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Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants.

Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV.

Nat Rev Microbiol. 2020 Feb;18(2):67-83. doi: 10.1038/s41579-019-0299-x. Epub 2019 Dec 19. Review.


Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length.

Songailiene I, Rutkauskas M, Sinkunas T, Manakova E, Wittig S, Schmidt C, Siksnys V, Seidel R.

Cell Rep. 2019 Sep 17;28(12):3157-3166.e4. doi: 10.1016/j.celrep.2019.08.033.


Structure of the DNA-Bound Spacer Capture Complex of a Type II CRISPR-Cas System.

Wilkinson M, Drabavicius G, Silanskas A, Gasiunas G, Siksnys V, Wigley DB.

Mol Cell. 2019 Jul 11;75(1):90-101.e5. doi: 10.1016/j.molcel.2019.04.020. Epub 2019 May 9.


CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement.

Young J, Zastrow-Hayes G, Deschamps S, Svitashev S, Zaremba M, Acharya A, Paulraj S, Peterson-Burch B, Schwartz C, Djukanovic V, Lenderts B, Feigenbutz L, Wang L, Alarcon C, Siksnys V, May G, Chilcoat ND, Kumar S.

Sci Rep. 2019 Apr 30;9(1):6729. doi: 10.1038/s41598-019-43141-6.


From Restriction Enzymes to CRISPR: An Interview with Virginijus Siksnys.

Davies K, Siksnys V.

CRISPR J. 2018 Apr;1:137-140. doi: 10.1089/crispr.2018.29008.vis. Epub 2018 Apr 9. No abstract available.


Genetic Dissection of the Type III-A CRISPR-Cas System Csm Complex Reveals Roles of Individual Subunits.

Mogila I, Kazlauskiene M, Valinskyte S, Tamulaitiene G, Tamulaitis G, Siksnys V.

Cell Rep. 2019 Mar 5;26(10):2753-2765.e4. doi: 10.1016/j.celrep.2019.02.029.


A pipeline for characterization of novel Cas9 orthologs.

Karvelis T, Young JK, Siksnys V.

Methods Enzymol. 2019;616:219-240. doi: 10.1016/bs.mie.2018.10.021. Epub 2018 Dec 27.


Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family.

Tamulaitiene G, Manakova E, Jovaisaite V, Tamulaitis G, Grazulis S, Bochtler M, Siksnys V.

Nucleic Acids Res. 2019 Jan 25;47(2):997-1010. doi: 10.1093/nar/gky1137.


BREX system of Escherichia coli distinguishes self from non-self by methylation of a specific DNA site.

Gordeeva J, Morozova N, Sierro N, Isaev A, Sinkunas T, Tsvetkova K, Matlashov M, Truncaite L, Morgan RD, Ivanov NV, Siksnys V, Zeng L, Severinov K.

Nucleic Acids Res. 2019 Jan 10;47(1):253-265. doi: 10.1093/nar/gky1125.


DNA recognition by Arabidopsis transcription factors ABI3 and NGA1.

Sasnauskas G, Manakova E, Lapėnas K, Kauneckaitė K, Siksnys V.

FEBS J. 2018 Nov;285(21):4041-4059. doi: 10.1111/febs.14649. Epub 2018 Sep 21.


Activity and structure of EcoKMcrA.

Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M.

Nucleic Acids Res. 2018 Oct 12;46(18):9829-9841. doi: 10.1093/nar/gky731.


DnaQ exonuclease-like domain of Cas2 promotes spacer integration in a type I-E CRISPR-Cas system.

Drabavicius G, Sinkunas T, Silanskas A, Gasiunas G, Venclovas Č, Siksnys V.

EMBO Rep. 2018 Jul;19(7). pii: e45543. doi: 10.15252/embr.201745543. Epub 2018 Jun 11.


Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.

Sasnauskas G, Kauneckaite K, Siksnys V.

Nucleic Acids Res. 2018 May 4;46(8):4316-4324. doi: 10.1093/nar/gky256.


The H-subunit of the restriction endonuclease CglI contains a prototype DEAD-Z1 helicase-like motor.

Toliusis P, Tamulaitiene G, Grigaitis R, Tuminauskaite D, Silanskas A, Manakova E, Venclovas C, Szczelkun MD, Siksnys V, Zaremba M.

Nucleic Acids Res. 2018 Mar 16;46(5):2560-2572. doi: 10.1093/nar/gky107.


UbaLAI is a monomeric Type IIE restriction enzyme.

Sasnauskas G, Tamulaitiene G, Tamulaitis G, Calyševa J, Laime M, Rimšeliene R, Lubys A, Siksnys V.

Nucleic Acids Res. 2017 Sep 19;45(16):9583-9594. doi: 10.1093/nar/gkx634.


CgII cleaves DNA using a mechanism distinct from other ATP-dependent restriction endonucleases.

Toliusis P, Zaremba M, Silanskas A, Szczelkun MD, Siksnys V.

Nucleic Acids Res. 2017 Aug 21;45(14):8435-8447. doi: 10.1093/nar/gkx580.


A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems.

Kazlauskiene M, Kostiuk G, Venclovas Č, Tamulaitis G, Siksnys V.

Science. 2017 Aug 11;357(6351):605-609. doi: 10.1126/science.aao0100. Epub 2017 Jun 29.


Harnessing the natural diversity and in vitro evolution of Cas9 to expand the genome editing toolbox.

Karvelis T, Gasiunas G, Siksnys V.

Curr Opin Microbiol. 2017 Jun;37:88-94. doi: 10.1016/j.mib.2017.05.009. Epub 2017 Jun 20. Review.


The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA.

Kostiuk G, Dikic J, Schwarz FW, Sasnauskas G, Seidel R, Siksnys V.

Nucleic Acids Res. 2017 Jun 2;45(10):5968-5979. doi: 10.1093/nar/gkx294.


Methods for decoding Cas9 protospacer adjacent motif (PAM) sequences: A brief overview.

Karvelis T, Gasiunas G, Siksnys V.

Methods. 2017 May 15;121-122:3-8. doi: 10.1016/j.ymeth.2017.03.006. Epub 2017 Mar 24. Review.


Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA.

Tamulaitiene G, Jovaisaite V, Tamulaitis G, Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V.

Nucleic Acids Res. 2017 Apr 7;45(6):3547-3558. doi: 10.1093/nar/gkw1310.


Type III CRISPR-Cas Immunity: Major Differences Brushed Aside.

Tamulaitis G, Venclovas Č, Siksnys V.

Trends Microbiol. 2017 Jan;25(1):49-61. doi: 10.1016/j.tim.2016.09.012. Epub 2016 Oct 20. Review.


Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging.

Labrie V, Buske OJ, Oh E, Jeremian R, Ptak C, Gasiūnas G, Maleckas A, Petereit R, Žvirbliene A, Adamonis K, Kriukienė E, Koncevičius K, Gordevičius J, Nair A, Zhang A, Ebrahimi S, Oh G, Šikšnys V, Kupčinskas L, Brudno M, Petronis A.

Nat Struct Mol Biol. 2016 Jun;23(6):566-73. doi: 10.1038/nsmb.3227. Epub 2016 May 9.


Spatiotemporal Control of Type III-A CRISPR-Cas Immunity: Coupling DNA Degradation with the Target RNA Recognition.

Kazlauskiene M, Tamulaitis G, Kostiuk G, Venclovas Č, Siksnys V.

Mol Cell. 2016 Apr 21;62(2):295-306. doi: 10.1016/j.molcel.2016.03.024.


Rewiring Cas9 to Target New PAM Sequences.

Siksnys V, Gasiunas G.

Mol Cell. 2016 Mar 17;61(6):793-4. doi: 10.1016/j.molcel.2016.03.002.


Streptococcus thermophilus CRISPR-Cas9 Systems Enable Specific Editing of the Human Genome.

Müller M, Lee CM, Gasiunas G, Davis TH, Cradick TJ, Siksnys V, Bao G, Cathomen T, Mussolino C.

Mol Ther. 2016 Mar;24(3):636-44. doi: 10.1038/mt.2015.218. Epub 2015 Dec 14.


Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements.

Karvelis T, Gasiunas G, Young J, Bigelyte G, Silanskas A, Cigan M, Siksnys V.

Genome Biol. 2015 Nov 19;16:253. doi: 10.1186/s13059-015-0818-7.


An Engineered SS Bridge Blocks the Conformational Change Required for the Nuclease Activity of BfiI.

Zaremba M, Siksnys V.

Biochemistry. 2015 Sep 1;54(34):5340-7. doi: 10.1021/acs.biochem.5b00437. Epub 2015 Aug 14.


Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI.

Tamulaitis G, Rutkauskas M, Zaremba M, Grazulis S, Tamulaitiene G, Siksnys V.

Nucleic Acids Res. 2015 Sep 18;43(16):8100-10. doi: 10.1093/nar/gkv768. Epub 2015 Aug 3.


Structure-guided sequence specificity engineering of the modification-dependent restriction endonuclease LpnPI.

Sasnauskas G, Zagorskaitė E, Kauneckaitė K, Tamulaitiene G, Siksnys V.

Nucleic Acids Res. 2015 Jul 13;43(12):6144-55. doi: 10.1093/nar/gkv548. Epub 2015 May 22.


Cas3 nuclease-helicase activity assays.

Sinkunas T, Gasiunas G, Siksnys V.

Methods Mol Biol. 2015;1311:277-91. doi: 10.1007/978-1-4939-2687-9_18.


Targeted gene editing by transfection of in vitro reconstituted Streptococcus thermophilus Cas9 nuclease complex.

Glemzaite M, Balciunaite E, Karvelis T, Gasiunas G, Grusyte MM, Alzbutas G, Jurcyte A, Anderson EM, Maksimova E, Smith AJ, Lubys A, Zaliauskiene L, Siksnys V.

RNA Biol. 2015;12(1):1-4. doi: 10.1080/15476286.2015.1017209. No abstract available.


DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis.

Zaremba M, Toliusis P, Grigaitis R, Manakova E, Silanskas A, Tamulaitiene G, Szczelkun MD, Siksnys V, Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V.

Nucleic Acids Res. 2015 Mar 31;43(6):3405. doi: 10.1093/nar/gkv049. Epub 2015 Mar 13. No abstract available.


Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection.

Rutkauskas M, Sinkunas T, Songailiene I, Tikhomirova MS, Siksnys V, Seidel R.

Cell Rep. 2015 Mar 10;10(9):1534-1543. doi: 10.1016/j.celrep.2015.01.067. Epub 2015 Mar 5.


Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus.

Tamulaitis G, Kazlauskiene M, Manakova E, Venclovas Č, Nwokeoji AO, Dickman MJ, Horvath P, Siksnys V.

Mol Cell. 2014 Nov 20;56(4):506-17. doi: 10.1016/j.molcel.2014.09.027. Epub 2014 Nov 6.


Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII.

Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V.

Nucleic Acids Res. 2014 Dec 16;42(22):14022-30. doi: 10.1093/nar/gku1237. Epub 2014 Nov 27.


DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis.

Zaremba M, Toliusis P, Grigaitis R, Manakova E, Silanskas A, Tamulaitiene G, Szczelkun MD, Siksnys V.

Nucleic Acids Res. 2014 Dec 16;42(22):13887-96. doi: 10.1093/nar/gku1236. Epub 2014 Nov 27. Erratum in: Nucleic Acids Res. 2015 Mar 31;43(6):3405.


Restriction enzyme Ecl18kI-induced DNA looping dynamics by single-molecule FRET.

Rutkauskas D, Petkelyte M, Naujalis P, Sasnauskas G, Tamulaitis G, Zaremba M, Siksnys V.

J Phys Chem B. 2014 Jul 24;118(29):8575-82. doi: 10.1021/jp504546v. Epub 2014 Jul 14.


Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes.

Szczelkun MD, Tikhomirova MS, Sinkunas T, Gasiunas G, Karvelis T, Pschera P, Siksnys V, Seidel R.

Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9798-803. doi: 10.1073/pnas.1402597111. Epub 2014 May 27.


Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme.

Golovenko D, Manakova E, Zakrys L, Zaremba M, Sasnauskas G, Gražulis S, Siksnys V.

Nucleic Acids Res. 2014 Apr;42(6):4113-22. doi: 10.1093/nar/gkt1368. Epub 2014 Jan 13.


Programmable DNA cleavage in vitro by Cas9.

Karvelis T, Gasiunas G, Siksnys V.

Biochem Soc Trans. 2013 Dec;41(6):1401-6. doi: 10.1042/BST20130164. Review.


RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing?

Gasiunas G, Siksnys V.

Trends Microbiol. 2013 Nov;21(11):562-7. doi: 10.1016/j.tim.2013.09.001. Epub 2013 Oct 1.


Molecular mechanisms of CRISPR-mediated microbial immunity.

Gasiunas G, Sinkunas T, Siksnys V.

Cell Mol Life Sci. 2014 Feb;71(3):449-65. Review.


crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus.

Karvelis T, Gasiunas G, Miksys A, Barrangou R, Horvath P, Siksnys V.

RNA Biol. 2013 May;10(5):841-51. doi: 10.4161/rna.24203. Epub 2013 Mar 27.


In vitro reconstitution of Cascade-mediated CRISPR immunity in Streptococcus thermophilus.

Sinkunas T, Gasiunas G, Waghmare SP, Dickman MJ, Barrangou R, Horvath P, Siksnys V.

EMBO J. 2013 Feb 6;32(3):385-94. doi: 10.1038/emboj.2012.352. Epub 2013 Jan 18.


Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria.

Gasiunas G, Barrangou R, Horvath P, Siksnys V.

Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):E2579-86. Epub 2012 Sep 4.


The link between restriction endonuclease fidelity and oligomeric state: a study with Bse634I.

Zaremba M, Sasnauskas G, Siksnys V.

FEBS Lett. 2012 Sep 21;586(19):3324-9. doi: 10.1016/j.febslet.2012.07.009. Epub 2012 Jul 22.


The recognition domain of the methyl-specific endonuclease McrBC flips out 5-methylcytosine.

Sukackaite R, Grazulis S, Tamulaitis G, Siksnys V.

Nucleic Acids Res. 2012 Aug;40(15):7552-62. doi: 10.1093/nar/gks332. Epub 2012 May 8.


Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease.

Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V.

Nucleic Acids Res. 2012 Aug;40(14):6741-51. doi: 10.1093/nar/gks300. Epub 2012 Apr 11.


Catalytic activity control of restriction endonuclease--triplex forming oligonucleotide conjugates.

Silanskas A, Zaremba M, Sasnauskas G, Siksnys V.

Bioconjug Chem. 2012 Feb 15;23(2):203-11. doi: 10.1021/bc200480m. Epub 2012 Jan 30.


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