Effects of 2-chloroadenine substitution in DNA on restriction endonuclease cleavage reactions

Hentosh, Patricia; McCastlain, J. Clay

doi:10.1093/nar/19.11.3143

Cited by 7 publications

(6 citation statements)

References 30 publications

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“…DNA MODIFICATIONS OTHER THAN m4C, m5C, hm5C, hm5U, AND m6A The effects of several other site-specific DNA modifications on the rate of restriction endonuclease cleavage, such as 5-bromodeoxycytidine, 5-bromodeoxyuridine, 5-iododeoxycytidine, deoxyinosine, 2-aminopurine, 2,6-diaminopurine, 2-chloroadenosine, 7-deazaguanosine, and deoxynucleotide phosphorothioates, are listed elsewhere (Bol,Be6,Mo4,Br2,Ta5,He4,Gr3,Se4,Vo2).…”

Section: Rate Of Cleavage At Methylated Restriction Sitesmentioning

confidence: 99%

Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases

McClelland¹,

Nelson²,

1994

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Restriction endonucleases have site-specific interactions with DNA that can often be inhibited by site-specific DNA methylation and other site-specific DNA modifications. However, such inhibition cannot generally be predicted. The empirically acquired data on these effects are tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific DNA modification methyltransferases and their specificities is presented along with EMBL database accession numbers for cloned genes.

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Section: Rate Of Cleavage At Methylated Restriction Sitesmentioning

confidence: 99%

Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases

McClelland¹,

Nelson²,

1994

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“…DNA modifications other than m4C, m5C, hm5C, 5U, and n,6A The effects of several other site-specific DNA modifications on the rate of restriction endonuclease cleavage, such as 5-bromodeoxycytidine, 5-bromodeoxyuridine, 5-iododeoxycytidine, deoxyinosine, 2-aminopurine, 2,6-diaminopurine, 2-chloroadenosine, 7-deazaguanosine, and deoxynucleotide phosphorothioate deoxynucleotides, are listed elsewhere (Bol ,Be6,Mo4,Br2,Ta5,He4,Gr3,Se4,Vo2).…”

mentioning

confidence: 99%

Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases

Nelson¹,

Raschke

McClelland³

1993

Nucl Acids Res

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We present in Table I an updated list of the sensitivities of 298 restriction endonucleases and 20 DNA methyltransferases to sitespecific modification at 4-methylcytosine (m4C), 5-methylcytosine ('OC), 5-hydroxymethylcytosine (hm5C), and 6-methyladenine (m6A) (McC 14), four modifications that are common m the DNA of prokaryotes, eukaryotes, and their viruses (Mc2,Mc5,Mc8,Mcl 1,Ne3,Ne4). In addition, new information is included on restriction endonuclease cleavage at sites modified with 5-hydroxymethyluracil (h'5U). Knowledge of the sensitivity of restriction endonucleases to site-specific modification can be used to study cellular DNA methylation. Several restriction-modification enzymes share the same recognition sequence specificity, but have different sensitivities to site-specific methylation. Table II lists 32 known isoschizomer pairs and one isomethylator pair, along with the modified recognition sites at which they differ. The data presented here and an additional three other tables are available in printed form or as a text file on a 3.5" Macintosh diskette. The extra tables include Table III which is a list of over 205 characterized DNA methyltransferases. A detailed list of cloned restriction-modification genes has been made by Wilson (Wi4). Table IV lists the sensitivities of over 20 Type II DNA methyltransferases to m4C, m5C, hm5C, and m6A modification. Most DNA methyltransferases are sensitive to non-canonical modifications within their recognition sequences (Bu9,Mc10, Ne3,Po4), and this sensitivity often differs from that of their restriction endonuclease partners. Table V gives a list of restriction systems in this review alphabetized by recognition sequence. The data can be supplied as a Microsoft Word, Macwrite or MS-DOS file. Please contact Michael McClelland at CIBR, phone 619 535 5486, FAX 619 535 5472. Molecular basis for sensitivity restriction enzymes to methylation m4C, m5C, hm5C, and m6A are bulky alkyl substitutions in the major groove of DNA. Site-specific DNA methylation can interfere with many sequence-specific DNA binding proteins (e.g. St2,Wa8), including binding of restriction endonucleases and DNA methyltransferases. At the molecular level, the inability of restriction enzymes to cut modified DNA can be explained using EcoRI and EcoRV endonucleases as instructive models. DNA modification can interfere with substrate binding and/or conformational changes of the enzyme: substrate complex. Based on the EcoRI: DNA co-crystal structure (MclS,Ro8), methylation of either adenine (Gm6AATTC or GAm6ATTC)

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“…The cells that survived the initial treatment with bromodeoxyadenosine progressed through one or two additional cell divisions before they too died. The Huang et al [49] finding, together with our data on the in vitro effects of template ClAde residues [16,17], suggests that the presence of bromodadenine or ClAde in template DNA inhibits further rounds of cellular DNA synthesis or other critical biochemical functions. However, active cellular repair of template ClAde residues would prevent such delayed cytotoxicity and enhance the survival of repaired cells.…”

Section: Discussionmentioning

confidence: 52%

A human factor that recognizes DNA substituted with 2‐chloroadenine, an antileukemic purine analog

Hentosh

Tibudan

Grippo

1995

Molecular Carcinogenesis

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2-Chloro-2'-deoxyadenosine (cladribine), an analog of deoxyadenosine, is an important new drug for the treatment of hairy cell leukemia and other forms of adult and pediatric leukemia. By a gel-shift binding assay, we identified an activity in HeLa nuclear extracts that recognizes and binds to oligonucleotides substituted with 2-chloroadenine (ClAde). The activity was specific for ClAde residues because control oligomers did not readily compete out the complex. The binding factor was a monomeric protein that was resistant to inactivation by heating at 45 degrees C but sensitive to heating at 65 degrees C, proteinase K treatment, and 5 mM ZnCl2. This protein, designated ClAde recognition protein (CARP), appeared to be related to a protein that recognized other forms of DNA damage. Gel-shift binding reactions with ultraviolet (UV)-irradiated oligomers revealed a UV-specific protein/DNA complex that had an electrophoretic mobility similar to that of the CARP/DNA complex, and CARP binding to ClAde-containing oligomers was readily competed out by UV-irradiated DNA. Moreover, CARP activity was present in extracts prepared from UV-sensitive xeroderma pigmentosum group A cells but not in a subset of cells from group E, suggesting that CARP was similar to a previously described repair associated factor, xeroderma pigmentosum-E binding factor. Our findings support a possible repair process for ClAde residues incorporated into cellular DNA.

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Effects of 2-chloroadenine substitution in DNA on restriction endonuclease cleavage reactions

Cited by 7 publications

References 30 publications

Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases

Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases

Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases

A human factor that recognizes DNA substituted with 2‐chloroadenine, an antileukemic purine analog

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