A Study on Endonuclease BspD6I and Its Stimulus-responsive Switching by Modified Oligonucleotides

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2018 Nov 27

PMID 30475809

Citations 2

Authors

Liudmila A Abrosimova

Anzhela Yu Migur

Elena A Kubareva

Timofei S Zatsepin

Aleksandra V Gavshina

Alfiya K Yunusova

Tatiana A Perevyazova

Alfred Pingoud

Tatiana S Oretskaya

Affiliations

Soon will be listed here.

Abstract

Nicking endonucleases (NEases) selectively cleave single DNA strands in double-stranded DNAs at a specific site. They are widely used in bioanalytical applications and in genome editing; however, the peculiarities of DNA-protein interactions for most of them are still poorly studied. Previously, it has been shown that the large subunit of heterodimeric restriction endonuclease BspD6I (Nt.BstD6I) acts as a NEase. Here we present a study of interaction of restriction endonuclease BspD6I with modified DNA containing single non-nucleotide insertion with an azobenzene moiety in the enzyme cleavage sites or in positions of sugar-phosphate backbone nearby. According to these data, we designed a number of effective stimulus-responsive oligonucleotide inhibitors bearing azobenzene or triethylene glycol residues. These modified oligonucleotides modulated the functional activity of Nt.BspD6I after cooling or heating. We were able to block the cleavage of T7 phage DNA by this enzyme in the presence of such inhibitors at 20-25°C, whereas the Nt.BspD6I ability to hydrolyze DNA was completely restored after heating to 45°C. The observed effects can serve as a basis for the development of a platform for regulation of NEase activity in vitro or in vivo by external signals.

Citing Articles

Types and Applications of Nicking Enzyme-Combined Isothermal Amplification.

Cao S, Tang X, Chen T, Chen G Int J Mol Sci. 2022; 23(9).

PMID: 35563012 PMC: 9100243. DOI: 10.3390/ijms23094620.

Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA.

Abrosimova L, Kuznetsov N, Astafurova N, Samsonova A, Karpov A, Perevyazova T Biomolecules. 2021; 11(10).

PMID: 34680052 PMC: 8533099. DOI: 10.3390/biom11101420.

References

Young D, Govan J, Lively M, Deiters A . Photochemical regulation of restriction endonuclease activity. Chembiochem. 2009; 10(10):1612-6. PMC: 2983471. DOI: 10.1002/cbic.200900090. View

Schierling B, Pingoud A . Controlling the DNA cleavage activity of light-inducible chimeric endonucleases by bidirectional photoactivation. Bioconjug Chem. 2012; 23(6):1105-9. DOI: 10.1021/bc3001326. View

Silanskas A, Foss M, Wende W, Urbanke C, Lagunavicius A, Pingoud A . Photocaged variants of the MunI and PvuII restriction enzymes. Biochemistry. 2011; 50(14):2800-7. DOI: 10.1021/bi2000609. View

Zheleznaya L, Perevyazova T, Zheleznyakova E, Matvienko N . Some properties of site-specific nickase BspD6I and the possibility of its use in hybridization analysis of DNA. Biochemistry (Mosc). 2002; 67(4):498-502. DOI: 10.1023/a:1015250426726. View

Cai H, Bloom L, Eritja R, Goodman M . Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase. J Biol Chem. 1993; 268(31):23567-72. View

Mougiakos I, Mohanraju P, Bosma E, Vrouwe V, Finger Bou M, Naduthodi M . Characterizing a thermostable Cas9 for bacterial genome editing and silencing. Nat Commun. 2017; 8(1):1647. PMC: 5698299. DOI: 10.1038/s41467-017-01591-4. View

Harrington L, Paez-Espino D, Staahl B, Chen J, Ma E, Kyrpides N . A thermostable Cas9 with increased lifetime in human plasma. Nat Commun. 2017; 8(1):1424. PMC: 5681539. DOI: 10.1038/s41467-017-01408-4. View

Wrenbeck E, Klesmith J, Stapleton J, Adeniran A, Tyo K, Whitehead T . Plasmid-based one-pot saturation mutagenesis. Nat Methods. 2016; 13(11):928-930. PMC: 5666567. DOI: 10.1038/nmeth.4029. View

Pyshnaya I, Pyshnyi D, Lomzov A, Zarytova V, Ivanova E . The influence of the non-nucleotide insert on the hybridization properties of oligonucleotides. Nucleosides Nucleotides Nucleic Acids. 2004; 23(6-7):1065-71. DOI: 10.1081/NCN-200026073. View

10.

Farzan V, Ulashchik E, Martynenko-Makaev Y, Kvach M, Aparin I, Brylev V . Automated Solid-Phase Click Synthesis of Oligonucleotide Conjugates: From Small Molecules to Diverse N-Acetylgalactosamine Clusters. Bioconjug Chem. 2017; 28(10):2599-2607. DOI: 10.1021/acs.bioconjchem.7b00462. View

11.

Koo T, Lee J, Kim J . Measuring and Reducing Off-Target Activities of Programmable Nucleases Including CRISPR-Cas9. Mol Cells. 2015; 38(6):475-81. PMC: 4469905. DOI: 10.14348/molcells.2015.0103. View

12.

Hu T, Wen W, Zhang X, Wang S . Nicking endonuclease-assisted recycling of target-aptamer complex for sensitive electrochemical detection of adenosine triphosphate. Analyst. 2016; 141(4):1506-11. DOI: 10.1039/c5an02484f. View

13.

Tang X, Swaminathan J, Gewirtz A, Dmochowski I . Regulating gene expression in human leukemia cells using light-activated oligodeoxynucleotides. Nucleic Acids Res. 2007; 36(2):559-69. PMC: 2241881. DOI: 10.1093/nar/gkm1029. View

14.

Li X, Du Y, Zhang Y, Kong D . Dual functional Phi29 DNA polymerase-triggered exponential rolling circle amplification for sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Sci Rep. 2017; 7(1):6263. PMC: 5524717. DOI: 10.1038/s41598-017-06594-1. View

15.

Kachalova G, Rogulin E, Yunusova A, Artyukh R, Perevyazova T, Matvienko N . Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit. J Mol Biol. 2008; 384(2):489-502. DOI: 10.1016/j.jmb.2008.09.033. View

16.

Havlicek S, Shen Y, Alpagu Y, Bruntraeger M, Zufir N, Phuah Z . Re-engineered RNA-Guided FokI-Nucleases for Improved Genome Editing in Human Cells. Mol Ther. 2017; 25(2):342-355. PMC: 5368403. DOI: 10.1016/j.ymthe.2016.11.007. View

17.

Hu Y, Li Z, Diamond A . Enhanced discrimination of single nucleotide polymorphism in genotyping by phosphorothioate proofreading allele-specific amplification. Anal Biochem. 2007; 369(1):54-9. DOI: 10.1016/j.ab.2007.04.042. View

18.

Asanuma H, Matsunaga D, Liu M, Liang X, Jhao J, Komiyama M . Photo-regulation of DNA function by azobenzene-tethered oligonucleotides. Nucleic Acids Res Suppl. 2003; (3):117-8. DOI: 10.1093/nass/3.1.117. View

19.

Nunez J, Harrington L, Doudna J . Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering. ACS Chem Biol. 2016; 11(3):681-8. DOI: 10.1021/acschembio.5b01019. View

20.

Lukyanchikova N, Petruseva I, Evdokimov A, Silnikov V, Lavrik O . DNA with Damage in Both Strands as Affinity Probes and Nucleotide Excision Repair Substrates. Biochemistry (Mosc). 2016; 81(3):263-74. DOI: 10.1134/S0006297916030093. View