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: 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…

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…

Research article: Multifluorophore DNA Origami Beacon as a Biosensing Platform

3D model of a Multifluorophore DNA Origami Sensor.
- Publication

Denis Selnihhin has published his work on a Multifluorophore DNA Origami Sensor in ACS Nano.

Research article: Development of a genetically encodable FRET system using fluorescent RNA aptamers

- Publication

Mette D. E. Jepsen and Steffen M. Sparvath have published their work on an RNA aptamer-based FRET system in Nature Communications.

Review article: Enzyme-functionalized DNA nanostructures as tools for organizing and controlling enzymatic reactions

A 3D model of a DNA origami with an encapsulated enzyme.
- Publication

Guido Grossi publishes a review in MRS Bulletin on DNA nanostructures and their use in organizing and controlling enzymes.

Review article: RNA nanotechnology – The knots and folds of RNA nanoparticle engineering

- Publication

Ebbe Sloth Andersen publishes a review in MRS Bulletin on the prospects and difficulties of engineering RNA nanostructures.

Research article: Control of enzyme reactions by a reconfigurable DNA nanovault

- Publication

Guido Grossi paper on the construction of a DNA nanovault to control enzyme activity is finally published in Nature Communications. Congratulations…

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Revised 07.12.2023
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Ebbe Sloth Andersen