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. On this page you will find descriptions of our latest research. For more extensive publication lists please see our CVs.

Cryo-EM structure and functional landscape of an RNA polymerase ribozyme

McRae, Wan, Kristoffersen, Hansen, Gianni, Gallego, Curran, Attwater, Holliger*, Andersen* 

In collaboration with the Holliger lab we here describe the first structure of an RNA polymerase ribozyme and determine its fitness landscape. We obtain the 5-Å structure of the apoenzyme and suggest a model for the holoenzyme. Model and map: 8T2P, EMD-40984 (not released yet).

Accepted in PNAS 2023 - Preprint (Aug 3, 2023) - Preprint (Aug 29, 2022) - Preprint (Aug 23, 2022).

Enzymatic assembly of small synthetic genes with repetitive elements

Nguyen*, Gobry, Sampedro Vallina, Pothoulakis, Andersen*

We have developed a method to assemble synthetic genes with repetitive elements, which can be used to construct RNA origamis with multiple aptamers on the same structure. We were forced to develop such a technique because many gene synthesis companies does not allow synthesis of repetitive elements.

In review - Preprint (Nov 23, 2022).

Structure, folding and flexibility of co-transcriptional RNA origami

McRae, Rasmussen, Liu, Bøggild, Nguyen, Sampedro Vallina, Boesen, Pedersen, Ren, Geary, Andersen*

We reveal the solution structure of RNA origami by cryo-EM and find important details about kissing loops and crossovers. In addition, we discover an interesting folding trap and demonstrate a nanosatellite shape. Read our press release. Structural data: 7PTQ - 7PTS - 7QDU - 7PTK - 7PTL.

Nature Nanotechnology (Feb 27, 2023) - Preprint (Sep 1, 2022).

Preprints

  • An RNA origami robot that traps and releases a fluorescent aptamer
    Sampedro Vallina, McRae, Geary, Andersen*
    bioRxiv 2023
  • Tertiary structure of single-instant RNA molecule reveals folding landscape
    Liu, McRae, Zhang, Geary, Andersen*, Ren*
    bioRxiv 2023 

  • Enzymatic assembly of small synthetic genes with repetitive elements
    Nguyen*, Gobry, Sampedro Vallina, Pothoulakis, Andersen*
    bioRxiv 2022

Research articles

  • Cryo-EM structure and functional landscape of an RNA polymerase ribozyme
    McRae, Wan, Kristoffersen, Hansen, Gianni, Gallego, Curran, Attwater, Holliger*, Andersen* 
    Accepted in PNAS 2023 - Preprint (Aug 3, 2023)

  • RNA target highlights in CASP15: Evaluation of predicted models by structure providers
    Kretsch, Andersen, Bujnicki, Chiu, Das, Luo, Masquida, McRae, Schroeder, Su, Wedekind, Xu, Zhang, Zheludev, Moult, Kryshtafovych 
    PROTEINS: Structure, Function and Bioinformatics 2023
    Preprint: AUthorea

  • RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli–Pepper aptamer FRET pair
    Sampedro Vallina, McRae, Hansen, Boussebayle, Andersen* 
    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 (free SharedIt link)
  • 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

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: CASP15 RNA contributors

- Publication

We provided RNA structures to the CASP15 competition and contributed to a paper analysing the results.

Book chapter: Design of RNA Origami as Protein Scaffolds and Biosensors

- Publication

Nestor publish a tutorial on RNA origami design as part of a methods book edited by Julian Valero Moreno.

Research paper: RNA origami as cryo-EM tool for aptamers

- Publication

We introduce RNA origami as a tool of cryo-EM characterization of aptamers and their ligand binding. As an example we introduce a new apta-FRET pair:…

Research paper: Cryo-EM reveals RNA origami structures

- Publication

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.

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Revised 07.12.2023
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Ebbe Sloth Andersen