Using DNA Origami Nanostructures To Determine Absolute Cross Sections for UV Photon-Induced DNA Strand Breakage

Abstract

We have characterized ultraviolet (UV) photon-induced DNA strand break processes by determination of absolute cross sections for photoabsorption and for sequence-specific DNA single strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowest-energy photons able to induce DNA strand breaks. Oligonucleotide targets are immobilized on a UV transparent substrate in controlled quantities through attachment to DNA origami templates. Photon-induced dissociation of single DNA strands is visualized and quantified using atomic force microscopy. The obtained quantum yields for strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA strand breakage by UV photons, which is clearly dependent on the photon energy. Above the ionization threshold strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also dependent on the nucleotide sequence.

Low‐Energy Electron‐Induced Strand Breaks in Telomere‐Derived DNA Sequences—Influence of DNA Sequence and Topology

“…The observed strand break cross sections are in the order of 10 −14 cm 2 , which underlines the high efficiency of the LEE‐induced strand breakage. The corresponding strand break cross sections for photon‐induced strand breakage using photons of approximately the same energy (8.4 eV) are almost two orders of magnitude smaller …”

“…Strand breaks are visualized in AFM images using the protein streptavidin (SAv), which binds specifically to a biotin (Bt) label at the intact oligonucleotide target strands. The determination of absolute cross sections is particularly valuable because the obtained values can be directly compared to absolute cross sections for related processes such as absorption, excitation, ionization, electron attachment, dissociative electron attachment, etc., if all these cross sections can be recorded with the same target configuration and substrate …”

FRET efficiency and antenna effect in multi-color DNA origami-based light harvesting systems

“…21,22 Since every staple strand can be addressed and modied individually and separately, different moieties can be arranged with a high local control since the exact position of each staple strand in the DNA origami structure is known. DNA origami structures have been used to create highly sensitive SERS substrates by attaching gold nanoparticle dimers, [23][24][25] to analyze DNA strand breaks induced by low energy electrons 26,27 and UV photons 28 and to arrange different uo-rophores 29,29,30 at precise distances to create nanoscale photonic devices which can be used for example as photonic wires, 15,18 to resolve conformational changes of biomolecules, [31][32][33][34] as logic gates 35,36 and articial light harvesting complexes. 8,10,18 The light harvesting efficiency is in this context typically expressed as an antenna effect (AE), i.e.…”

Evaluating experimental molecular physics studies of radiation damage in DNA*

“…Therefore it became possible not only to detect but also to accurately quantify the yields of oligonucleotide strand breaks formed directly upon irradiation with electrons [73] or photons [74].…”