Author

D. Dulin

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 7 Biochemistry· 2

Signature Assays, Organisms & Methods

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Approach:experimental assay· 8 Organism:bacteria (other)· 3 Organism:virus· 3 Research Focus:cell signaling & trafficking· 2 Research Focus:chromatin & epigenetic regulation· 2 Research Focus:host-pathogen & immune response· 2 Approach:biophysical modeling· 1 Assay:DNA methylation· 1

Frequent Co-Authors

M. Seifert· 6 shared F. S. Papini· 5 shared M. Depken· 5 shared C. E. Cameron· 4 shared J. J. Arnold· 4 shared A. M. Malinen· 3 shared P. van Nies· 3 shared S. C. Bera· 3 shared

Activity by Year

2017-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 34 mutual co-author links

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6 shared papersBiophysics

M. Seifert

Mutual co-authors in cluster

Author profile →

9 papers

Recent·Most cited

Temperature-dependent twist of double-stranded RNA probed by magnetic tweezers experiments and molecular dynamics simulations

H. Dohnalova, M. Seifert, E. Matouskova, F. S. Papini, J. Lipfert, D. Dulin, F. Lankas

This study investigates how temperature affects the twist of double-stranded RNA using magnetic tweezers and molecular dynamics simulations, finding RNA unwinds more than DNA with increasing temperature.

bioRxiv · May 31, 2023Biophysics

Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease

R. Chinthapatla, M. S. Sotoudegan, T. Anderson, I. M. Moustafa, K. T. Passow, S. A. Kennelly, R. Moorthy, D. Dulin, J. Y. Feng, D. A. Harki, R. Kirchdoerfer, C. E. Cameron, J. J. Arnold

This study investigates how SARS-CoV-2's ExoN enzyme processes RNA and identifies modifications that block its activity, offering potential for new antiviral strategies.

bioRxiv · Aug 11, 2022Biochemistry

Quantitative parameters of bacterial RNA polymerase open-complex formation, stabilization and disruption on a consensus promoter

S. C. Bera, P. P. B. America, S. Maatsola, M. Seifert, E. Ostrofet, J. Cnossen, M. Spermann, F. S. Papini, M. Depken, A. M. Malinen, D. Dulin

The paper quantifies the kinetics of bacterial RNA polymerase open-complex formation, stabilization, and disruption on a consensus promoter using single-molecule magnetic tweezers.

bioRxiv · Oct 13, 2021Biophysics

The nucleotide addition cycle of the SARS-CoV-2 polymerase

S. C. Bera, M. Seifert, R. Kirchdoerfer, P. van Nies, Y. Wubulikasimu, S. Quack, F. S. Papini, J. J. Arnold, B. Canard, C. E. Cameron, M. Depken, D. Dulin

This study describes the mechanochemical behavior of the SARS-CoV-2 polymerase using magnetic tweezers, revealing three catalytic conformations and a thermal ratchet mechanism for nucleotide incorporation.

bioRxiv · Mar 27, 2021Biophysics

The formation of the bacterial RNA polymerase-promoter open complex involves a branched pathway

A. M. Malinen, J. Bakermans, E. Aalto-Setälä, M. Blessing, D. L. Bauer, O. Parilova, G. A. Belogurov, D. Dulin, A. N. Kapanidis

This study uses single-molecule fluorescence microscopy to show that bacterial RNA polymerase-promoter open complex formation follows a branched pathway with varying stability.

bioRxiv · Mar 27, 2021 · PreprintBiochemistry

Inhibition of SARS-CoV-2 polymerase by nucleotide analogs: a single moleculeperspective

M. Seifert, S. C. Bera, P. van Nies, R. N. Kirchdoerfer, A. Shannon, T.-T.-N. Le, X. Meng, H. Xia, J. M. Wood, L. D. Harris, F. S. Papini, J. J. Arnold, S. C. Almo, T. L. Grove, P.-Y. Shi, , D. Dulin

This study investigates how nucleotide analogs like Remdesivir affect SARS-CoV-2 polymerase activity using single-molecule techniques, revealing backtracking rather than termination and evasion of ddhCTP.

bioRxiv · Aug 6, 2020 · PreprintBiophysics

Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases.

M. Seifert, P. van Nies, F. S. Papini, J. J. Arnold, M. M. Poranen, C. E. Cameron, M. Depken, D. Dulin

This study uses temperature-controlled magnetic tweezers to compare replication kinetics of RdRps from three RNA viruses, finding temperature-dependent activation differences.

bioRxiv · Jan 15, 2020Biophysics

High-yield fabrication of DNA and RNA scaffolds for single molecule force and torque spectroscopy experiments.

F. Stal Papini, M. Seifert, D. Dulin

The paper presents new protocols for high-yield fabrication of DNA and RNA scaffolds for single molecule force and torque spectroscopy experiments, showing improved efficiency over standard methods.

bioRxiv · Jun 6, 2019 · PreprintBiophysics

Pausing controls branching between productive and non-productive pathways during initial transcription

D. Dulin, D. L. V. Bauer, A. M. Malinen, J. J. W. Bakermans, M. Kaller, Z. Morichaud, I. Petushkov, M. Depken, K. Brodolin, A. Kulbachinskiy, A. N. Kapanidis

The paper investigates how RNA polymerase pausing controls transcriptional pathways in bacteria, showing that paused RNA synthesis directs RNAP to productive or abortive pathways.

bioRxiv · Oct 6, 2017Biophysics