-state lifetimes and redox properties, these complexes represent a new class of light absorbers with potential application as dyes for charge injection into semiconductor solar cells and in sensitizer-catalyst assemblies for photocatalysis that operate with irradiation from the ultraviolet to ∼800 nm.

The Nucleotide Excision Repair Pathway Limits L1 Retrotransposition.

Long interspersed elements 1 (L1) are active mobile elements that constitute almost 17% of the human genome. They amplify through a "copy-and-paste" mechanism termed retrotransposition, and de novo insertions related to these elements have been reported to cause 0.2% of genetic diseases. Our previous data demonstrated that the endonuclease complex ERCC1-XPF, which cleaves a 3' DNA flap structure, limits L1 retrotransposition. Although the ERCC1-XPF endonuclease participates in several different DNA repair pathways, such as single-strand annealing, or in telomere maintenance, its recruitment to DNA lesions is best characterized in the nucleotide excision repair (NER) pathway. To determine if the NER pathway prevents the insertion of retroelements in the genome, we monitored the retrotransposition efficiencies of engineered L1 elements in NER-deficient cells and in their complemented versions. Core proteins of the NER pathway, XPD and XPA, and the lesion binding protein, XPC, are involved in limiting L1 retrotransposition. In addition, sequence analysis of recovered de novo L1 inserts and their genomic locations in NER-deficient cells demonstrated the presence of abnormally large duplications at the site of insertion, suggesting that NER proteins may also play a role in the normal L1 insertion process. Here, we propose new functions for the NER pathway in the maintenance of genome integrity: limitation of insertional mutations caused by retrotransposons and the prevention of potentially mutagenic large genomic duplications at the site of retrotransposon insertion events.

A comprehensive approach to expression of L1 loci.

L1 elements represent the only currently active, autonomous retrotransposon in the human genome, and they make major contributions to human genetic instability. The vast majority of the 500 000 L1 elements in the genome are defective, and only a relatively few can contribute to the retrotransposition process. However, there is currently no comprehensive approach to identify the specific loci that are actively transcribed separate from the excess of L1-related sequences that are co-transcribed within genes. We have developed RNA-Seq procedures, as well as a 1200 bp 5΄ RACE product coupled with PACBio sequencing that can identify the specific L1 loci that contribute most of the L1-related RNA reads. At least 99% of L1-related sequences found in RNA do not arise from the L1 promoter, instead representing pieces of L1 incorporated in other cellular RNAs. In any given cell type a relatively few active L1 loci contribute to the 'authentic' L1 transcripts that arise from the L1 promoter, with significantly different loci seen expressed in different tissues.

Cationic dirhodium(ii,ii) complexes for the electrocatalytic reduction of CO2 to HCOOH.

Two formamidinate bridged dirhodium(ii,ii) complexes with chelating diimine ligands L, [Rh2(µ-DTolF)2(L)2]2+, were shown to electrocatalytically reduce CO2 in the presence of H2O. Analysis of the reaction mixture and headspace following bulk electrolysis revealed H2 and HCOOH as the major products. The variation in relative product formation is discussed.

Judicious Ligand Design in Ruthenium Polypyridyl CO2 Reduction Catalysts to Enhance Reactivity by Steric and Electronic Effects.

A series of RuII polypyridyl complexes of the structural design [RuII (R-tpy)(NN)(CH3 CN)]2+ (R-tpy=2,2':6',2''-terpyridine (R=H) or 4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine (R=tBu); NN=2,2'-bipyridine with methyl substituents in various positions) have been synthesized and analyzed for their ability to function as electrocatalysts for the reduction of CO2 to CO. Detailed electrochemical analyses establish how substitutions at different ring positions of the bipyridine and terpyridine ligands can have profound electronic and, even more importantly, steric effects that determine the complexes' reactivities. Whereas electron-donating groups para to the heteroatoms exhibit the expected electronic effect, with an increase in turnover frequencies at increased overpotential, the introduction of a methyl group at the ortho position of NN imposes drastic steric effects. Two complexes, [RuII (tpy)(6-mbpy)(CH3 CN)]2+ (trans-[3]2+ ; 6-mbpy=6-methyl-2,2'-bipyridine) and [RuII (tBu-tpy)(6-mbpy)(CH3 CN)]2+ (trans-[4]2+ ), in which the methyl group of the 6-mbpy ligand is trans to the CH3 CN ligand, show electrocatalytic CO2 reduction at a previously unreactive oxidation state of the complex. This low overpotential pathway follows an ECE mechanism (electron transfer-chemical reaction-electron transfer), and is a direct result of steric interactions that facilitate CH3 CN ligand dissociation, CO2 coordination, and ultimately catalytic turnover at the first reduction potential of the complexes. All experimental observations are rigorously corroborated by DFT calculations.

Activating a Low Overpotential CO2 Reduction Mechanism by a Strategic Ligand Modification on a Ruthenium Polypyridyl Catalyst.

The introduction of a simple methyl substituent on the bipyridine ligand of [Ru(tBu3 tpy)(bpy)(NCCH3 )](2+) (tBu3 tpy=4,4',4''-tri-tert-butyl-2,2':6',2''-terpyridine; bpy=2,2'-bipyridine) gives rise to a highly active electrocatalyst for the reduction of CO2 to CO. The methyl group enables CO2 binding already at the one-electron reduced state of the complex to enter a previously not accessible catalytic cycle that operates at the potential of the first reduction. The complex turns over with a Faradaic efficiency close to unity and at an overpotential that is amongst the lowest ever reported for homogenous CO2 reduction catalysts.