Daniel Summerer

A Genetically Encoded Spin Label for Electron Paramagnetic Resonance Distance Measurements

We report the genetic encoding of a noncanonical, spin-labeled amino acid in Escherichia coli. This enables the intracellular biosynthesis of spin-labeled proteins and obviates the need for any chemical labeling step usually required for protein electron paramagnetic resonance (EPR) studies. The amino acid can be introduced at multiple, user-defined sites of a protein and is stable in E. coli even for prolonged expression times. It can report intramolecular distance distributions in proteins by double-electron electron resonance measurements. Moreover, the signal of spin-labeled protein can be selectively detected in cells. This provides elegant new perspectives for in-cell EPR studies of endogenous proteins.

A Genetically Encoded Diazirine Photocrosslinker in Escherichia coli

Photoaffinity labels and crosslinkers have been used to map biomolecular interactions, as well as to identify the biological targets of small molecules. Benzophenones are among the most useful photocrosslinking agents and preferentially insert into C H bonds upon excitation with UV light. Aryl azides and [3-(trifluoromethyl)-3H-diazin-3yl]phenones generate reactive nitrenes and carbenes, respectively, that undergo relatively nonspecific insertion and addition reactions. 6] To facilitate the selective incorporation of photocrosslinking agents into proteins in living cells, we recently genetically encoded para-benzoyl-l-phenylalanine (pBpa) and para-azido-l-phenylalanine (pAzpa) in response to the amber nonsense codon in E. coli, yeast and mammalian cells. These photocrosslinkers were site-specifically incorporated into proteins by means of heterologous amber suppressor tRNA/aminoacyl–tRNA synthetase (aaRS) pairs that recognize the unnatural amino acid, but do not cross-react with endogenous host cell tRNAs, aaRSs or amino acids. To expand the photoaffinity label repertoire, we now report that 4’-[3-(trifluoromethyl)-3H-diazirin-3-yl]-l-phenylalanine (TfmdPhe; Figure 1A) can also be genetically encoded with excellent efficiency and fidelity in bacteria. TfmdPhe has useful photochemical properties and is stable under physiological conditions. Upon excitation by ~350 nm light, TfmdPhe undergoes fragmentation to N2 and a reactive carbene, which readily inserts into C H or O H bonds. In contrast, pAzpa requires relatively short wavelength UV excitation and can rearrange to less reactive secondary products prior to crosslinking. TfmdPhe is also somewhat smaller than pBpa, which can facilitate its incorporation into proteins at sites that are involved in biomolecular interactions. TfmdPhe has been incorporated into proteins previously by a chemically misacylated amber suppressor tRNA in a cell-free protein expression system. However, this method severely limits the protein yield, and is not amenable to studies directly in living cells. TfmdPhe was synthesized by using a previously reported method. To selectively incorporate TfmdPhe into proteins in E. coli, an orthogonal amber suppressor tRNA/aaRS was generated from a Methanococcus jannaschii amber suppressor tRNA (MjtRNACUA)/para-bromo-l-phenylalanyl-tRNA synthetase (BrPheRS) pair by using a previously reported, directed evolution strategy. BrPheRS was used as a template for mutagenesis because para-bromo-l-phenylalanine (BrPhe) is structurally similar to TfmdPhe, and BrPheRS has polypeptide backbone ACHTUNGTRENNUNGrearrangements that enlarge the substrate-binding pocket. Based on the structure of the BrPheRS–BrPhe complex, a library of aaRS active-site mutants was generated, in which residues L32, L65, H70, Q109, H160 and Y161 of BrPheRS were randomized by overlap extension polymerase chain reaction with synthetic oligonucleotide primers; the intended mutations were encoded by NNK (N=A+T+C+G; K=T+G). This library of aaRS mutants (on pBK plasmids under the control of the E. coli GlnRS promoter and terminator) was then passed through rounds of alternating positive and negative selections. In the positive selection, cell survival is dependent on the suppression of an amber codon that was introduced at a permissive site in the chloramphenicol acetyl transferase (CAT) gene in the presence of chloramphenicol and 1 mm TfmdPhe. The negative selection utilizes the toxic barnase gene with amber mutations at two permissive sites, and is carried out in the absence of TfmdPhe. Cells that contain MjTyrRS variants that acylate MjtRNACUA with TfmdPhe, but not any endogenous amino acids survive both positive and negative selections, whereas cells that contain MjTyrRS variants that acylate MjtRNACUA with endogenous amino acids express barnase and die in the negative selection. Five rounds of selection afforded five colonies that survived on chloramphenicol only in the presence of TfmdPhe. DNA sequencing of MjTyrRS mutants in these five colonies revealed one unique TfmdPheRS that had three new mutation sites : Y32I, H70F, and Q109M as well as four mutations (E107S, D158P, I159L, and L162E) that were inherited from BrPheRS. To determine the efficiency and fidelity of the incorporation of TfmdPhe into proteins, an amber codon was substituted for [a] Dr. E. M. Tippmann , Dr. W. Liu , Dr. D. Summerer, A. V. Mack, Prof. Dr. P. G. Schultz Department of Chemistry and the Skaggs Institute for Chemical Biology The Scripps Research Institute 10550 N. Torrey Pines Rd, La Jolla, CA 92037 (USA) Fax: (+1)858-784-9440 E-mail : schultz@scripps.edu [b] Dr. E. M. Tippmann + Present address: Cardiff School of Chemistry, Cardiff University Cardiff, Wales, CF10 3XQ (UK) [c] Dr. W. Liu + Present address: Department of Chemistry, Texas A&M University College Station, TX 77842 (USA) [] These authors contributed equally to this work. Figure 1. A) Structure of 4’-[3-(trifluoromethyl)-3H-diazin-3-yl]-l-phenylalanine (TfmdPhe); B) Specificity and efficiency of TfmdPhe incorporation by TfmdPheRS–MjtRNA CUA pair. TfmdPhe was incorporated in response to an amber codon at position 7 in Z domain, analyzed by SDS-PAGE, and stained by gel code blue. Proteins were purified by Ni-affinity chromatography.

Site-specific labeling of proteins with NMR-active unnatural amino acids

A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling of proteins for NMR studies. In this perspective, we discuss these opportunities including new photocaged unnatural amino acids, outline usage of metal chelating and spin-labeled unnatural amino acids and expand the approach to in-cell NMR experiments.

DNA-Templated Synthesis : More Versatile than Expected

It has been known for almost twenty years that nucleic acids may promote chemical reactions. Catalytic nucleic acids can be found in nature or evolved through in vitro selection processes. [1] Structural and functional investigations suggest that catalytically active nucleic acids act in a similar manner to enzymes: they promote chemical reactions through the precise spatial alignment of the reaction partners, the stabilization of transition states, and binding of reaction products in an elaborate manner. [1] Recent reports reveal new facets of nucleic acid promoted chemistry and indicate that DNA strands are able to promote chemical reactions by bringing reaction partners in close proximity of each other rather than by precisely aligning the reactive groups. Herein we focus on recent progress made in this diverse field. [2] For deeper insights we refer to the literature cited in the references. The ability of nucleic acid templates to promote coupling of adjacently annealed reaction partners to form the corresponding ligation products has been known. [3] This feature has been exploited in the race for the development of new and efficient methods for the detection of nucleotide variations such as single nucleotide polymorphisms (SNPs) in genes. Kool and co-workers have reported chemical autoligation processes, including the reaction of a phosphothioate or -selenoate anion 1 on one strand with a 5-carbon atom 2 that bears an iodide leaving group on the other strand (Scheme 1). [4] Efficient ligation is only observed when complementary templates are applied for the binding of the oligonucleotide reagents 1 and 2. Mattes and Seitz recently demonstrated that

Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing

The lack of efficient high-throughput methods for enrichment of specific sequences from genomic DNA represents a key bottleneck in exploiting the enormous potential of next-generation sequencers. Such methods would allow for a systematic and targeted analysis of relevant genomic regions. Recent studies reported sequence enrichment using a hybridization step to specific DNA capture probes as a possible solution to the problem. However, so far no method has provided sufficient depths of coverage for reliable base calling over the entire target regions. We report a strategy to multiply the enrichment performance and consequently improve depth and breadth of coverage for desired target sequences by applying two iterative cycles of hybridization with microfluidic Geniom biochips. Using this strategy, we enriched and then sequenced the cancer-related genes BRCA1 and TP53 and a set of 1000 individual dbSNP regions of 500 bp using Illumina technology. We achieved overall enrichment factors of up to 1062-fold and average coverage depths of 470-fold. Combined with high coverage uniformity, this resulted in nearly complete consensus coverages with >86% of target region covered at 20-fold or higher. Analysis of SNP calling accuracies after enrichment revealed excellent concordance, with the reference sequence closely mirroring the previously reported performance of Illumina sequencing conducted without sequence enrichment.

Red-Light-Controlled Protein–RNA Crosslinking with a Genetically Encoded Furan†

Well red: A protein-RNA crosslinker has been genetically encoded that can be controlled with red light, thus offering high penetration depths in biological materials. This should enable the discovery and mapping of transient protein-RNA interactions and enable the design of peptide- and protein-based drugs for RNA-targeted photodynamic therapy.

Targeted high throughput sequencing of a cancer-related exome subset by specific sequence capture with a fully automated microarray platform

Sequence capture methods for targeted next generation sequencing promise to massively reduce cost of genomics projects compared to untargeted sequencing. However, evaluated capture methods specifically dedicated to biologically relevant genomic regions are rare. Whole exome capture has been shown to be a powerful tool to discover the genetic origin of disease and provides a reduction in target size and thus calculative sequencing capacity of >90-fold compared to untargeted whole genome sequencing. For further cost reduction, a valuable complementing approach is the analysis of smaller, relevant gene subsets but involving large cohorts of samples. However, effective adjustment of target sizes and sample numbers is hampered by the limited scalability of enrichment systems. We report a highly scalable and automated method to capture a 480 Kb exome subset of 115 cancer-related genes using microfluidic DNA arrays. The arrays are adaptable from 125 Kb to 1 Mb target size and/or one to eight samples without barcoding strategies, representing a further 26 - 270-fold reduction of calculative sequencing capacity compared to whole exome sequencing. Illumina GAII analysis of a HapMap genome enriched for this exome subset revealed a completeness of >96%. Uniformity was such that >68% of exons had at least half the median depth of coverage. An analysis of reference SNPs revealed a sensitivity of up to 93% and a specificity of 98.2% or higher.

Programmable and Highly Resolved In Vitro Detection of 5‐Methylcytosine by TALEs

Gene expression is extensively regulated by specific patterns of genomic 5-methylcytosine (mC), but the ability to directly detect this modification at user-defined genomic loci is limited. One reason is the lack of molecules that discriminate between mC and cytosine (C) and at the same time provide inherent, programmable sequence-selectivity. Programmable transcription-activator-like effectors (TALEs) have been observed to exhibit mC-sensitivity in vivo, but to only a limited extent in vitro. We report an mC-detection assay based on TALE control of DNA replication that displays unexpectedly strong mC-discrimination ability in vitro. The status and level of mC modification at single positions in oligonucleotides can be determined unambiguously by this assay, independently of the overall target sequence. Moreover, discrimination is reliably observed for positions bound by N-terminal and central regions of TALEs. This indicates the wide scope and robustness of the approach for highly resolved mC detection and enabled the detection of a single mC in a large, eukaryotic genome.

Evolved Sequence Contexts for Highly Efficient Amber Suppression with Noncanonical Amino Acids

The expansion of the genetic code with noncanonical amino acids (ncAA) enables the function of proteins to be tailored with high molecular precision. In this approach, the ncAA is charged to an orthogonal nonsense suppressor tRNA by an aminoacyl-tRNA-synthetase (aaRS) and incorporated into the target protein in vivo by suppression of nonsense codons in the mRNA during ribosomal translation. Compared to sense codon translation, this process occurs with reduced efficiency. However, it is still poorly understood, how the local sequence context of the nonsense codon affects suppression efficiency. Here, we report sequence contexts for highly efficient suppression of the widely used amber codon in E. coli for the orthogonal Methanocaldococcus jannaschii tRNA(Tyr)/TyrRS and Methanosarcina mazei tRNA(Pyl)/PylRS pairs. In vivo selections of sequence context libraries consisting of each two random codons directly up- and downstream of an amber codon afforded contexts with strong preferences for particular mRNA nucleotides and/or amino acids that markedly differed from preferences of contexts obtained in control selections with sense codons. The contexts provided high amber suppression efficiencies with little ncAA-dependence that were transferrable between proteins and resulted in protein expression levels of 70-110% compared to levels of control proteins without amber codon. These sequence contexts represent stable tags for robust and highly efficient incorporation of ncAA into proteins in standard E. coli strains and provide general design rules for the engineering of amber codons into target genes.

Programmable Sensors of 5-Hydroxymethylcytosine

5-Hydroxymethylcytosine (hmC), the sixth base of the mammalian genome, is increasingly recognized as an epigenetic mark with important biological functions. We report engineered, programmable transcription-activator-like effectors (TALEs) as the first DNA-binding receptor molecules that provide direct, individual selectivities for cytosine (C), 5-methylcytosine (mC), and hmC at user-defined DNA sequences. Given the wide applicability of TALEs for programmable targeting of DNA sequences in vitro and in vivo, this provides broad perspectives for epigenetic research.