illumina-based deep sequencing data  (Illumina Inc)

Journal: Nucleic Acids Research

Article Title: High-throughput methods enabling random duplications, deletions, or nucleotide-constrained mutagenesis of entire DNA motifs

doi: 10.1093/nar/gkag236

Figure Lengend Snippet: RADDIM creates random duplications or deletions at one random position within a circular DNA molecule. ( A ) Illustration of the RADDIM workflow when starting from a plasmid template. Illustration created with BioRender.com . ( B ) An ExoChase-treated pUC19 plasmid (Fig. ) containing a CcdB toxin gene was nicked on the forward DNA-strand by the site-specific nickase Nt.BbvCI. The resulting double-nicked plasmids were incubated with Bst DNAP, with or without either the 5′–3′ single-strand-specific RecJ exonuclease, or the 3′–5′ single-strand-specific Thermolabile Exonuclease I, to determine if single-strand exonucleases could remove unwanted DNA-amplifications during a convergent nick-translation reaction. ( C ) Characterization of the DNA-ends that were created by a convergent nick-translation reaction using Bst DNAP and either RecJ or Thermolabile Exo I (Fig. ). ConNickTra linearized plasmids were purified and T7 DNAP was used to repair all DNA-ends. Next, T4 DNA ligase was used to re-circularize the linear plasmids, which were transformed into CcdB-sensitive E. coli cells. This selected for plasmids with a mutation in the ccdB toxin gene. The ccdB gene of 40 successfully sequenced plasmids from the RecJ library ( n = 40), and 39 successfully sequenced plasmids from the Thermolabile Exo I library ( n = 39) were sequenced by single-colony Sanger sequencing. ( D ) A synthetic 196 bp dsDNA fragment was incubated together with Bst DNAP alone, and/or Thermolabile Exo I, for 3 h with or without 1 mM MnCl 2 , to evaluate if manganese could reprogram the Bst DNAP and/or ExoI to degrade the ends of linear DNA molecules. ( E ) A pUC19 plasmid containing a CcdB toxin gene was randomly linearized by a ConNickTra reaction using Bst DNAP and ExoI, followed by an addition of 1 mM MnCl 2 for 10–30 min. After a T7 DNAP-mediated DNA end-repair, and a T4 DNA ligase-mediated re-circularization, plasmids were transformed into CcdB-sensitive E. coli cells. ( F ) The ccdB gene of 25 successfully sequenced plasmids from the 10 min library ( n = 25), 21 plasmids from the 20 min library ( n = 21), and 22 successfully sequenced plasmids from the 30 min library ( n = 22) were analyzed by single-colony Sanger sequencing.

Article Snippet: The RADDIM PacBio Revio deep sequencing data analysis and the Python scripts used to calculate the theoretical mutational landscapes possible with NSM are available from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) GitHub for this project ( https://github.com/biosustain/raddim ) and on Zenodo ( https://doi.org/10.5281/zenodo.18863538 ).

Techniques: Plasmid Preparation, Incubation, Nick Translation, Purification, Transformation Assay, Mutagenesis, Sequencing

Journal: Nucleic Acids Research

Article Title: High-throughput methods enabling random duplications, deletions, or nucleotide-constrained mutagenesis of entire DNA motifs

doi: 10.1093/nar/gkag236

Figure Lengend Snippet: RADDIM allows for in-frame and multi-residue InDels enabling functional protein structure modifications. ( A ) Illustration of an alternative RADDIM workflow to insert random DNA sequences into a RADDIM library by ligating a random DNA sequence oligo library to ConNickTra linearized plasmids, followed by a T7 DNAP-mediated DNA-end-repair/fill-in. Illustration created with BioRender.com . ( B ) Representative β-lactamase compensatory mutations able to restore phenotypic ampicillin resistance of the enzymatically inactivated (A40P and R41W) TEM-1 protein, superimposed onto the wild-type TEM-1 protein structure (PDB: 1ZG4). Red spheres = original inactivating mutations (A40P and R41W), Green spheres = compensatory AA substitutions. Purple marking = site of multi-residue compensatory deletion. Brown marking = site of multi-residue compensatory insertions.

Article Snippet: The RADDIM PacBio Revio deep sequencing data analysis and the Python scripts used to calculate the theoretical mutational landscapes possible with NSM are available from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) GitHub for this project ( https://github.com/biosustain/raddim ) and on Zenodo ( https://doi.org/10.5281/zenodo.18863538 ).

Techniques: Residue, Functional Assay, Sequencing

Journal: Nucleic Acids Research

Article Title: High-throughput methods enabling random duplications, deletions, or nucleotide-constrained mutagenesis of entire DNA motifs

doi: 10.1093/nar/gkag236

Figure Lengend Snippet: Deep sequencing confirms the diversity of RADDIM-generated InDel libraries. ( A ) Size distribution of insertions and deletions across a RADDIM plasmid library and the location of all variants (insertions and deletions) that are 1 nt and >1 nt in length. InDels are shown by their start position in the 5′–3′ direction in the plasmid sequence. Positive values represent insertions and negative values represent deletions. CAT = chloramphenicol acetyltransferase, tCYC1 = transcriptional terminator of iso-1-cytochrome c from S. cerevisiae , ori = pUC19 origin-of-replication, BLA* = inactivated (A40P and R41W) β-lactamase (TEM-1), CcdB = bacterial DNA gyrase toxin, CcdA* = inactivated cognate immunity protein of CcdB. ( B ) Illustration of the plasmid linearization mechanisms attained by combining the ExoChase and ConNickTra methods, enabling random and singular double-stranded DNA-breaks to be enriched within only one half of a plasmid molecule, down-stream of the site-specific DNA-nick. Illustration created with BioRender.com . ( C ) Quantification of all identified deletions ranging from 1 to 30 nt in length. ( D ) Quantification of all identified insertions ranging from 1 to 30 nt in length. ( E ) The number of identified mismatches for all insertions ranging from 2 to 30 nt in length.

Article Snippet: The RADDIM PacBio Revio deep sequencing data analysis and the Python scripts used to calculate the theoretical mutational landscapes possible with NSM are available from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) GitHub for this project ( https://github.com/biosustain/raddim ) and on Zenodo ( https://doi.org/10.5281/zenodo.18863538 ).

Techniques: Sequencing, Generated, Plasmid Preparation

Journal: Nucleic Acids Research

Article Title: High-throughput methods enabling random duplications, deletions, or nucleotide-constrained mutagenesis of entire DNA motifs

doi: 10.1093/nar/gkag236

Figure Lengend Snippet: RADDIM enables a random duplication or deletion of entire regulatory DNA motifs. ( A ) Illustration of the last steps in the RADDIM workflow when starting from a linear PCR-product (Fig. ). Illustration created with BioRender.com . Relative mNeonGreen fluorescent protein expression by S. cerevisiae cells transformed with RADDIM-mutated ( B ) pACT1 ( n = 90) or ( C ) pTEF1 promoter variants ( n = 86) following a FACS of top 1% of fluorescent cells. ( D ) Relative mNeonGreen fluorescent protein expression by reconstituted pACT1 and pTEF1 promoter variants ( n = 3). Statistical significance was calculated by two-way ANOVA with ns: P > 0.05, *: P ≤ 0.05, **: P ≤ 0.005, ***: P ≤ 0.0005, and ****: P ≤ 0.0001. ( E) Relative mNeonGreen fluorescent protein expression by wild-type pACT1 and pTEF1 promoters ( n = 3). Statistical significance was calculated by unpaired t -test with ns: P > 0.05 and *: P ≤ 0.0001.

Article Snippet: The RADDIM PacBio Revio deep sequencing data analysis and the Python scripts used to calculate the theoretical mutational landscapes possible with NSM are available from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) GitHub for this project ( https://github.com/biosustain/raddim ) and on Zenodo ( https://doi.org/10.5281/zenodo.18863538 ).

Techniques: Expressing, Transformation Assay

Journal: bioRxiv

Article Title: Functional and structural characterization of a combination of pan-sarbecovirus antibodies with potent antiviral activity

doi: 10.1101/2025.03.30.646023

Figure Lengend Snippet: (A) Cryo-EM density map of PRO-37587 Fab bound to SARS-CoV-2 Omicron BA.1 spike trimer. Spike chains (S chain A, B or C) are colored either gray, cyan, or green. PRO-37587 Fab heavy (HC) and light (LC) chains are colored brown and beige, respectively. (B) Molecular model of PRO-37587 Fab bound to a single SARS-CoV-2 Omicron BA.1 RBD. PRO-37587 Fab backbone is depicted as cartoon with colors as shown in (A). SARS-CoV-2 RBD is depicted with a surface representation, with contacts colored red, non-contacts colored cyan, and glycans colored orange. Contacting residues on the RBD are highlighted. (C) Comparison of contacting residues for PRO-37587 Fab (PDB: 9NFT, left) and reference molecule S2X259 Fab (PDB: 7RAL, right). Backbone is depicted as a transparent cartoon and contacts on the Fabs are shown as sticks. Mutational differences between PRO-37587 and S2X259 Fabs that make contacts at the interface are highlighted. SARS-CoV-2 RBD is colored as in (B). (D) SARS-CoV-2 Omicron BA.1 RBD contacts (left) contrasted against sequence conservation (right). Contacts are highlighted with text and are colored as in (B). Sequence conservation is measured as the positional sequence entropy (in bits) of 18 different SARS-CoV-2 variants, including Omicron lineages (SARS-CoV-2 WIV04, D614G, Delta, Omicron BA.1, BA.2, BA.4, BA.5, JN.1, XBB.1.1, LB.1, XBB.1.5, EG.5.1, BQ.1.1, KP.2, XBB.1.16.1, BA.2.86, KP.3 and KP.3.1.1). A higher entropy (red) indicates a larger variation of mutations at that position, and a lower entropy (cyan) indicates less variation. (E) Sequence population of SARS-CoV-2 RBD contacting residues, as measured across the variants used in (D). (F) From left to right, model of SARS-CoV-2 Omicron BA.1 spike with PRO-37587 Fabs bound to all three RBDs, a close up of PRO-37587 Fab bound to SARS-CoV-2 Omicron BA.1 RBD with an overlay of SARS-CoV-2 pre-Omicron RBD (PDB: 7RAL), and a close-up of the altered helix conformation observed in our structure and previously reported. Molecules are colored as in (B), with SARS-CoV-2 pre-Omicron RBD reference colored orange.

Article Snippet: Illumina-based deep sequencing data from the resistance passaging experiments are available from the NCBI Sequence Read Archive (SRA), BioProject: PRJNA1234183, BioSample Accession Numbers: SAMN47134171-SAMN47134194.

Techniques: Cryo-EM Sample Prep, Comparison, Sequencing

Journal: bioRxiv

Article Title: Functional and structural characterization of a combination of pan-sarbecovirus antibodies with potent antiviral activity

doi: 10.1101/2025.03.30.646023

Figure Lengend Snippet: Combination of GB-0669 and PRO-37587 increases barrier of resistance to SARS-CoV-2 Omicron BA.1 live virus escape. GB-0669 and PRO-37587 were tested in vitro as single agents and combination with SARS-CoV-2 Omicron BA.1 live virus for 10 passages. (A) Table indicating passage number (reported as P x , with x being the passage number) and associated mutations that resulted in the virus partially or completely escaping neutralizing activity of the mAbs. Mutation coordinates are relative to the SARS-CoV-2 Omicron BA.1 spike sequence. Complete and partial escape were determined by cytopathic effect (CPE) at each passage. CPE observed at an antibody concentration of 10 µg/ml or above was considered complete escape (indicated with red), while CPE observed at antibody concentrations between 1-10 µg/ml was considered partial escape (indicated as yellow). CPE observed at antibody concentrations < 1 µg/ml, or no CPE, was considered no escape (indicated as gray). (B) Table reporting EC50 (µg/ml) values of GB-0669 and PRO-37587 as single agent and in combination (GB-0669 + PRO-37587) against resistance passaged viruses harvested after emergence of resistance for GB-0669 and PRO-37587 as single agents (respectively at P3 [GB-0669 P3 virus] and P10 [PRO-37587 P10 virus]) or at P10 for the GB-0669 + PRO-37587 combination (GB-0669 + PRO-37587 P10 virus). Viruses passaged with no antibodies and harvested at P3 (untreated P3 virus) and P10 (untreated P10 virus) were used as controls. (C) Table reporting relative frequencies of mutations identified in the escape experiment outlined in (A) among publicly available SARS-CoV-2 genomes representative of the indicated time periods (March [Mar] 2023 - Mar 2024, or January [Jan] 2020 - Mar 2024). Mutation coordinates are referenced relative to the SARS-CoV-2 Omicron BA.1 spike protein. (D) Replication kinetics (TCID50/ml) of the PRO-37587 P10 virus and the respective control (untreated P10 virus). Results are shown as mean ± SD (representative of one experiment, two technical replicates). ** indicates p ≤ 0.01 when comparing PRO-37587 P10 virus and untreated P10 virus across the same timepoints.

Article Snippet: Illumina-based deep sequencing data from the resistance passaging experiments are available from the NCBI Sequence Read Archive (SRA), BioProject: PRJNA1234183, BioSample Accession Numbers: SAMN47134171-SAMN47134194.

Techniques: Virus, In Vitro, Activity Assay, Mutagenesis, Sequencing, Concentration Assay, Control