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List of works by Mark Helm

2'-O-Methylation within Bacterial RNA Acts as Suppressor of TLR7/TLR8 Activation in Human Innate Immune Cells.

scientific article published on 20 March 2015

2'-O-methylation within prokaryotic and eukaryotic tRNA inhibits innate immune activation by endosomal Toll-like receptors but does not affect recognition of whole organisms

scientific article published on 24 April 2019

5-methylcytosine in RNA: detection, enzymatic formation and biological functions

scientific article

A Methyl Group Controls Conformational Equilibrium in Human Mitochondrial tRNALys

scientific article published on 17 October 2007

A Vastly Increased Chemical Variety of RNA Modifications Containing a Thioacetal Structure

scientific article published on 6 April 2018

A Watson-Crick base-pair-disrupting methyl group (m1A9) is sufficient for cloverleaf folding of human mitochondrial tRNALys.

scientific article published in October 1999

A modified dinucleotide motif specifies tRNA recognition by TLR7.

scientific article published on 22 July 2014

A modified guanosine phosphoramidite for click functionalization of RNA on the sugar edge

scientific article published on 01 November 2012

A monomer-to-trimer transition of the human mitochondrial transcription termination factor (mTERF) is associated with a loss of in vitro activity

scientific article

A multifunctional bioconjugate module for versatile photoaffinity labeling and click chemistry of RNA.

scientific article

A new mechanism for mtDNA pathogenesis: impairment of post-transcriptional maturation leads to severe depletion of mitochondrial tRNASer(UCN) caused by T7512C and G7497A point mutations

scientific article

A new nuclear function of the Entamoeba histolytica glycolytic enzyme enolase: the metabolic regulation of cytosine-5 methyltransferase 2 (Dnmt2) activity

scientific article

A post-labeling approach for the characterization and quantification of RNA modifications based on site-directed cleavage by DNAzymes.

scientific article

A tRNA half modulates translation as stress response in Trypanosoma brucei

scientific article published in Nature Communications

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders

scientific article

Absolute Quantification of Noncoding RNA by Microscale Thermophoresis

scientific article published on 02 May 2019

Absolute and relative quantification of RNA modifications via biosynthetic isotopomers.

scientific article published on 16 August 2014

Against Expectations: Unassisted RNA Adsorption onto Negatively Charged Lipid Bilayers

scientific article published on 31 October 2019

AlkAniline-Seq: profiling of m7G and m3C RNA modifications at single nucleotide resolution

scientific article published on 16 November 2018

AlkAniline‐Seq: Profiling of m 7 G and m 3 C RNA Modifications at Single Nucleotide Resolution

Alkyne-Functionalized Coumarin Compound for Analytic and Preparative 4-Thiouridine Labeling

scientific article

Allosterically activated Diels-Alder catalysis by a ribozyme

scientific article published in August 2005

Aminoacylation properties of pathology-related human mitochondrial tRNA(Lys) variants

scientific article

An epigenetic "extreme makeover": the methylation of flaviviral RNA (and beyond)

scientific article published on 23 December 2020

Analysis of RNA modifications by liquid chromatography–tandem mass spectrometry

scientific article published on 25 March 2016

Analysis of the Cellular Roles of MOCS3 Identifies a MOCS3-Independent Localization of NFS1 at the Tips of the Centrosome

scientific article published on 13 March 2019

Bioconjugation of Small Molecules to RNA Impedes Its Recognition by Toll-Like Receptor 7.

scientific article published on 24 March 2017

Cationic nanohydrogel particles as potential siRNA carriers for cellular delivery

scientific article

Characterization and selectivity of catalytic antibodies from human serum with RNase activity.

scientific article published on December 1998

Comprehensive DNA methylation analysis of the Aedes aegypti genome

scientific article (publication date: 2 November 2016)

CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles

scientific article published on 10 November 2016

Cytosine methylation of tRNA-Asp by DNMT2 has a role in translation of proteins containing poly-Asp sequences

scientific article published on 09 June 2015

DNA and RNA Pyrimidine Nucleobase Alkylation at the Carbon-5 Position.

scientific article published on January 2016

Detecting RNA modifications in the epitranscriptome: predict and validate

scientific article published on 20 February 2017

Detection of RNA modifications.

scientific article

Determination of enrichment factors for modified RNA in MeRIP experiments

Diastereoselectivity of 5-Methyluridine Osmylation Is Inverted inside an RNA Chain

scientific article published on 19 August 2016

Double methylation of tRNA-U54 to 2'-O-methylthymidine (Tm) synergistically decreases immune response by Toll-like receptor 7

Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor.

scientific article published on 9 October 2014

Dye selection for live cell imaging of intact siRNA.

scientific article published on January 2012

Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine

scientific article published on 30 September 2015

Editorial: RNA modifications - what to read first?

scientific article published on 10 August 2017

Effect of a quaternary pentamine on RNA stabilization and enzymatic methylation.

scientific article published in September 2009

Engineering of a DNA Polymerase for Direct m6 A Sequencing.

scientific article published on 8 November 2017

Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120.

scientific article

Expanding the chemical scope of RNA:methyltransferases to site-specific alkynylation of RNA for click labeling

scientific article published on 30 October 2010

FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA

scientific article published on 01 November 2019

FRET imaging of cells transfected with siRNA/liposome complexes

scientific article

Formation of a stalled early intermediate of pseudouridine synthesis monitored by real-time FRET.

scientific article published on 27 January 2010

Functional redundancy in tRNA dihydrouridylation

scientific article published in 2024

Functionalization of Liposomes with Hydrophilic Polymers Results in Macrophage Uptake Independent of the Protein Corona

scientific article published on 17 July 2019

GADD45a physically and functionally interacts with TET1

scientific article published on 3 November 2015

HITS-CLIP analysis of human ALKBH8 points towards its role in tRNA and noncoding RNA regulation

scientific article published on 17 January 2022

HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs

scientific article published in December 2022

Hakai is required for stabilization of core components of the m<sup>6</sup>A mRNA methylation machinery

scientific article published on 18 June 2021

High-Throughput Mapping of 2'-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol).

scientific article published on January 2017

High-throughput sequencing for 1-methyladenosine (m(1)A) mapping in RNA.

scientific article

Human DNMT2 methylates tRNA(Asp) molecules using a DNA methyltransferase-like catalytic mechanism

scientific journal article

Identification of an optimized 2'-O-methylated trinucleotide RNA motif inhibiting Toll-like receptors 7 and 8.

scientific article published on 02 June 2017

Identification of modifications in microbial, native tRNA that suppress immunostimulatory activity

scientific article published on 6 February 2012

Identification of the 3-amino-3-carboxypropyl (acp) transferase enzyme responsible for acp3U formation at position 47 in Escherichia coli tRNAs

scientific article published on 01 February 2020

Illumina-based RiboMethSeq approach for mapping of 2'-O-Me residues in RNA.

scientific article

In vitro tRNA methylation assay with the Entamoeba histolytica DNA and tRNA methyltransferase Dnmt2 (Ehmeth) enzyme

scientific article

In vivo down-regulation of mouse brain capillary P-glycoprotein: a preliminary investigation

scientific article published on 11 August 2009

Intermolecular 'cross-torque': the N4-cytosine propargyl residue is rotated to the 'CH'-edge as a result of Watson-Crick interaction

scientific article published on 30 April 2015

Isoleucylation properties of native human mitochondrial tRNAIle and tRNAIle transcripts. Implications for cardiomyopathy-related point mutations (4269, 4317) in the tRNAIle gene

scientific journal article

Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator.

scientific article

LC-MS Analysis of Methylated RNA

scientific article published on 01 January 2017

Limited antibody specificity compromises epitranscriptomic analyses

scientific article published on 11 December 2019

Live cell imaging of duplex siRNA intracellular trafficking

scientific article

Loss of anticodon wobble uridine modifications affects tRNA(Lys) function and protein levels in Saccharomyces cerevisiae

scientific article published on 6 March 2015

MODOMICS: a database of RNA modification pathways--2013 update

scientific article

MODOMICS: a database of RNA modification pathways. 2017 update

scientific article published on 2 November 2017

Manganese Ions Individually Alter the Reverse Transcription Signature of Modified Ribonucleosides

scientific article published on 18 August 2020

Mapping the tRNA binding site on the surface of human DNMT2 methyltransferase

scientific article published on 23 May 2012

Measuring single small molecule binding via rupture forces of a split aptamer.

scientific article

Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation.

scientific article published on 27 May 2016

Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

article

Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis

scientific article published on 7 March 2007

Modulation of Mitochondriotropic Properties of Cyanine Dyes by in Organello Copper-Free Click Reaction.

scientific article published on 13 July 2017

Molecular dysfunction associated with the human mitochondrial 3302A>G mutation in the MTTL1 (mt-tRNALeu(UUR)) gene

scientific article

Monitoring drug nanocarriers in human blood by near-infrared fluorescence correlation spectroscopy

scientific article published in Nature Communications

New Techniques to Assess In Vitro Release of siRNA from Nanoscale Polyplexes.

scientific article published on 9 December 2014

Next-Generation Sequencing-Based RiboMethSeq  Protocol for Analysis of tRNA 2'-O-Methylation

scientific article published on 9 February 2017

Nuclear control of cloverleaf structure of human mitochondrial tRNA(Lys).

scientific article published in March 2004

Optimizing splinted ligation of highly structured small RNAs.

scientific article published on 26 October 2005

Partial methylation at Am100 in 18S rRNA of baker's yeast reveals ribosome heterogeneity on the level of eukaryotic rRNA modification

scientific article

Phosphorylation of Elp1 by Hrr25 is required for elongator-dependent tRNA modification in yeast.

scientific article published in January 2015

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

scientific article published on 19 April 2018

Post-transcriptional nucleotide modification and alternative folding of RNA

scientific article

Post-transcriptional nucleotide modification and alternative folding of RNA.

scientific article published on 11 October 2007

Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland

scientific article

Preparation of small amounts of sterile siRNA-liposomes with high entrapping efficiency by dual asymmetric centrifugation (DAC).

scientific article published on 13 December 2008

Profiling of RNA modifications by multiplexed stable isotope labelling.

scientific article published on 24 February 2014

Pseudouridine: still mysterious, but never a fake (uridine)!

scientific article

RNA Modifications Modulate Activation of Innate Toll-Like Receptors

RNA Sex

scientific article published on 01 December 2003

RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis.

scientific article published on 12 August 2012

RNA intramolecular dynamics by single-molecule FRET.

scientific article

RNA mediated Toll-like receptor stimulation in health and disease

scientific article

RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage

scientific article

RNA nucleotide methylation ⬇️

scientific article published on March 23, 2011

RNase activity of a DNA minor groove binder with a minimalist catalytic motif from RNase A.

scientific article

Recognition of Specified RNA Modifications by the Innate Immune System

scientific article

Regulatory RNAs and beyond

scientific article

Related haloarchaeal pleomorphic viruses contain different genome types

scientific article published in July 2012

Sculpting an RNA Conformational Energy Landscape by a Methyl Group Modification—A Single-Molecule FRET Study

scientific article published on 01 January 2008

Search for characteristic structural features of mammalian mitochondrial tRNAs.

scientific article

Search for differences in post-transcriptional modification patterns of mitochondrial DNA-encoded wild-type and mutant human tRNALys and tRNALeu(UUR).

scientific article published on February 1999

Sequences Outside Recognition Sets Are Not Neutral for tRNA Aminoacylation

scientific article published on 01 May 1998

Single-Molecule FRET Studies of Counterion Effects on the Free Energy Landscape of Human Mitochondrial Lysine tRNA

scientific article published on 24 March 2011

Single-molecule FRET reveals a cooperative effect of two methyl group modifications in the folding of human mitochondrial tRNA(Lys).

scientific article published in July 2011

Single-molecule Förster resonance energy transfer studies of RNA structure, dynamics and function

scientific article

Stability of Alkyl Chain-Mediated Lipid Anchoring in Liposomal Membranes

scientific article published on 29 September 2020

Stability of a Split Streptomycin Binding Aptamer

scientific article published on 24 June 2016

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

scientific article

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation

scientific article (publication date: 2013)

Sulfur transfer and activation by ubiquitin-like modifier system Uba4•Urm1 link protein urmylation and tRNA thiolation in yeast

scientific article published on 24 October 2016

Surveillance of siRNA integrity by FRET imaging

scientific article

Tackling the Limitations of Copolymeric Small Interfering RNA Delivery Agents by a Combined Experimental-Computational Approach

scientific article published on 04 November 2019

The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu

scientific article

The Guanidinium Group as a Key Part of Water-Soluble Polymer Carriers for siRNA Complexation and Protection against Degradation

scientific article published on 4 April 2014

The RNA methyltransferase Dnmt2 methylates DNA in the structural context of a tRNA.

scientific article

The marbled crayfish as a paradigm for saltational speciation by autopolyploidy and parthenogenesis in animals

scientific article

The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA

scientific journal article

The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent

scientific article published on 13 September 2015

Urmylation and tRNA thiolation functions of ubiquitin-like Uba4·Urm1 systems are conserved from yeast to man.

scientific article

Use of DNAzymes for site-specific analysis of ribonucleotide modifications

scientific article published on 12 November 2007

Use of Specific Chemical Reagents for Detection of Modified Nucleotides in RNA ⬇️

scientific article published on April 13, 2011

Variability of Substrate Specificity of Serum Antibodies Obtained from Patients with Different Autoimmune and Viral Diseases in Reaction of tRNA Hydrolysis

scientific article published on 01 April 1999

Variable presence of 5-methylcytosine in commercial RNA and DNA.

scientific article published on 14 August 2015

Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d

scientific article published on 13 March 2018

m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin

scientific article published on 01 June 2021

m6A modulates neuronal functions and sex determination in Drosophila

scientific article published on 30 November 2016

tRNA stabilization by modified nucleotides

scientific article published on June 2010

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