Base-specific reactions useful for DNA sequencing: methylene blue – sensitized photooxidation of guanine and osmium tetraoxide modification of thymine

Friedmann, Theodore; Brown, D. M.

doi:10.1093/nar/5.2.615

Cited by 175 publications

(71 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, most protocols nowadays are based on various DNA-modified electrodes to enhance their detection limit, because the intercalative association of the planar tricyclic phenothiazine ring system (Scheme 1) with the immobilized DNA layer can be utilized for their accumulation onto the electrode surface. [15][16][17] Recently, nanomaterials have been used in bioanalytical chemistry for their unique properties. Colloidal gold is a kind of nanomaterial which possesses tremendous specific surface area and good biocompatibility.…”

Section: Introductionmentioning

confidence: 99%

Sensing Phenothiazine Drugs at a Gold Electrode Co-modified with DNA and Gold Nanoparticles

Zhong

Han

et al. 2003

ANAL. SCI.

View full text Add to dashboard Cite

Section: Introductionmentioning

confidence: 99%

Sensing Phenothiazine Drugs at a Gold Electrode Co-modified with DNA and Gold Nanoparticles

Zhong

Han

et al. 2003

ANAL. SCI.

View full text Add to dashboard Cite

“…Subsequent alkali treatment is known to give products having identical mobility to that of the Maxam-Gilbert products. 8 While a more extensive series of experiments will be required to determine the mechanism responsible for the guanine-specific cleavage of DNA following pulsed u .v. laser excitation, some comments can be made at this stage.…”

mentioning

confidence: 99%

Base-specific photocleavage of DNA induced by nanosecond U.V. pulsed laser radiation or methylene blue sensitisation

Blau¹,

Croke²,

Kelly³

et al. 1987

J. Chem. Soc., Chem. Commun.

View full text Add to dashboard Cite

Excitation of DNA in neutral solution either with short-duration, intense pulses of excimer laser (248 nm) radiation or with l o w intensity red-light (633 nm) sensitisation by methylene blue causes cleavage of the DNA backbone selectively at guanine.The development of photochemical procedures which could complement (or even replace) current DNA sequencing methods is of considerable interest. One appoach could be to use base-specific photocleavage of DNA to replace the chemical methods of Maxam and Gilbert.1 However as it is known that the photochemistry of DNA is dominated by photoreactions of the bases (e.g. thymine dimerisation) and that breaking of the sugar-phosphate backbone is a very inefficient process,2 such a strategy might seem unlikely. We report here that excitation of DNA with short-duration pulses of U.V. radiation causes such cleavage, base-selectively at guanine.Irradiation of DNA with 'picosecond' 314 or 'nanosecond' 5-7 pulses of U.V. radiation has recently been shown to cause rupture of the DNA backbone. Our present experiments have been carried out with a standard (Lambda Physik EMG 102) KrF excimer laser used to provide U.V. pulses (248 mm; pulse-width 22 ns; energy 70 mJ). The laser beam is focussed down so as to excite uniformly a small (4-50 pl) sample of DNA solution contained in a tube of diameter 1.5 or 2.3 nm. By suitable focussing and filtering of the beam it is possible to control the intensity of the pulse within the range 1 x 109-5 x 1012 W m-2. The cleavage of DNA by this radiation has been studied using covalently closed circular (plasmid pBR322) DNA. As expected from the earlier reports,sJj it was found that low intensity light caused little change in the electrophoretic behaviour of this DNA, whereas at the same fluence but at intensities greater than lo9 W m-2 single strand nicking occurred and the open circular and linear forms were produced. This intensity dependence indicates that the bond-rupture reaction is initiated by multi-photon (probably consecutive two photon) excitation, as previously observed with picosecond e~citation.3.~ At an intensity of 5 x 1010 W m-2, the quantum yield for single strand cleavage was found to be ca. 1-2 x 10-5. The base specificity of the cleavage was determined using a 5'-terminus 32P-labelled DNA sample (4.3 kbase EcoRI-Hind I11 restriction fragment of pBR322) and subsequent electrophoresis on sequencing gels in parallel with the products formed by conventional were irradiated for 30 min. Samples were then dried, resuspended in 80% formamide, denatured for 5 min at 95 "C, and electrophoresed as above. It may be noted that the denaturing conditions used (2-5 min at 90°C) might possibly be sufficient to induce some additional cleavage at sites where the bases had been modified during irradiation. before electrophoresis. Sections of the autoradiograph obtained in these experiments are shown in Figure 1 (Lanes 3-5). It may be noted from the pattern of the bands that cleavage is observed only at guanine and that a band is present for each guan...

show abstract

“…Because the bands in the T ϩ C lane of Fig. 4A were not very clear, a separate T-specific reaction was carried out for the 5Ј-A-PdG-C-3Ј sequence and the analysis showed no band at the site of the adduct, which confirmed the exclusive insertion of dAMP opposite the adduct (data not shown) (41).…”

Section: Dna Synthesis On a Pdg-adducted Template-the Effect Ofmentioning

confidence: 87%

“…The bands were cut out of the gel and extracted by shaking overnight in distilled water. The extracted products were purified by ethanol precipitation and ultracentrifugation then subjected to Maxam-Gilbert chemical sequencing and a T-specific reaction (40,41).…”

Section: Chemicals and Enzymesmentioning

confidence: 99%

Replication of Template-Primers Containing Propanodeoxyguanosine by DNA Polymerase β

Hashim

Schnetz-Boutaud

Marnett

1997

Journal of Biological Chemistry

View full text Add to dashboard Cite

Propanodeoxyguanosine (PdG) is a model for several unstable exocyclic adducts formed by reaction of DNA with bifunctional carbonyl compounds generated by lipid peroxidation. The effect of PdG on DNA synthesis by human DNA polymerase ␤ was evaluated using template-primers containing PdG at defined sites. DNA synthesis was conducted in vitro and the products were analyzed by polyacrylamide gel electrophoresis and DNA sequencing. The extent of PdG bypass was low and the products comprised a mixture of base pair substitutions and deletions. Sequence analysis of all of the products indicated that the deoxynucleoside monophosphate incorporated "opposite" PdG was complementary to the base 5 to PdG in the template strand. These findings are very similar to recent results of Efrati et al. (Efrati, E., Tocco, G., Eritja, R., Wilson, S. H., and Goodman, M. F. (1997) J. Biol. Chem. 272, 2559 -2569) obtained in DNA replication of template-primers containing abasic sites and suggest that PdG is a non-informational lesion when acted upon by polymerase (pol) ␤. In addition to base pair substitutions and one-or two-base deletions, a four-base deletion was observed and the mechanism of its formation was probed by site-specific mutagenesis. The results indicated that this deletion occurred by one-base insertion followed by slippage to form a four-base loop followed by extension. All of the observations on pol ␤ replication of PdG-containing template-primers are consistent with a mechanism of lesion bypass that involves template slippage and dNTP stabilization followed by deoxynucleoside monophosphate incorporation and extension. This mechanism of PdG bypass is completely different than that previously determined for the Klenow fragment of DNA polymerase I and is consistent with recent structural models for DNA synthesis by pol ␤.Mutations are the cause of genetic disease and arise during the copying of normal or damaged DNA templates. The factors that determine the frequency and types of mutations include the identity of the DNA polymerase, the composition of the deoxynucleotide pool, the local sequence context of the template, and, in the case of damaged templates, the structure of the DNA lesion (1-16). Our laboratory and others have investigated the effect of propanodeoxyguanosine (PdG) 1 on the fidelity of DNA replication in vivo and in vitro (17)(18)(19)(20)(21)(22). PdG has been used as a model with which to assess the biological effects of several unstable DNA adducts derived from the reaction of dG residues with bifunctional aldehydes (23, 24). PdG is a relatively small lesion that completely blocks Watson-Crick base pairing but induces little distortion in the local structure of DNA molecules to which it is introduced (25, 26). Transformation of recombinant viral genomes or shuttle vectors containing site-specifically positioned PdG residues into bacterial and mammalian cells demonstrates that PdG is highly mutagenic and capable of inducing a range of base pair substitutions and frameshift mutations in vivo (17)(18)(19)22...

show abstract

Base-specific reactions useful for DNA sequencing: methylene blue – sensitized photooxidation of guanine and osmium tetraoxide modification of thymine

Cited by 175 publications

References 10 publications

Sensing Phenothiazine Drugs at a Gold Electrode Co-modified with DNA and Gold Nanoparticles

Sensing Phenothiazine Drugs at a Gold Electrode Co-modified with DNA and Gold Nanoparticles

Base-specific photocleavage of DNA induced by nanosecond U.V. pulsed laser radiation or methylene blue sensitisation

Replication of Template-Primers Containing Propanodeoxyguanosine by DNA Polymerase β

Contact Info

Product

Resources

About