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)
  • Tertiary structure of single-instant RNA molecule reveals folding landscape
    Liu, McRae, Zhang, Geary, Andersen*, Ren* (bioRxiv)

  • An RNA origami robot that traps and releases a fluorescent aptamer
    Sampedro Vallina, McRae, Geary, Andersen* (bioRxiv)

  • 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 (AUthorea)

Research articles

  • 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 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…

Review article: A visual review of Streptococcus pneumoniae

- Publication

Ditte Høyer Engholm publishes her visual review of Streptococcus pneumoniae in FEMS Microbiology Reviews.

Book chapter: Visualizing the bacterium Streptococcus pneumoniae

- Publication

Ditte Høyer Engholm has published an article in the book "The Aesthetics of Scientific Data Representation - More than Pretty Pictures” edited by…

Research article: Construction of a Polyhedral DNA 12-Arm Junction for Self-Assembly of Wireframe DNA Lattices

- Publication

Ilenia Manuguerra published a work on ACS Nano about design, assembly and characterization of a new DNA motif for self-assembly of DNA wireframe…

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Revised 26.05.2023
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Ebbe Sloth Andersen