Andersen Lab for Biomolecular Design

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Publications

The main product of our research effort is the presentation of the results in journal articles. In these pages you will find lists of our publications.

Preprints

  • Enzymatic assembly of small synthetic genes with repetitive elements
    Nguyen*, Gobry, Sampedro Vallina, Pothoulakis, Andersen* (bioRxiv)
  • An RNA paranemic crossover triangle as a 3D module for cotranscriptional nanoassembly
    Sampedro Vallina, McRae, Geary, Andersen* (accepted in Small)
  • Cryo-EM structure and functional landscape of an RNA polymerase ribozyme
    McRae, Wan, Kristoffersen, Hansen, Gianni, Gallego, Curran, Attwater, Holliger*, Andersen* (bioRxiv 2022) (ResearchSquare 2022)

  • RNA origami scaffolds as a cryo-EM tool for investigating aptamer-ligand binding of a Broccoli-Pepper FRET pair 
    Sampedro Vallina, McRae, Hansen, Boussebayle, Andersen* (bioRxiv 2022)

  • High-resolution structures and conformational dynamics of RNA origami during folding
    McRae, Rasmussen, Liu, Bøggild, Nguyen, Sampedro Vallina, Boesen, Pedersen, Ren, Geary, Andersen* (ResearchSquare 2022) (accepted in Nature Nanotechnology)

Research articles

Review articles

Research commentary

Book chapters

  • Design and production of RNA origami as protein scaffolds and biosensors
    Vallina, Geary, Jepsen, Andersen, Methods in Molecular Biology (in press 2022)

  • Computer-Aided Design of RNA Origami Structures
    Sparvath, Geary & Andersen, Methods in Molecular Biology 2017

PhD theses

  • Taking RNA nanotechnology in vivo
    Ane Andreassen, 2018
  • Visual Review of the Human Pathogen Streptococcus pneumoniae
    Ditte Høyer Engholm, 2017
  • RNA Origami — Developing Cotranscriptionally Folded RNA Nanostructures for in vivo Applications
    Steffen Lynge Sparvath, 2017
  • DNA Nanostructures to Control Enzymatic Activities
    Guido Grossi, 2016
  • Development of DNA Origami Single Molecule Biosensor
    Denis Selnihhin, 2015

Master theses

  • (Title will be added later)
    Michael Nguyen (Part A - progress report), 2018
  • (Title will be added later)
    Mads Jeppesen, 2018
  • Stability and Sensing Studies using Co-transcriptional single stranded RNA Origami in Escherichia coli
    Ane Helene Langvad Andreassen (Part A - progress report), 2017
  • E. coli as a Biosensor using Fluorescent RNA Aptamers for in vivo Detection
    Maria Færch Jensen, 2017
  • Aptamer-based detection of small molecules for DNA origami nanotechnology
    Caroline Filippa Langfeldt Knabe, 2016
  • A DNA Origami Nanostructure to Control Enzymatic Activities
    Guido Grossi (Part A - progress report), 2015
  • Programming Biosynthetic Pathways using RNA Origami Structures
    Ane Helene Langvad Andreassen, 2015
  • RNA Origami Designs: Developing Novel 3D RNA Structures with Multiple Functionalities
    Steffen Lynge Sparvath (Part A - progress report), 2014

Bachelor theses

  • (Title will be added later)
    Jakob Smidt, 2018
  • A Broad Range RNA Biosensor for miRNA Detection
    Tenna Vesterman Henriksen, 2016
  • A Biosensor Based on Rolling Circle Transcription
    Mads Jeppesen, 2016
  • (Title will be added later)
    Peter Loof Møller, 2016
  • (Title will be added later)
    Maria Færch Jensen, 2014
  • (Title will be added later)
    Christina Moeslund Madsen, 2014
  • (Title will be added later)
    Leandro Andrés Escobar-Herrera, 2014
  • (Title will be added later)
    Trine Tamberg, 2014
  • Cellular Interfacing with Self-assembled Nucleic Acids
    Ane Helene Langvad Andreassen, 2013
  • (Title will be added later)
    Caroline Filippa Langfeldt Knabe, 2013
  • (Title will be added later)
    Minh Lon Lu, 2013
  • Self-Assembly of a Dynamic 3D RNA-DNA Origami Structure Characterized by FRET Studies
    Steffen Lynge Sparvath, 2011

Publication news

Research paper: Controlling transcriptional activation using RNA origami scaffolds

- News type

George's work on ''Utilizing RNA origami scaffolds in Saccharomyces cerevisiae for dCas9-mediated transcriptional control'' has been published in Nucleic Acid Research.

Research paper: Controlling gene expression with RNA origami scaffolds

In Focus - News type

Michael's work on "Synthetic Translational Regulation by Protein-Binding RNA Origami Scaffolds" has been published in ACS Synthetic Biology.

Research paper: RNA origami software and scaffolds

- Publication

Cody's paper published online in Nature Chemistry describing novel software and its use to create bigger and better scaffolds for proteins. Great contributions by Guido and Ewan and done in collaboration with Paul Rothemund. Free SharedIt link above.

Research paper: Enhanced RNA origami anticoagulant

- Publication

Together with our collaborators in the Thom LaBean lab we have published a new paper on enhanced RNA origami anticoagulants.

Research paper: Flexibility of RNA junctions

- Publication

We have published a paper with our collaborators on the application of apta-FRET for studying the flexibility of RNA junctions.

Research paper: Branched Kissing Loop motif

- Publication

We publish a new motif called the branched kissing loop (bKL) together with the Weizmann and Rothemund labs in Nature Chemistry.

Research paper: RNA Origami Anticoagulant

- Publication

Together with our collaborators in the Thom LaBean lab we have published a paper on the application of RNA origamis for control of blood clotting.

Research paper: Out-of-Plane Aptamer Functionalization of RNA Origami

- Publication

Together with the Simmel lab we published a study on functionalization of RNA origami structures.

Research article: Topological complexity of biomolecules

- Publication

We introduce genus trace and find that it encodes interesting physical and biological information about the three dimensional structural complexity of RNA and protein molecules.

Research article: An RNA origami octahedron with intrinsic siRNAs for potent gene knockdown

RNA octahedron with instrinsic siRNAs. (1) The enzyme Dicer binds the structure and (2) cleaves the siRNAs from the structure.
- Publication

Hans Christian Høiberg and Steffen M. Sparvath have published their work on an RNA origami with intrinsic siRNAs in Biotechnology Journal. The project started out as a contribution to the 2011 BIOMOD competition.

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Revised 24.11.2022
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Ebbe Sloth Andersen