About

Burckhard Seelig, PhD, is a professor with a background in biochemistry from Freie Universität Berlin. His research focuses on implementing Darwinian molecular evolution in a test tube to generate novel proteins for applications in synthetic biology and biomedicine. He studies the origin and evolution of functional proteins and investigates the history of the genetic code. His lab generates de novo proteins with custom properties through in vitro and in vivo selection and evolution, analyzing these proteins to elucidate fundamental principles of protein biochemistry and the origins of protein-based life.

Research topics

• Computer Science
• Biology
• Computational biology
• Materials science
• Algorithm
• Genetics
• Biochemistry
• Combinatorics
• Cell biology
• Chemistry
• Physics
• Mathematics

Selected publications

• BPS2026 – Functional characterization of de novo, primordial-like proteins

  Biophysical Journal · 2026-02-01

  articleSenior author
  PublisherDOI

• EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids

  Journal of Molecular Evolution · 2025-04-01

  letterOpen access

  In vitro evolution is a powerful technique for identifying functional nucleic acids and peptides, but the analysis of the resulting high-throughput sequencing data poses significant challenges, particularly in peptide selections. Existing bioinformatics tools often lack the specificity needed for this task, leaving researchers to navigate complex datasets with inadequate resources. To address these challenges, we present EasyDIVER + , an enhanced pipeline building on the foundation of the original EasyDIVER tool, which was designed for pre-processing sequencing data. EasyDIVER + not only processes raw, paired-end, demultiplexed Illumina read files but also introduces advanced analytical capabilities, including the calculation of enrichment values for each unique sequence across consecutive selection rounds. Furthermore, EasyDIVER + offers a highly flexible and customizable visualization platform, enabling detailed graphical representations of sequence metrics. These new features mark a significant advance in bioinformatics for peptide and protein data, providing researchers with intuitive tools for comprehensive data analysis and interpretation.

  PublisherOA PDFDOI

• Intellectual frameworks to understand complex biochemical systems at the origin of life

  Nature Chemistry · 2025-01-01 · 10 citations

  article1st authorCorresponding
  PublisherDOI

• Comprehensive protease specificity profiling

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-11-07 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Protease enzymes are of great importance in medicine, industry, and as research tools. Despite the crucial need for detailed knowledge of their proteolytic cleavage specificity, many proteases are poorly characterized. We present a method for fully characterizing the cleavage specificity of proteases through the comprehensive profiling of all possible permutations of octamer peptide substrates in a single experiment. The powerful combination of in vitro selection with high-throughput sequencing, mass spectrometry, and automated motif mining enabled the screening of mixtures of >10 12 peptides. We developed freely available software that easily integrates the massive amounts of cleavage data into user-friendly specificity information. We applied this method to three different proteases that had either narrow (factor Xa) or broad specificity (ADAM17 and streptopain). The resulting specificity maps revealed motifs that corroborate canonical known cleavage sites, yet step further into extended spectrum preferences and yield insights into the function of broad specificity proteases.

  PublisherOA PDFDOI

• mRNA Display

  Encyclopedia of Astrobiology · 2023-01-01

  book-chapter1st authorCorresponding
  PublisherDOI

• Nanodroplet-based reagent delivery into water-in-fluorinated-oil droplets

  ChemRxiv · 2023-04-25

  preprintOpen accessSenior author

  In vitro compartmentalization is a technique for generating water-in-oil microdroplets to establish the genotype (DNA information)-phenotype (biomolecule function) linkage required by many biological applications. Recently, fluorinated oils have become more widely used for making microdroplets due to their better biocompatibility. However, it is difficult to perform multi-step reactions requiring the addition of reagents in water-in-fluorinated-oil microdroplets. On-chip droplet manipulation is usually used for such purposes, but it may encounter some technical issues of low throughput or time delay of reagent delivery into different microdroplets. Hence, we evaluated the feasibility of employing a nanodroplet-based approach to address these issues using copper ions and a middle-size peptide (2 kDa) molecule.

  PublisherOA PDFDOI

• Nanodroplet-based reagent delivery into water-in-fluorinated-oil droplets

  ChemRxiv · 2023-04-26 · 1 citations

  preprintOpen accessSenior author

  In vitro compartmentalization is a technique for generating water-in-oil microdroplets to establish the genotype (DNA information)-phenotype (biomolecule function) linkage required by many biological applications. Recently, fluorinated oils have become more widely used for making microdroplets due to their better biocompatibility. However, it is difficult to perform multi-step reactions requiring the addition of reagents in water-in-fluorinated-oil microdroplets. On-chip droplet manipulation is usually used for such purposes, but it may encounter some technical issues of low throughput or time delay of reagent delivery into different microdroplets. Hence, to address the above issues, we evaluated the feasibility of employing a nanodroplets-based approach for the delivery of copper ions and peptide molecules of middle-size (2 kDa).

  PublisherOA PDFDOI

• Facile immobilization of pyridoxal 5′-phosphate using p-diazobenzoyl-derivatized Sepharose 4B

  Results in Chemistry · 2023-07-19

  articleOpen accessSenior authorCorresponding

  Pyridoxal 5′-phosphate (PLP) is a ubiquitous and versatile cofactor utilized by numerous enzymes involved in amino acid biosynthetic pathways. Immobilized PLP is a valuable tool to isolate unknown PLP-dependent enzymes in nature or to perform in vitro selection or directed evolution on existing or de novo PLP-dependent enzymes. The C-6 position is preferred for covalent immobilization of PLP because it maintains all important functional groups in their native, unmodified form. Previously reported diazonium derivatization methods for C-6 immobilization utilized an azide linker compound that is hazardous and not readily available. Here we report a safer and more accessible method to synthesize p-diazobenzoyl-derivatized Sepharose 4B using the N-hydroxysuccinimide (NHS) ester chemistry. The derivative was used to immobilize PLP, and the resulting C-6 immobilized PLP had a loading of ∼ 2.6 µmol PLP per mL of resin, comparable to commercially available products of other immobilized cofactors.

  PublisherDOI

• Cell Survival Enabled by Leakage of a Labile Metabolic Intermediate

  Molecular Biology and Evolution · 2023-02-09 · 4 citations

  articleOpen access

  Many metabolites are generated in one step of a biochemical pathway and consumed in a subsequent step. Such metabolic intermediates are often reactive molecules which, if allowed to freely diffuse in the intracellular milieu, could lead to undesirable side reactions and even become toxic to the cell. Therefore, metabolic intermediates are often protected as protein-bound species and directly transferred between enzyme active sites in multi-functional enzymes, multi-enzyme complexes, and metabolons. Sequestration of reactive metabolic intermediates thus contributes to metabolic efficiency. It is not known, however, whether this evolutionary adaptation can be relaxed in response to challenges to organismal survival. Here, we report evolutionary repair experiments on Escherichia coli cells in which an enzyme crucial for the biosynthesis of proline has been deleted. The deletion makes cells unable to grow in a culture medium lacking proline. Remarkably, however, cell growth is efficiently restored by many single mutations (12 at least) in the gene of glutamine synthetase. The mutations cause the leakage to the intracellular milieu of a highly reactive phosphorylated intermediate common to the biosynthetic pathways of glutamine and proline. This intermediate is generally assumed to exist only as a protein-bound species. Nevertheless, its diffusion upon mutation-induced leakage enables a new route to proline biosynthesis. Our results support that leakage of sequestered metabolic intermediates can readily occur and contribute to organismal adaptation in some scenarios. Enhanced availability of reactive molecules may enable the generation of new biochemical pathways and the potential of mutation-induced leakage in metabolic engineering is noted.

  PublisherDOI

• Nanodroplet-Based Reagent Delivery into Water-in-Fluorinated-Oil Droplets

  Biosensors · 2023-07-28 · 3 citations

  articleOpen accessSenior authorCorresponding

  In vitro compartmentalization (IVC) is a technique for generating water-in-oil microdroplets to establish the genotype (DNA information)-phenotype (biomolecule function) linkage required by many biological applications. Recently, fluorinated oils have become more widely used for making microdroplets due to their better biocompatibility. However, it is difficult to perform multi-step reactions requiring the addition of reagents in water-in-fluorinated-oil microdroplets. On-chip droplet manipulation is usually used for such purposes, but it may encounter some technical issues such as low throughput or time delay of reagent delivery into different microdroplets. Hence, to overcome the above issues, we demonstrated a nanodroplet-based approach for the delivery of copper ions and middle-sized peptide molecules (human p53 peptide, 2 kDa). We confirmed the ion delivery by microscopic inspection of crystal formation inside the microdroplet, and confirmed the peptide delivery using a fluorescent immunosensor. We believe that this nanodroplet-based delivery method is a promising approach to achieving precise control for a broad range of fluorocarbon IVC-based biological applications, including molecular evolution, cell factory engineering, digital nucleic acid detection, or drug screening.

  PublisherOA PDFDOI

Recent grants

• Developing a synthetic evolution approach to create de novo enzymes

  NIH · $286k · 2014–2019

• Developing a synthetic evolution approach to create de novo enzymes

  NIH · $858k · 2014–2018

• Developing methods to engineer therapeutic proteases

  NIH · $401k · 2015–2018

Frequent coauthors

• Matilda Newton

  University of Colorado Boulder

  37 shared

• Misha Golynskiy

  University of Minnesota

  29 shared

• Dušan Petrović

  AstraZeneca (Sweden)

  16 shared

• Adrian Romero‐Rivera

  University of Girona

  14 shared

• Shina Caroline Lynn Kamerlin

  Uppsala University

  14 shared

• Aleardo Morelli

  University of Minnesota

  14 shared

• John C. Haugner

  Bristol-Myers Squibb (Germany)

  14 shared

• J.A. Gavira

  Instituto Andaluz de Ciencias de la Tierra

  12 shared

Awards & honors

• Dr. James E. Rubin Medical Memorial Award
• Graduating Medical Student Research Award
• Veneziale-Steer Award
• Dr. Marvin and Hadassah Bacaner Research Awards
• Schmidt Steer Award