{"id":208,"date":"2019-06-20T13:04:53","date_gmt":"2019-06-20T06:04:53","guid":{"rendered":"http:\/\/dnape.online\/?page_id=208"},"modified":"2019-06-20T13:06:05","modified_gmt":"2019-06-20T06:06:05","slug":"publications","status":"publish","type":"page","link":"https:\/\/dnape.online\/en\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n<\/span>

[vc_row][vc_column]

\t\t

\r\n\r\n\t\t\r\n\t\t\t\t\t\t\t\r\n\t\t\t\t\t\t\u041d\u0435\u0434\u0430\u0432\u043d\u0438\u0435 \u041f\u043e\u0441\u0442\u044b\t\t\t\t\t<\/span>\r\n\t\t\t\r\n\t\t\r\n\t\t<\/h3>\r\n\t\t\t
\r\n\t\t
\r\n\t\t
\r\n\t\t\t\t\t\t\t
\r\n\t\t\t\t\t
New enzymes<\/a><\/span>\u0422\u043e\u043c 2025<\/a><\/span><\/div>\t\t\t\t\t<\/a>\r\n\t\t\t\t\t\t\t\t\t<\/div>\r\n\t\t\t

\t\t\t\r\n\t\t\t\tThe restriction endonuclease EmiI, an isoschizomer of Ksp632I, recognizes the non-palindromic DNA sequence 5\u2032-CTCTTC(1\/4)-3\u2032\t\t\t<\/a>\r\n\t\t\t<\/h2>

M.A. Abdurashitov, D.A. Gonchar, V.A. Chernukhin, V.S. Dedkov, N.A. Mikhnenkova, A.A. Nikonova, S.Kh. Degtyarev<\/h3>\t\t
\r\n\r\n\t\t\t\t\t\t\t<\/i> 0<\/a>\t\t<\/div>\r\n\t\t\t\t\t\t
\r\n\t\t\t\t\tA bacterial strain, Exiguobacterium mexicanum 6, was identified as a producer of a novel restriction endonuclease designated EmiI. The enzyme recognizes the non-palindromic hexanucleotide DNA sequence 5\u2032-CTCTTC-3\u2032 and cleaves DNA outside the recognition site at positions 1\/4, generating three-nucleotide 5\u2032-protruding ends: 5\u2032-CTCTTC(N)\u2081\u2193-3\u2032 \/ 3\u2032-GAGAAG(N)\u2084\u2193-5\u2032.\r\nThus, EmiI is an isoschizomer of the restriction endonucleases Ksp632I and Bst6I . The producer strain was identified based on morphological and biochemical characteristics as well as analysis of the primary structure of a fragment of the 16S rRNA gene. A preparation of restriction endonuclease EmiI with an activity of 5000 U\/ml was obtained through purification using three chromatographic steps. Optimal reaction conditions for EmiI include SE buffer Y (33 mM Tris\u2013acetate, pH 7.9; 10 mM Mg\u2013acetate; 66 mM potassium acetate; 1 mM DTT) at a temperature of 37 \u00b0C.\t\t\t\t<\/div>\r\n\t\t\t\t\t\t<\/div>\r\n\t<\/article>\r\n\t
\r\n\t\t
\r\n\t\t\t\t\t\t\t
\r\n\t\t\t\t\t
New enzymes<\/a><\/span>\u0422\u043e\u043c 2025<\/a><\/span><\/div>\t\t\t\t\t<\/a>\r\n\t\t\t\t\t\t\t\t\t<\/div>\r\n\t\t\t

\t\t\t\r\n\t\t\t\tA novel 5mC-directed site-specific DNA endonuclease MoxI efficiently cleaves the DNA sequence 5\u2032-R(5mC)GY-3\u2032\t\t\t<\/a>\r\n\t\t\t<\/h2>

V.A. Chernukhin, V.S. Dedkov, D.A. Gonchar, V.N. Baimak, O.A. Belichenko, S.Kh. Degtyarev<\/h3>\t\t
\r\n\r\n\t\t\t\t\t\t\t<\/i> 0<\/a>\t\t<\/div>\r\n\t\t\t\t\t\t
\r\n\t\t\t\t\tA bacterial strain of Microbacterium oxydans was identified as a producer of a 5-methylcytosine-dependent, site-specific DNA endonuclease, MoxI. The enzyme recognizes and cleaves the DNA sequence 5\u2032-R(5mC)\u2193GY-3\u2032 \/ 3\u2032-YG\u2193(5mC)R-5\u2032.\r\nThe moxI gene was cloned and expressed in Escherichia coli, and the recombinant enzyme was purified and biochemically characterized. The recognition sequence of MoxI was shown to be identical to that of the previously described 5mC-directed site-specific DNA endonuclease GlaI. In contrast to GlaI, however, MoxI exhibits maximal catalytic activity at 37 \u00b0C and demonstrates higher cleavage efficiency toward substrates containing two 5-methylcytosine residues within the recognition site\t\t\t\t<\/div>\r\n\t\t\t\t\t\t<\/div>\r\n\t<\/article>\r\n\t
\r\n\t\t
\r\n\t\t\t\t\t\t\t
\r\n\t\t\t\t\t
New enzymes<\/a><\/span>\u0422\u043e\u043c 2025<\/a><\/span><\/div>\t\t\t\t\t<\/a>\r\n\t\t\t\t\t\t\t\t\t<\/div>\r\n\t\t\t

\t\t\t\r\n\t\t\t\tBmoI Restriction Endonuclease from the Bacterial Strain Brevundimonas mongoliensis 53 Recognizes the DNA Sequence 5\u2019-GG^GWCCC-3\u2019\t\t\t<\/a>\r\n\t\t\t<\/h2>\t\t
\r\n\r\n\t\t\t\t\t\t\t<\/i> 0<\/a>\t\t<\/div>\r\n\t\t\t\t\t\t
\r\n\t\t\t\t\tWe identified a bacterial strain, Brevundimonas mongoliensis 53, which produces a new Type II restriction endonuclease, designated BmoI.\r\nBmoI recognizes the palindromic heptanucleotide sequence 5\u2019-GG^GWCCC-3\u2019 (W = A or T) and cleaves at the indicated position to generate three-nucleotide 5\u2032 overhangs.\r\nBmoI is an isoschizomer of the previously described restriction enzyme SanDI.\r\nThe producing strain was identified based on morphological and biochemical characteristics and by sequencing a fragment of the 16S rRNA gene.\r\nA preparation of BmoI with an activity of 2000 U\/ml was obtained using a three-step chromatographic purification workflow.\r\nOptimal reaction conditions for BmoI were determined to be SE buffer W (10 mM Tris-HCl, pH 8.5; 10 mM MgCl\u2082; 100 mM NaCl; 1 mM DTT) and an incubation temperature of 37\u00b0C.\t\t\t\t<\/div>\r\n\t\t\t\t\t\t<\/div>\r\n\t<\/article>\r\n\t
\r\n\t\t
\r\n\t\t\t\t\t\t\t
\r\n\t\t\t\t\t
New enzymes<\/a><\/span><\/div>\t\t\t\t\t<\/a>\r\n\t\t\t\t\t\t\t\t\t<\/div>\r\n\t\t\t

\t\t\t\r\n\t\t\t\tRestriction Endonuclease Pse31I from Bacterial Strain Peribacillus Species 31, an Isoschizomer of Eco31I, Recognizes the Non-palindromic DNA Sequence 5\u2019-GGTCTC-3\u2019 (1\/5)\t\t\t<\/a>\r\n\t\t\t<\/h2>\t\t
\r\n\r\n\t\t\t\t\t\t\t<\/i> 0<\/a>\t\t<\/div>\r\n\t\t\t\t\t\t
\r\n\t\t\t\t\tWe have discovered a bacterial strain, Peribacillus species 31, which produces a novel restriction endonuclease named Pse31I. The enzyme recognizes a six-nucleotide non-palindromic DNA sequence, 5\u2019-GGTCTC-3\u2019, and cleaves it away from the recognition site at positions 1\/5: 5\u2019-GGTCTC(N)1^\/3\u2019-CCAGAG(N)5^-5\u2019. Thus, Pse31I is a true isoschizomer of the restriction enzyme Eco31I .\r\nThe producer strain was identified based on morphological and biochemical characteristics, as well as by analyzing the primary structure of a fragment of the 16S rRNA gene. Pse31I exhibits maximal activity at 37\u00b0C and is inactivated by incubation at 55\u00b0C and 65\u00b0C. The enzyme does not cleave sites containing a methylated cytosine in the top strand (5\u2019-GGTCT(5mC)-3\u2019) and\/or in the bottom strand (3\u2019-(5mC)CAGAG).\r\nThe optimal reaction conditions for the enzyme include SE-buffer 5 (Y) (33 mM Tris-acetate (pH 7.9), 10 mM Mg-acetate, 66 mM K-acetate, 1 mM DTT) and a temperature of 37\u00b0C\t\t\t\t<\/div>\r\n\t\t\t\t\t\t<\/div>\r\n\t<\/article>\r\n\t
\r\n\t\t
\r\n\t\t\t\t\t\t\t
\r\n\t\t\t\t\t
New enzymes<\/a><\/span>\u0422\u043e\u043c 2025<\/a><\/span><\/div>\t\t\t\t\t<\/a>\r\n\t\t\t\t\t\t\t\t\t<\/div>\r\n\t\t\t

\t\t\t\r\n\t\t\t\tThe restriction endonuclease PecI from the bacterial strain Paracoccus species 12 recognizes the DNA sequence 5\u2019-TTA^TAA-3\u2019 and is an isoschizomer of PsiI\t\t\t<\/a>\r\n\t\t\t<\/h2>

D.A. Gonchar, V.A. Chernukhin, V.S. Dedkov, N.A. Mikhnenkova, M.A. Abdurashitov, O.A. Belichenko, S.Kh. Degtyarev<\/h3>\t\t
\r\n\r\n\t\t\t\t\t\t\t<\/i> 0<\/a>\t\t<\/div>\r\n\t\t\t\t\t\t
\r\n\t\t\t\t\tWe identified a bacterial strain, Paracoccus species 12, which produces a novel restriction endonuclease, named PecI. This enzyme recognizes the hexanucleotide palindromic DNA sequence 5\u2019-TTA^TAA-3\u2019 and cleaves it, as indicated by the arrow, generating blunt ends. Thus, PecI is a true isoschizomer of the restriction enzyme PsiI.\r\nA preparation of PecI restriction endonuclease at a concentration of 10,000 U\/mL was obtained through a four-step chromatographic purification process. The optimal reaction conditions for the enzyme are SE-buffer 5 (Y) (33 mM Tris-acetate (pH 7.9), 10 mM Mg-acetate, 66 mM K-acetate, 1 mM DTT) and a temperature of 37oC.\t\t\t\t<\/div>\r\n\t\t\t\t\t\t<\/div>\r\n\t<\/article>\r\n\t
\r\n\t\t
\r\n\t\t\t\t\t\t\t
\r\n\t\t\t\t\t
Applications<\/a><\/span>Methods<\/a><\/span>Volume 2021<\/a><\/span><\/div>\t\t\t\t\t<\/a>\r\n\t\t\t\t\t\t\t\t\t<\/div>\r\n\t\t\t

\t\t\t\r\n\t\t\t\tCutting out the amplicon with restriction endonuclease \u2013 a way to exclude the false results of RT PCR with TaqMan probe\t\t\t<\/a>\r\n\t\t\t<\/h2>

Akishev A.G., Netesova N.A., Abdurashitov M.A., Degtyarev S.Kh.<\/h3>\t\t
\r\n\r\n\t\t\t\t\t\t\t<\/i> 0<\/a>\t\t<\/div>\r\n\t\t\t\t\t\t
\r\n\t\t\t\t\tReal-time PCR with TaqMan probe (RT PCR) is one of the main methods for analyzing the structure of human DNA and is widely used in medicine. In this work, PCR RT of 4 fragments of human genomic DNA (chr1: 90717178-90717300, chr9: 97464604-97464756, chr11: 65647215-65647307, chr17: 4560027-4560175) was performed with DNA preparations from human blood obtained both by the standard method of phenol deproteinization and isolated on columns. Preparations of the original DNA and DNA after a treatment with a restriction endonuclease that cuts out the amplified fragment were used in PCR. In the case of native DNA preparations purified by column, PCR of 3 from 4 DNA fragments provided an overestimated Cq value. In the case of the phenol purification, an overestimated Cq value for native DNA preparations was obtained for 2 from 4 DNA fragments. For DNA preparations obtained by the column purification, treatment of DNA with a restriction endonuclease that cuts out the amplified fragment leads to normal Cq values for all four analyzed DNA fragments. Thus, RT PCR of native DNA obtained by the column purification may result in an overestimation of Cq, which is avoided if DNA previously has been hydrolyzed by a restriction endonuclease that cuts out the amplicon.\t\t\t\t<\/div>\r\n\t\t\t\t\t\t<\/div>\r\n\t<\/article>\r\n\t
\r\n\t\t
\r\n\t\t\t\t\t\t\t
\r\n\t\t\t\t\t
Enzyme studies<\/a><\/span>Volume 2019<\/a><\/span><\/div>\t\t\t\t\t<\/a>\r\n\t\t\t\t\t\t\t\t\t<\/div>\r\n\t\t\t

\t\t\t\r\n\t\t\t\tComparison of the substrate specificity of GlaI recombinant site-specific methyl-directed DNA endonuclease and the native enzyme isolated from Glacial ice bacterium strain\t\t\t<\/a>\r\n\t\t\t<\/h2>

Valery A. Chernukhin, Vladimir S. Dedkov, Danila A. Gonchar, Murat A. Abdurashitov, Alexander G. Akishev, Tatyana N. Nayakshina, Elena N. Lomakovskaya and Sergey Kh. Degtyarev<\/h3>\t\t
\r\n\r\n\t\t\t\t\t\t\t<\/i> 0<\/a>\t\t<\/div>\r\n\t\t\t\t\t\t
\r\n\t\t\t\t\tcloning of GlaI site-specific methyl-directed DNA endonuclease gene and the comparison of the substrate specificity of recombinant and native enzymes is described. The analysis of recombinant GlaI endonuclease properties showed that the substrate specificity of native and recombinant enzymes didn't differ, but the concentration of recombinant enzyme exceeded 10 times of native enzyme\t\t\t\t<\/div>\r\n\t\t\t\t\t\t<\/div>\r\n\t<\/article>\r\n\t
\r\n\t\t
\r\n\t\t\t\t\t\t\t
\r\n\t\t\t\t\t
New enzymes<\/a><\/span>Volume 2019<\/a><\/span><\/div>\t\t\t\t\t<\/a>\r\n\t\t\t\t\t\t\t\t\t<\/div>\r\n\t\t\t

\t\t\t\r\n\t\t\t\tA new restriction endonuclease LmnI recognizes the nonpalindromic DNA sequence 5\u2019-GCTCC(1\/-1)-3\u2019\t\t\t<\/a>\r\n\t\t\t<\/h2>

Valery A. Chernukhin, Danila A. Gonchar, Murat A. Abdurashitov, Tatyana N. Nayakshina, Vladimir S. Dedkov, Natalya A. Mikhnenkova, Elena N. Lomakovskaya and Sergey Kh. Degtyarev<\/h3>\t\t
\r\n\r\n\t\t\t\t\t\t\t<\/i> 0<\/a>\t\t<\/div>\r\n\t\t\t\t\t\t
\r\n\t\t\t\t\tWe have discovered a bacterial strain Lysinibacillus manganicus An22 that produces the new prototype of restriction endonuclease named LmnI. This enzyme recognizes a nonpalindromic DNA sequence 5\u2019-GCTCC-3\u2019\/3\u2019-CGAGG-5\u2019. \r\nThe LmnI restriction endonuclease preparation with the concentration of 1000 units\/ml was isolated using four chromatographic steps. It was shown that new enzyme cuts its recognition sequence forming 3\u2019-protruding ends as indicated by the arrows: 5\u2019-GCTCCN\u2193-3\u2019\/3\u2019-CGAG\u2191GN-5\u2019, and can be applied to a IIS type of restriction-modification systems.\t\t\t\t<\/div>\r\n\t\t\t\t\t\t<\/div>\r\n\t<\/article>\r\n\t<\/div>\r\n\t<\/div>[\/vc_column][\/vc_row]<\/p>\n","protected":false},"excerpt":{"rendered":"

[vc_row][vc_column][\/vc_column][\/vc_row]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"coauthors":[23],"class_list":["post-208","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/dnape.online\/en\/wp-json\/wp\/v2\/pages\/208","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/dnape.online\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/dnape.online\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/dnape.online\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/dnape.online\/en\/wp-json\/wp\/v2\/comments?post=208"}],"version-history":[{"count":3,"href":"https:\/\/dnape.online\/en\/wp-json\/wp\/v2\/pages\/208\/revisions"}],"predecessor-version":[{"id":212,"href":"https:\/\/dnape.online\/en\/wp-json\/wp\/v2\/pages\/208\/revisions\/212"}],"wp:attachment":[{"href":"https:\/\/dnape.online\/en\/wp-json\/wp\/v2\/media?parent=208"}],"wp:term":[{"taxonomy":"author","embeddable":true,"href":"https:\/\/dnape.online\/en\/wp-json\/wp\/v2\/coauthors?post=208"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}