Author

V. Siksnys

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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Biochemistry· 3 Biophysics· 3 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 7 Assay:DNA methylation· 3 Organism:bacteria (other)· 1 Research Focus:drug response / drug discovery· 1 Organism:E. coli· 1 Research Focus:host-pathogen & immune response· 1 Research Focus:protein folding & dynamics· 1

Frequent Co-Authors

I. Songailiene· 3 shared M. Rutkauskas· 3 shared R. Seidel· 3 shared T. Karvelis· 3 shared T. Sinkunas· 3 shared C. Venclovas· 2 shared D. J. Kauert· 2 shared F. E. Kemmerich· 2 shared

Activity by Year

2020-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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Curved chords = mutual co-authorship

3 shared papersBiophysics

I. Songailiene

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex

D. J. Kauert, J. Madariaga Marcos, M. Rutkauskas, A. Wulfken, I. Songailiene, T. Sinkunas, V. Siksnys, R. Seidel

This paper uses ultrafast DNA unwinding experiments to study the energy landscape of R-loop formation by the Cascade complex, revealing a downhill bias followed by an uphill bias and showing base flips and mismatches modulate the landscape.

bioRxiv · Mar 17, 2023Biophysics

Dynamic interplay between target search and recognition for the Cascade surveillance complex of type I-E CRISPR-Cas systems

P. Aldag, M. Rutkauskas, J. Madariaga-Marcos, I. Songailiene, T. Sinkunas, F. E. Kemmerich, D. J. Kauert, V. Siksnys, R. Seidel

This study investigates how the Type I-E CRISPR-Cas Cascade complex searches and recognizes DNA targets, showing that recognition probabilities are low and increased by DNA supercoiling and limited 1D diffusion.

bioRxiv · Dec 18, 2022Biophysics

A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex

M. Rutkauskas, I. Songailiene, P. Irmisch, F. E. Kemmerich, T. Sinkunas, V. Siksnys, R. Seidel

The paper develops a quantitative model to predict CRISPR-Cas Cascade off-target recognition dynamics using single-molecule experiments and shows it accurately captures target recognition with mutations.

bioRxiv · Jan 26, 2022 · PreprintBiophysics

Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion

J. Garb, A. Lopatina, A. Bernheim, M. Zaremba, V. Siksnys, S. Melamed, A. Leavitt, A. Millman, G. Amitai, R. Sorek

The paper shows DSR proteins deplete NAD+ during phage infection, inhibiting propagation, and identifies SIR2 domains as effector NADases in bacterial immunity.

bioRxiv · Dec 14, 2021Microbiology

Biochemically diverse CRISPR-Cas9 orthologs

G. Gasiunas, J. K. Young, T. Karvelis, D. Kazlauskas, T. Urbaitis, M. Jasnauskaite, M. Grusyte, S. Paulraj, P.-H. Wang, Z. Hou, S. K. Dooley, M. Cigan, C. Alarcon, N. D. Chilcoat, G. Bigelyte, , V. Siksnys

The paper characterizes the biochemical diversity of CRISPR-Cas9 orthologs, identifying varied PAM recognition and gRNA requirements across 79 Cas9 proteins.

bioRxiv · Apr 29, 2020 · PreprintBiochemistry

5' modifications to CRISPR Cas9 gRNA can change the dynamics and size of R-loops and inhibit DNA cleavage

G. Mullally, K. van Aelst, M. M. Naqvi, F. M. Diffin, T. Karvelis, G. Gasiunas, V. Siksnys, M. D. Szczelkun

The paper investigates how 5' modifications to CRISPR gRNA affect R-loop dynamics and DNA cleavage, finding that certain modifications inhibit cleavage while others do not.

bioRxiv · Apr 9, 2020Biochemistry

PAM recognition by miniature CRISPR nucleases triggersprogrammable double-stranded DNA target cleavage

T. Karvelis, G. Bigelyte, J. K. Young, Z. Hou, R. Zedaveinyte, K. Budre, S. Paulraj, V. Djukanovic, S. Gasior, A. Silanskas, C. Venclovas, V. Siksnys

This study identifies and characterizes miniature CRISPR-Cas nucleases that cleave double-stranded DNA in a PAM-dependent manner, showing their potential for programmable genome editing.

bioRxiv · Feb 20, 2020Biochemistry