Synthesis and Hydrolysis of Oligodeoxyribonucleotides Containing 2-Aminopurine

Fujimoto, June; Nuesca, Zoraida M.; Mazurek, Mark; Sowers, Lawrence C.

doi:10.1093/nar/24.4.754

Cited by 28 publications

(19 citation statements)

References 32 publications

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“…A number of fluorescent base analogs have been incorporated into nucleoside phosphoramidites and thus synthetic nucleic acids. One of the most popular fluorescent nucleobases is 2-aminopurine, an analog of the purines adenine and guanine (Ward et al 1969;Doudna et al 1990;Fujimoto et al 1996;Millar 1996;Rist and Marino 2002). It specifically Watson-Crick base-pairs with thymine or uracil and has proven its utility as a probe to monitor local conformational changes in nucleic acid structure, for example, in catalytic RNA and upon formation of nucleic acid-protein complexes (Millar 1996;O'Neill and Barton 2002;Walter et al 2002;Patel and Bandwar 2003;Roy 2003;Bradrick and Marino 2004;Clerte and Hall 2004).…”

Section: Introductionmentioning

confidence: 99%

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation

Tinsley¹,

Walter²

2006

RNA

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Pyrrolo-C (PC), or 3-[b-D-2-ribofuranosyl]-6-methylpyrrolo [2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G. Due to its red-shifted absorbance, it can be selectively excited in the presence of natural nucleosides, making it a potential site-specific probe for RNA structure and dynamics. Similar to 2-aminopurine nucleoside, which base-pairs with uridine (or thymidine), PC's fluorescence becomes reversibly quenched upon base-pairing, most likely due to stacking interactions with neighboring bases. To test its utility as an RNA probe, we examined PC's fluorescent properties over a wide range of ionic strengths, pH, organic cosolvents, and temperatures. Incorporation of PC into a single-stranded RNA results in an $60% reduction of fluorescence intensity, while duplex formation reduces the fluorescence by $75% relative to the free ribonucleoside. We find that the fluorescence intensity of PC is only moderately affected by ionic strength, pH, and temperature, while it is slightly enhanced by organic cosolvents, making it a versatile probe for a broad range of buffer conditions. We demonstrate two applications for PC: fluorescent measurements of the kinetics of formation and dissociation of an RNA/DNA complex, and fluorescent monitoring of the thermal denaturation of the central segment of an RNA duplex. Taken together, our data showcase the potential of pyrrolo-C as an effective fluorescent probe to study RNA structure, dynamics, and function, complementary to the popular 2-aminopurine ribonucleoside.

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Section: Introductionmentioning

confidence: 99%

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation

Tinsley¹,

Walter²

2006

RNA

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“…The formation of C C (15) and N N (18) bridged dimers can be accounted for on the basis of the rapid dimerization of the radical species (12) and (13), respectively. The ribose triphosphate moieties in both the dimers seem to hydrolyze either during dimerization due to steric hindrance or during silylation at 110 • C. The second possibility can be ruled out on the basis that several purine derivatives have been found to give products having ribose unit attached during silylation [38] and addition of 0.1 M HCl to the electrolyzed sample to convert the sodium salt into the free acid would further cause the cleavage of ␤-N-glycosidic linkage as well documented in the literature [39]. Interestingly, during silylation all the reactive hydrogen atoms attached to nitrogen atoms are replaced with trimethylsilyl units to give the corresponding tetrasilylated C C dimer (16) and disilylated N N dimer (19) having m/z 558 and 414, respectively.…”

Section: Redox Mechanismmentioning

confidence: 80%

Electrochemical oxidation of inosine-5′-triphosphate at pyrolytic graphite electrode

Goyal

Dhawan

2006

Electrochimica Acta

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“…Oligonucleotide Synthesis and Characterization-Oligonucleotides were prepared by solid phase synthesis methods as described previously (26,27). Following synthesis and deprotection, oligonucleotides were purified with Poly-Pak II cartridges, and denaturing gel purified when necessary.…”

Section: Methodsmentioning

confidence: 99%

Mechanisms of Base Selection by the Escherichia coli Mispaired Uracil Glycosylase

Liu

Theruvathu

Darwanto

et al. 2008

Journal of Biological Chemistry

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The repair of the multitude of single-base lesions formed daily in cells of all living organisms is accomplished primarily by the base excision repair pathway that initiates repair through a series of lesion-selective glycosylases. In this article, singleturnover kinetics have been measured on a series of oligonucleotide substrates containing both uracil and purine analogs for the Escherichia coli mispaired uracil glycosylase (MUG). The relative rates of glycosylase cleavage have been correlated with the free energy of helix formation and with the size and electronic inductive properties of a series of uracil 5-substituents. Data are presented that MUG can exploit the reduced thermodynamic stability of mispairs to distinguish U:A from U:G pairs. Discrimination against the removal of thymine results primarily from the electron-donating property of the thymine 5-methyl substituent, whereas the size of the methyl group relative to a hydrogen atom is a secondary factor. A series of parameters have been obtained that allow prediction of relative MUG cleavage rates that correlate well with observed relative rates that vary over 5 orders of magnitude for the series of base analogs examined. We propose that these parameters may be common among DNA glycosylases; however, specific glycosylases may focus more or less on each of the parameters identified. The presence of a series of glycosylases that focus on different lesion properties, all coexisting within the same cell, would provide a robust and partially redundant repair system necessary for the maintenance of the genome.

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Synthesis and Hydrolysis of Oligodeoxyribonucleotides Containing 2-Aminopurine

Cited by 28 publications

References 32 publications

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation

Electrochemical oxidation of inosine-5′-triphosphate at pyrolytic graphite electrode

Mechanisms of Base Selection by the Escherichia coli Mispaired Uracil Glycosylase

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