Base pairing involving deoxyinosine: implications for probe design

Martin, Francis H.; Castro, Miguel; Aboul‐ela, Fareed; Tinoco, Ignacio

doi:10.1093/nar/13.24.8927

Cited by 328 publications

(257 citation statements)

References 23 publications

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“…The C/I base pair has the highest level of stability, in keeping with its structural similarity to a C/G base pair (34). The outcome of the computational analysis on the stability of the hypoxanthinecontaining base pairs is consistent with experimental analyses previously reported (35)(36)(37). The stability of the base pairs as estimated by the PMF calculation suggests that the G/I base pair is more prone to base flipping.…”

Section: Discussionsupporting

confidence: 81%

Specificity and Catalytic Mechanism in Family 5 Uracil DNA Glycosylase

Xia

Liu

et al. 2014

Journal of Biological Chemistry

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Section: Discussionsupporting

confidence: 81%

Specificity and Catalytic Mechanism in Family 5 Uracil DNA Glycosylase

Xia

Liu

et al. 2014

Journal of Biological Chemistry

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“…A rate-limiting nucleotide flipping step for Hx excision would also explain the base pair specificity observed previously (16,20). Hypoxanthine is excised more slowly from a more stable Hx⅐C Watson-Crick type pair than an Hx⅐T wobble pair (31)(32)(33). Two explanations are possible to explain why excision of ⑀A is not affected to a great degree by its base pairing partner.…”

Section: Effects Of Hydrogen Bonding Within a Basementioning

confidence: 84%

Effects of Hydrogen Bonding within a Damaged Base Pair on the Activity of Wild Type and DNA-intercalating Mutants of Human Alkyladenine DNA Glycosylase

Vallur¹,

Feller²,

Abner³

et al. 2002

Journal of Biological Chemistry

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Human alkyladenine DNA glycosylase "flips" damaged DNA bases into its active site where excision occurs. Tyrosine 162 is inserted into the DNA helix in place of the damaged base and may assist in nucleotide flipping by "pushing" it. Mutating this DNA-intercalating Tyr to Ser reduces the DNA binding and base excision activities of alkyladenine DNA glycosylase to undetectable levels demonstrating that Tyr-162 is critical for both activities. Mutation of Tyr-162 to Phe reduces the single turnover excision rate of hypoxanthine by a factor of 4 when paired with thymine. Interestingly, when the base pairing partner for hypoxanthine is changed to difluorotoluene, which cannot hydrogen bond to hypoxanthine, single turnover excision rates increase by a factor of 2 for the wild type enzyme and about 3 to 4 for the Phe mutant. In assays with DNA substrates containing 1,N 6 -ethenoadenine, which does not form hydrogen bonds with either thymine or difluorotoluene, base excision rates for both the wild type and Phe mutant were unaffected. These results are consistent with a role for Tyr-162 in pushing the damaged base to assist in nucleotide flipping and indicate that a nucleotide flipping step may be rate-limiting for excision of hypoxanthine.Human alkyladenine DNA glycosylase (AAG) 1 is one of several damage-specific DNA glycosylases that function in the base excision repair pathway (reviewed in Refs. 1-4). These DNA glycosylases initiate repair by identifying and removing damaged bases from DNA. Monofunctional DNA glycosylases, including AAG, hydrolyze the glycosylic bond between the base and sugar to leave an abasic sugar residue in DNA. Other enzymes in the pathway remove this apurinic/apyrimidinic lesion and resynthesize DNA to complete repair. The ability of DNA glycosylases to identify and excise damaged DNA bases is key to the overall success of base excision repair.Structural studies of AAG (5, 6) and other DNA glycosylases have revealed that they use a nucleotide "flipping" mechanism for damaged base recognition and excision where the damaged base is flipped out of the DNA helix and bound in an enzyme active site. In these nucleotide-flipped DNA glycosylase⅐DNA complexes, an enzyme amino acid side chain is inserted into the base stack at the site vacated by the flipped base and may assist in nucleotide flipping by pushing the damaged base from the helix. It is believed that DNA glycosylases actively flip damaged bases out of the helix rather than passively capturing bases that have transiently adopted extrahelical conformations. This active nucleotide flipping mechanism is supported by detailed kinetic studies of Escherichia coli uracil DNA glycosylase which show a two-step binding mechanism where UDG initially binds DNA to form an unflipped protein⅐DNA complex prior to flipping uracil from the helix (7).Many questions remain about how nucleotide flipping enables DNA glycosylases to discriminate between damaged and undamaged bases. For DNA glycosylases that have a narrow substrate specificity, a mechanism where a...

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“…It has a similar structure to guanosine, but lacks the 2-amino group, and pairs with the natural bases as shown in Figure 1 (2)(3)(4)(5)(6)(7)(8)(9). Deoxyinosine has been investigated as a universal base for use in oligonucleotide probes and primers (10)(11)(12). Martin et al using an optical melting technique concluded that it does not pair equally with the four naturally occurring bases, the thermodynamic stabilities being in the order I-C > I-A > I-G -I-T.…”

Section: Introductionmentioning

confidence: 99%