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)
  • 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)

Research articles

  • RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli–Pepper aptamer FRET pair
    Sampedro Vallina, McRae, Hansen, Boussebayle, Andersen* (bioRxiv 2022) Accepted in Nucleic Acid Research 2023

  • Structure, folding and flexibility of co-transcriptional RNA origami
    McRae, Rasmussen, Liu, Bøggild, Nguyen, Sampedro Vallina, Boesen, Pedersen, Ren, Geary, Andersen* Nature Nanotechnology 2023
  • An RNA Paranemic Crossover Triangle as A 3D Module for Cotranscriptional Nanoassembly
    Sampedro Vallina, McRae, Geary, Andersen* Small 2022
  • Utilizing RNA origami scaffolds in Saccharomyces cerevisiae for dCas9-mediated transcriptional control 
    Pothoulakis, Nguyen, Andersen* Nucleic Acid Research 2022
  • Synthetic Translational Regulation by Protein-Binding RNA Origami Scaffolds 
    Nguyen, Pothoulakis, Andersen* ACS Syn Bio 2022
  • RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds
    Geary, Grossi, McRae, Rothemund* & Andersen* Nature Chemistry 2021 (free SharedIt link)
  • Multivalent Aptamer‐Functionalized Single‐Strand RNA Origami as Effective, Target‐Specific Anticoagulants with Corresponding Reversal Agents
    Krissanaprasit, Key, Froehlich, Pontula, Mihalko, Dupont, Andersen, Kjems, Brown & LaBean Adv. Healthcare Mater. 2021
  • Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET
    Jeng, Trachman, Weissenboek, Troung, Link, Jepsen, Knutson, Andersen, Ferré-D'Amaré & Unrau RNA 2021
  • Branched Kissing Loops for the Construction of Diverse RNA Homooligomeric Nanostructures
    Liu, Geary, Chen, Shao, Li, Mao, Andersen, Piccirilli, Rothemund & Weizmann, Nature Chemistry 2020
  • Out-of-Plane Aptamer Functionalization of RNA Three-Helix Tiles
    Chopra, Sagredo, Grossi, Andersen, Simmel, Nanomaterials 2019

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

New paper: Cryo-EM reveals RNA origami structures

In Focus - News type

Paper published in Nature Nanotechnology on Cryo-EM of RNA origami structures. Amazing work by Ewan McRae and the rest of the team from Aarhus and…

Research paper: New tensegrity triangle motif for RNA origami

- Publication

Great collaborative work by Néstor, Ewan and Cody to develop a novel RNA motif for 3D nano construction using cryo-EM published in Small.

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…

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…

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.

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Revised 23.03.2023
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Ebbe Sloth Andersen