DNA Modifications

Purification and recovery of bulky hydrophobic DNA adducts

For many years (32)P postlabeling has detected DNA adducts at very low levels and yet has not been able to identify unknown adducts. Mass spectrometry offers substantially improved identification powers, albeit at some loss in detection limits. With this ultimate utilization of mass spectrometry in mind, the current research presents a new method to quantitatively purify bulky hydrophobic DNA adducts at levels that are pertinent to ongoing DNA adduct research in human health and environmental fields. This method was demonstrated with benzo[a]pyrene adducts. Purification was accomplished with the use of small columns (7.5-mm frits) with an 11 mg bed of polystyrene-divinlybenzene beads which retained the adducts while permitting the nonadducted nucleotides to be washed out with water. Subsequently, the adducts were eluted with 50% MeOH and the sample was reduced in volume in an evacuated centrifuge. Purification was demonstrated at adduct levels ranging from 4 adducts in 10(6) nonadducted nucleotides to 4 in 10(8). For these levels, analyses by capillary electrophoresis with sample stacking and UV detection determined that recoveries ranged from 91 to 54%, respectively. The adduct quantities isolated should be sufficient to allow the use of current MS capabilities that are linked on-line to separation methodologies such as capillary electrophoresis, capillary electrochromatography, and high-pressure liquid chromatography.

Analysis of nucleotides and oligonucleotides immobilized as self-assembled monolayers by static secondary ion mass spectrometry

Nucleic acid constituents can be bound to a metal surface in the form of self-assembled monolayers. Binding is achieved either through ionic interactions with a self-assembled 2-aminoethanethiol monolayer or by direct covalent binding of a dithiophosphate oligonucleotide to a metal surface through a sulfur-metal bond. Nucleotides, polynucleotides (both normal and a dithiophosphate analog) and double-stranded DNA have all been bound to surfaces. When the surfaces are interrogated using static secondary ion mass spectrometry (SIMS), the surface-bound nucleic acid constituents are observed in the form of the characteristic protonated nucleic acid base ions (BH2+). While a silver foil substrate was found to provide the highest absolute signal, vapor-deposited gold yields the best signal-to-noise ratio for ionically bound deoxyguanosine monophosphate. Under comparable conditions, a Cs+ projectile produces a 10-fold increase in the secondary ion signal relative to a Ga+ projectile. The experiment has been extended to a triple-quadrupole instrument where tandem mass spectrometric experiments on ionically immobilized dGMP showed the characteristic loss of ammonia from the released BH2+ ion. When a 'biomimetic' surface formed by ionically immobilizing double-stranded DNA is exposed to a solution containing ethidium bromide, ions corresponding to the non-covalent adduct are readily detectable using SIMS. This adduct and the nucleic acid constituents can be monitored at levels below 10 fmol.