Speeding up biomolecular interactions by molecular sledding

Numerous biological processes involve association of a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Similarly, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptide and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions

Author Correction: Accurate detection of circulating tumor DNA using nanopore consensus sequencing

The Data Availability statement in the original version of the paper reads: “The sequencing datasets generated during the current study are available upon request at EGA, under accession number EGAS00001003759”. However, as this data upload was not successful, the authors reuploaded the data under a different accession number and have amended the Data Availability statement to read “The sequencing datasets generated during the current study are available upon request at EGA, under accession number EGAS00001007090”. The original article has been corrected.</p

Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor. To detect lowly abundant ctDNA molecules based on somatic variants, extremely sensitive sequencing methods are required. Here, we describe a new technique, CyclomicsSeq, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule. Consensus calling of the DNA copies increased the base-calling accuracy ~60×, enabling accurate detection of TP53 mutations at frequencies down to 0.02%. We demonstrate that a TP53-specific CyclomicsSeq assay can be successfully used to monitor tumor burden during treatment for head-and-neck cancer patients. CyclomicsSeq can be applied to any genomic locus and offers an accurate diagnostic liquid biopsy approach that can be implemented in clinical workflows

Harnessing phages for supramolecular and materials chemistry

Het eerste gedeelte van de scriptie betreft het onderzoek naar de toepassing van phage display, om korte aptamers te selecteren voor zeer verschillende moleculen. Door deze techniek te gebruiken hebben we een peptide kunnen selecteren die de bateriele enzym dxs in-vitro verhinderd. Dit soort peptide realiseert een begin voor de ontwikkeling van nieuw soort antibiotica. Wederom, door de toepassing van phage display, hebben we een bibliotheek van circulaire peptides die CB8 tegengaan bekeken. Dit zijn macrocyclische moleculen met de bekende eigenschap dat ze complexen vormen met N-terminal aromatische aminozuren. Met dit onderzoek, laten we voor het eerst zien dat CB8 complexen kan vormen met cyclische peptiden. Naast phage display, benoemen we ook de toepassing van genetische gemodificeerde virus capsid als een veel beloofde bouwsteen voor liquid crystals. Hiernaast hebben we het major coat protein ook succesvol genetisch geengineerd (p8) van M13 voor de aanpassing van de chemisch-fysieke eigenschappen van het materiaal. Als laatst, melden we de resultaten van een uitgebreide bacteriële activiteitstest waaraan verschillende nieuwe aminoglycoside antibiotica zijn onderworpen. Deze zijn geproduceerd met verschillende benadering, waaronder de door ons ontwikkelde “aptameric protective groups” technologie

Methods for chemical synthesis of biologically active compounds using supramolecular protective groups and novel compounds obtainable Thereby

Title: Methods for chemical synthesis of biologically active compounds using supramolecular protective groups and novel compounds obtainable thereby. Abstract The invention relates to drug development and synthetic chemistry, in particular to the manufacture of biologically active compounds based on naturally occurring molecules. It also relates to novel biologically active compounds, for example aminoglycoside antibiotics, in a substantially pure regioisomeric form