Reaction of O6-alkylguanine-DNA alkyltransferase with O6-methylguanine analogs: evidence that the oxygen of O6-methylguanine is protonated by the protein to effect methyl transfer

Spratt, Thomas E.; Santos, Hannah De los

doi:10.1021/bi00129a018

Cited by 39 publications

(28 citation statements)

References 53 publications

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“…The oligonucleotides were synthesized and characterized similarly to as previously described (26,27). The oligodeoxynucleotides synthesized include the primer and the template strands of the sequences described below.…”

Section: Synthesis Of Oligodeoxynucleotidesmentioning

confidence: 99%

Structure of the hydrogen bonding complex of O6-methylguanine with cytosine and thymine during DNA replication

Spratt

Levy

1997

Nucleic Acids Research

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During DNA replication, mutations occur when an incorrect dNTP is incorporated opposite a carcinogen-modified nucleotide. We have probed the structures of the interaction between O 6-methylguanine ( O 6mG) and cytosine and thymine during replication by kinetic means in order to examine the structure during the rate determining step. The kinetics of incorporation of dCTP and dTTP opposite O 6mG and three analogs, S 6-methyl-6-thioguanine, O 6-methyl-1-deazaguanine and O 6-methylhypoxanthine, have been measured with four polymerases, the Klenow fragment of DNA polymerase I, the Klenow fragment with the proof-reading exonuclease inactivated, Taq and Tth polymerases. In the insertion of dTTP opposite O 6mG, a large decrease in V max/ K m was observed only upon modification of the N1 position. This result is consistent with a Watson-Crick type configuration. For the incorporation of dCTP, the V max/ K m was significantly decreased only with removal of the exocyclic amino group at the 2 position. The pH dependence of the ratio of incorporation of dCTP and dTTP was independent of pH at physiological pH. This result suggests that dCTP is incorporated via an uncharged complex such as the wobble configuration.

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Section: Synthesis Of Oligodeoxynucleotidesmentioning

confidence: 99%

Structure of the hydrogen bonding complex of O6-methylguanine with cytosine and thymine during DNA replication

Spratt

Levy

1997

Nucleic Acids Research

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“…The synthesis and properties of 3-deazaguanosine and 3-deaza-2′-deoxyguanosine derivatives have been widely studied in the development of anti-bacterial, anti-viral and anti-tumor agents ( 1 – 9 ). The usefulness of 3-deaza-6- O -methyldeoxyguanosine in studying the reaction mechanism of O 6 -alkylguanine-DNA alkyltransferase was also reported ( 10 ). Besides such studies on the biological activities of 3-deazaguanine nucleosides, Seela and co-workers ( 11 , 12 ) have reported studies on the synthesis and physicochemical properties of oligonucleotides incorporating 3-deazaguanine, focusing on the thermal stability of DNA duplexes and the importance of the N 3 atom of the guanine residue on the catalytic activity of hammerhead ribozymes ( 13 ).…”

Section: Introductionmentioning

confidence: 99%

Synthesis of 2′-O-methyl-RNAs incorporating a 3-deazaguanine, and UV melting and computational studies on its hybridization properties

Seio

Sasami

Tawarada

et al. 2006

Nucleic Acids Research

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2′-O-Methyl-RNAs incorporating 3-deazaguanine (c3G) were synthesized by use of N,N-diphenylcarbamoyl and N,N-dimethylaminomethylene as its base protecting groups to suppress sheared-type 5′-GA-3′/5′-GA-3′ tandem mismatched base pairing which requires the N3 atom. These modified RNAs hybridized more weakly with the complementary and single mismatch-containing RNAs than the unmodified RNAs. The Tm experiments were performed to clarify the effects of replacement of the fifth G with c3G on stabilization of 2′-O-methyl-(5′-CGGCGAGGAG-3′)/5′-CUCCGAGCCG-3′ and 2′-O-methyl-(5′-CGGGGACGAG-3′)/5′-CUCGGACCCG-3′duplexes, which form sheared-type and face-to-face type 5′-GA-3′/5′-GA-3′ tandem mismatched base pairs, respectively. Consequently, this replacement led to more pronounced destabilization of the former duplex that needs the N3 atom for the sheared-type base pair than the latter that does not need it for the face-to-face type base pair. A similar tendency was observed for 2′-O-methyl-RNA/DNA duplexes. These results suggest that the N3 atom of G plays an important role in stabilization of the canonical G/C base pair as well as the base discrimination and its loss suppressed formation of the undesired sheared-type mismatched base pair. Computational studies based on ab initio calculations suggest that the weaker hydrogen bonding ability and larger dipole moment of c3G can be the origin of the lower Tm.

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“…The structural data further suggested that the efficiency of alkyl transfer could be reduced by impairing the substrate binding to SNAP‐tag. Based on this, two BG derivatives, that is, BI lacking the 2‐amino group and 7‐deaza‐benzylguanine (deBG) replacing N7 with C7 (Figure 2b), were chosen as the candidates [42,49,50] . Subsequently these substrates were synthesized as described in the Experimental Section and Supporting Information.…”

Section: Resultsmentioning

confidence: 99%

Tuning the Reactivity of a Substrate for SNAP‐Tag Expands Its Application for Recognition‐Driven DNA‐Protein Conjugation

Zhang

Nakata

Dinh

et al. 2021

Chemistry A European J

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Recognition‐driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site‐specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition‐driven modification of DNA as they consist of both a sequence‐specific DNA‐binding domain (DBD) and a self‐ligating protein‐tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence‐specific reaction. However, combining an MA consisting of a reactive protein‐tag and its substrate, for example, SNAP‐tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP‐tag have been designed to realize sequence‐selective rapid crosslinking reactions of MAs with SNAP‐tag. The reactions of substrates with SNAP‐tag were verified by kinetic analyses to enable the sequence‐selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP‐tag against CLIP‐tag to achieve orthogonal DNA‐protein crosslinking by six unique MAs.

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Reaction of O6-alkylguanine-DNA alkyltransferase with O6-methylguanine analogs: evidence that the oxygen of O6-methylguanine is protonated by the protein to effect methyl transfer

Cited by 39 publications

References 53 publications

Structure of the hydrogen bonding complex of O6-methylguanine with cytosine and thymine during DNA replication

Structure of the hydrogen bonding complex of O6-methylguanine with cytosine and thymine during DNA replication

Synthesis of 2′-O-methyl-RNAs incorporating a 3-deazaguanine, and UV melting and computational studies on its hybridization properties

Tuning the Reactivity of a Substrate for SNAP‐Tag Expands Its Application for Recognition‐Driven DNA‐Protein Conjugation

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