Structure determination of isomeric hexadeoxynucleotide photoproducts by high-field NMR and fast atom bombardment/ tandem mass spectrometry

Detection of UVA/UVC-induced damage of p53 fragment by rolling circle amplification with AIEgens

A new strategy combining the rolling circle amplification and the aggregation-induced emission molecule is achieved to differentiate damaged and undamaged p53 fragments.

UV-induced TA photoproducts: formation and hydrolysis in double-stranded DNA

Hydrolysis of TA photoproduct leads to two derivatives presenting different formation kinetic profiles depending on the oligomer content. The formation efficiency of TA photoproducts in UV-C-irradiated DNA slightly exceeds the formation of the trans,syn cyclobutane pyrimidine dimer at TT sites.

Characterization of activation energy distribution for ultraviolet irradiation of T-rich oligonucleotide using high-performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry

Exposure to solar UV radiation gives rise to mutations that may lead to skin cancer of human being. Series of experiments were carried out in order to reveal activation energy distribution of DNA mutation caused by UV radiation. The T-rich oligonucleotides were exposed to UV radiation with increasing intensity for different durations. Photoproducts of T-rich oligonucleotide were investigated using ion-pair reversed-phase high-performance liquid chromatography/tandem electrospray ionization mass spectrometry (IP-RP-HPLC/ESI-MS) at room temperature. Two photoproducts of T-rich oligonucleotide were cis-syn cyclobutane pyrimidine dimmer (T[c,s]T) and the pyrimidine(6,4)pyrimidone product (T[6,4]T). Activation energy distribution of DNA mutation was calculated using a commercial kinetics analysis programs by Robert L. Braun and Alan K. Burnham , Lawrance Livermore International Laboratory (version 2.4.1). To use the software for deriving the kinetics parameters, the factor T (temperature) in the software was substituted with k1R, in which k1 is a factor, R is radiation intensity. The activation energy derived ranges from 55 to 110 kJ mol(-1). By the same software, those kinetics parameters were extrapolated to natural UV radiation process to predict DNA damage degree without the DNA repair process.

Location of abasic sites in oligodeoxynucleotides by tandem mass spectrometry and by a chemical cleavage initiated by an unusual reaction of the ODN with MALDI matrix

We describe two approaches employing electrospray ionization (ESI) tandem mass spectrometry (MS/MS) and matrix assisted laser desorption/ionization (MALDI) post-source decay (PSD) for determining the location of an abasic site in modified oligodeoxynucleotides (ODNs). With MS/MS, we found both complementary fragment ions (a(n)' and w(n)') produced at the abasic site were predominant in the mass spectra and allowed the location to be determined. Under MALDI conditions, most ODNs carrying an abasic site are singly charged, and PSD gives predominately w(n)' ions at the abasic sites, revealing their location. We also describe another approach for identifying and locating abasic sites in model ODNs; namely, an "in situ" derivatization coupled with MALDI mass spectrometry (MS). In general, an ODN n-mer containing an abasic site at the m-th position from the 5-terminus can react with the matrix component, anthranilic acid, to form a Schiff base. The adduct upon MALDI breaks into 3' and 5' fragments (w(n-m), b(m), a(m), d(m-1)) at the abasic site, revealing its location. ESI MS methods are also applicable for detecting the hydrazone derivatives of abasic sites, and the fragmentation of hydrazones shows the location of the abasic site.

Determination of photomodified oligodeoxynucleotides by exonuclease digestion, matrix-assisted laser desorption/ionization and post-source decay mass spectrometry

A fast method to detect and sequence photomodified oligodeoxynucleotides (ODNs) by exonuclease digestion and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is reported. Upon treatment of modified ODNs with both phosphodiesterase I and phosphodiesterase II, the digestion stops at the sites of photomodification. Post-source decay (PSD) of MALDI-produced ions from two enzymatic digestion end products distinguishes isomers such as 5'-d(T[cis-syn]TAAGC) and 5'-d(CGAAT[cis-syn]T), which have symmetrical or identical compositions at the 3' and 5' ends, respectively. Studies have also been done to follow the kinetics for enzyme degradation of photomodified ODNs. The calculated rate constants from a mathematical treatment of the time-dependent MALDI data clearly show that the enzymatic digestion rate slows as the enzyme approaches the modified site.

Fragmentation of electrospray-produced oligodeoxynucleotide ions adducted to metal ions

In this article, we describe the unique fragmentations of oligodeoxynucleotides (ODNs) whose phosphate groups are completely depleted of protons and replaced with metal ions. The production of the ubiquitous [a(n) - base] ions still occurs, but no longer by transfer of an acidic phosphate proton to an adjoining 3' base. Nor is the extent of the reaction determined by the proton affinity of that base. Rather, the reaction now occurs via a cleavage 3' to both pyrimidines and purines; cleavage 3' to pyrimidine is more favorable than that 3' to purine. We also demonstrate that an ODN is more stable in the gas phase when its phosphate groups are bound to metal ions than when its phosphate groups are attached to hydrogens. This study also provides further evidence for the ODN fragmentation mechanism that involves H transfer to a nucleobase. To establish the structural utility of this new fragmentation, we applied it to distinguishing small ODNs containing a photomodified cis,syn-cyclobutane pyrimidine dimer from the parent ODNs, a system that cannot be distinguished by collisional activation of precursor species that do not contain metal ions.

Matrix-assisted laser desorption/ionization mass spectrometry methods for oligodeoxynucleotides: improvements in matrix, detection limits, quantification, and sequencing

A comatrix of anthranilic acid and nicotinic acid is optimum for the matrix-assisted laser desorption/ionization time of flight determination of oligodeoxynucleotides that are comprised of up to 21 nucleotides. A detection limit of approximately 200 amol was obtained for an oligonucleotide 21mer. The comatrix system is also suitable for quantification of oligodeoxynucleotides provided an internal standard having one more or less nucleotide than the number in the analyte is used. Furthermore, the matrix, when used in combination with the ladder method of sequencing, allows the complete sequence of tens of picomoles of model oligodeoxynucleotides to be determined.

Differentiation of isomeric photomodified oligodeoxynucleotides by fragmentation of ions produced by matrix-assisted laser desorption ionization and electrospray ionization

UV irradiation of oligodeoxynucleotides at 254 nm generates several different types of DNA photoproducts, including cis-syn cyclobutane pyrimidine dimers, pyrimidine[6-4] pyrimidone photoproducts and their Dewar valence isomers, and thymine-adenine photoproducts (TA*). Studies of photoproducts in oligodeoxynucleotides require the development of suitable structure determination methods such as mass spectrometry. In an earlier study (Vollmer et al. Int. J. Mass Spectrom. Ion Processes 1997, 165/166, 487-496), we showed that fast atom bombardment and tandem sector mass spectrometry can be used to locate the site of photomodification and identify most of the photoproducts of d(TATTAT). One goal of the present research was to expand the method to the more sensitive electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) methods. A second goal was to test the generality of the methods by investigating not only the photoproducts of d(TATTAT) but also those of three other oligodeoxynucleotides, d(GTATTAT), d(GGCTATAA), and d(AATTAA). The photoproducts of these sequences were separated by HPLC and gave characteristic fragment ions in postsource decompositions of MALDI-produced ions and collisionally activated decompositions of ESI-produced ions.