Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low‐Energy Electrons (0.5–9 eV)

Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low‐energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross‐section for oligonucleotides modified with 8‐bromoadenine (^8BrA). These results were evaluated against DEA measurements with isolated ^8BrA in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks.     

Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks – Influence of the DNA Sequence and Substrate

DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF₂ as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7–2.3×10⁻¹⁶ cm². The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.     

Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low‐Energy Electron Attachment

To elucidate the role of guanosine in DNA strand breaks caused by low‐energy electrons (LEEs), theoretical investigations of the LEE attachment‐induced C? O σ‐bonds and N‐glycosidic bond breaking of 2′‐deoxyguanosine‐3′,5′‐diphosphate (3′,5′‐dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3′,5′‐diphosphate in the gas phase excludes either C? O bond cleavage or N‐glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3′,5′‐dGDP and the VDE of 3′,5′‐dGDP^?. Furthermore, the solvent–solute interactions greatly reduce the activation barriers of the C? O bond cleavage to 1.06–3.56 kcal mol^?1. These low‐energy barriers ensure that either C_5′? O_5′ or C_3′? O_3′ bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N‐glycosidic bond rupture implies that this reaction pathway is inferior to C? O bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE‐induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE‐induced DNA damage resembles that of the solvent.     

Induction of strand breaks in DNA films by low energy electrons and soft X-ray under nitrous oxide atmosphere

Five-monolayer (5 ML) plasmid DNA films deposited on glass and tantalum substrates were exposed to Al K_α X-rays of 1.5 keV under gaseous nitrous oxide (N₂O) at atmospheric pressure and temperature. Whereas the damage yields for DNA deposited on glass are due to soft X-rays, those arising from DNA on tantalum are due to both the interaction of low energy photoelectrons from the metal and X-rays. Then, the differences in the yields of damage on glass and tantalum substrates, essentially arises from interaction of essentially low-energy electrons (LEEs) with DNA molecules and the surrounding atmosphere. The G-values (i.e., the number of moles of product per Joule of energy absorbed) for DNA strand breaks induced by LEEs (G_LEE) and the lower limit of G-values for soft X-ray photons (G_XL) were calculated and the results compared to those from previous studies under atmospheric conditions and other ambient gases, such as N₂ and O₂. Under N₂O, the G-values for loss of supercoiled DNA are 103±15 nmol/J for X-rays, and 737±110 nmol/J for LEEs. Compared to corresponding values in an O₂ atmosphere, the effectiveness of X-rays to damage DNA in N₂O is less, but the G value for LEEs in N₂O is more than twice the corresponding value for an oxygenated environment. This result indicates a higher effectiveness for LEEs relative to N₂ and O₂ environments in causing SSB and DSB in an N₂O environment. Thus, the previously observed radiosensitization of cells by N₂O may not be only due to OH radicals but also to the reaction of LEE with N₂O molecules near DNA. The previous experiments with N₂ and O₂ and the present one demonstrate the possibility to investigate damage induced by LEEs to biomolecules under various types of surrounding atmospheres.     

Low energy electron induced damage to plasmid DNA pQE30

Low energy electrons (LEEs) are produced in copious amounts by the primary radiation used in radiation therapy. The damage caused to the DNA by these secondary electrons in the energy range 5-22 eV has been studied to understand their possible role in radiation induced damage. Electrons are irradiated on dried films of plasmid DNA (pQE30) and analysed using agarose gel electrophoresis. Single strand breaks (SSBs) induced by LEE to supercoiled plasmid DNA show resonance structures at 7, 12, and 15 eV for low doses and 6, 10, and ～18 eV at saturation doses. The present measurements have an overall agreement with the literature that LEEs resonantly induce SSBs in DNA. Resonant peaks in the SSBs induced by LEEs at 7, 12, and 15 eV with the lowest employed dose in the current study are somewhat different from those reported earlier by two groups. The observed differences are perhaps related to the irradiation dose, conditions and the nature of DNA employed, which is further elaborated.     

Reactions in Nitroimidazole Triggered by Low‐Energy (0–2 eV) Electrons: Methylation at N1‐H Completely Blocks Reactivity

Low‐energy electrons (LEEs) at energies of less than 2 eV effectively decompose 4‐nitroimidazole (4NI) by dissociative electron attachment (DEA). The reactions include simple bond cleavages but also complex reactions involving multiple bond cleavages and formation of new molecules. Both simple and complex reactions are associated with pronounced sharp features in the anionic yields, which are interpreted as vibrational Feshbach resonances acting as effective doorways for DEA. The remarkably rich chemistry of 4NI is completely blocked in 1‐methyl‐4‐nitroimidazole (Me4NI), that is, upon methylation of 4NI at the N1 site. These remarkable results have also implications for the development of nitroimidazole based radiosensitizers in tumor radiation therapy.     

The Equally Important Role of Adenine Derivatives to That of Pyrimidine Derivatives in Near‐0 eV Electron‐Induced DNA Lesions

The role of adenine (A) derivatives in DNA damage is scarcely studied due to the low electron affinity of base A. Experimental studies demonstrate that low‐energy electron (LEE) attachment to adenine derivatives complexed with amino acids induces barrier‐free proton transfer producing the neutral N₇‐hydrogenated adenine radicals rather than conventional anionic species. To explore possible DNA lesions at the A sites under physiological conditions, probable bond ruptures in two models—N₇‐hydrogenated 2′‐deoxyadenosine‐3′‐monophosphate (3′‐dA(N7H)MPH) and 2′‐deoxyadenosine‐5′‐monophosphate (5′‐dA(N7H)MPH), without and with LEE attachment—are studied by DFT. In the neutral cases, DNA backbone breakage and base release resulting from C_3′?O_3′ and N₉?C_1′ bond ruptures, respectively, by an intramolecular hydrogen‐transfer mechanism are impossible due to the ultrahigh activation energies. On LEE attachment, the respective C_3′?O_3′ and N₉?C_1′ bond ruptures in [3′‐dA(N7H)MPH]^? and [5′‐dA(N7H)MPH]^? anions via a pathway of intramolecular proton transfer (PT) from the C_2′ site of 2′‐deoxyribose to the C₈ atom of the base moiety become effective, and this indicates that substantial DNA backbone breaks and base release can occur at non‐3′‐end A sites and the 3′‐end A site of a single‐stranded DNA in the physiological environment, respectively. In particular, compared to the results of previous theoretical studies, not only are the electron affinities of 3′‐dA(N7H)MPH and 5′‐dA(N7H)MPH comparable to those of hydrogenated pyrimidine derivatives, but also the lowest energy requirements for the C_3′?O_3′ and N₉‐glycosidic bond ruptures in [3′‐dA(N7H)MPH]^? and [5′‐dA(N7H)MPH]^? anions, respectively, are comparable to those for the C_3′?O_3′ and N₁‐glycosidic bond cleavages in corresponding anionic hydrogenated pyrimidine derivatives. Thus, it can be concluded that the role of adenine derivatives in single‐stranded DNA damage is equally important to that of pyrimidine derivatives in an irradiated cellular environment.     

Electron‐induced dissociation of doubly protonated betaine clusters: controlling fragmentation chemistry through electron energy

The [M₂₁+2H]²⁺ cluster of the zwitterion betaine, M = (CH₃)₃NCH₂CO₂, formed via electrospray ionisation (ESI), has been allowed to interact with electrons with energies ranging from >0 to 50 eV in a Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometer. The types of gas‐phase electron‐induced dissociation (EID) reactions observed are dependent on the energy of the electrons. In the low‐energy region up to 10 eV, electrons are mainly captured, forming the charge‐reduced species, {[M₂₁+2H]^{+ .} }*, in an excited state, which stabilises via the ejection of an H atom and one or more neutral betaines. In the higher energy region, above 12 eV, a Coulomb explosion of the multiply charged clusters is observed in highly asymmetric fission with singly charged fragments carrying away more than 70% of the parent mass. Neutral betaine evaporation is also observed in this energy region. In addition, a series of singly charged fragments appears which arise from C? X bond cleavage reactions, including decarboxylation and CH₃ group transfer. These latter reactions may arise from access of electronic excited states of the precursor ions. Copyright © 2009 John Wiley & Sons, Ltd.     

Impact of Single Basepair Mismatches on Electron‐Transfer Processes at Fc‐PNA⋅DNA Modified Gold Surfaces

Gold‐surface grafted peptide nucleic acid (PNA) strands, which carry a redox‐active ferrocene tag, present unique tools to electrochemically investigate their mechanical bending elasticity based on the kinetics of electron‐transfer (ET) processes. A comparative study of the mechanical bending properties and the thermodynamic stability of a series of 12‐mer Fc‐PNA?DNA duplexes was carried out. A single basepair mismatch was integrated at all possible strand positions to provide nanoscopic insights into the physicochemical changes provoked by the presence of a single basepair mismatch with regard to its position within the strand. The ET processes at single mismatch Fc‐PNA?DNA modified surfaces were found to proceed with increasing diffusion limitation and decreasing standard ET rate constants k⁰ when the single basepair mismatch was dislocated along the strand towards its free‐dangling Fc‐modified end. The observed ET characteristics are considered to be due to a punctual increase in the strand elasticity at the mismatch position. The kinetic mismatch discrimination with respect to the fully‐complementary duplex presents a basis for an electrochemical DNA sensing strategy based on the Fc‐PNA?DNA bending dynamics for loosely packed monolayers. In a general sense, the strand elasticity presents a further physicochemical property which is affected by a single basepair mismatch which may possibly be used as a basis for future DNA sensing concepts for the specific detection of single basepair mismatches.     

Comparison between X-ray photon and secondary electron damage to DNA in vacuum

Both monolayer and thick (20 microm) films of dry pGEM-3Zf(-) plasmid DNA deposited on tantalum foil were exposed to Al Kalpha X-rays (1.5 keV) for various times in an ultrahigh vacuum chamber. For monolayer DNA, the damage was induced mainly by low energy secondary electrons (SEs) emitted from the tantalum. For the thick films, DNA damage was induced chiefly by X-ray photons. Different forms of plasmid DNA were separated and quantified by agarose gel electrophoresis. The exposure curves for the formation of nicked circular (single strand break, SSB), linear (double strand break, DSB), and interduplex cross-link forms 1 and 2 were obtained for both monolayer and thick films of DNA, respectively. The lower limits of G values for SSB and DSB induced by SEs were derived to be 86 +/- 2 and 8 +/- 2 nmol J(-1), respectively. These values are 1.5 and 1.6 times larger than those obtained with 1.5 keV photons. The projected X-ray energy dependence of the low energy electron (LEE) enhancement factor for the SSB and DSB in monolayer DNA is also discussed. This new method of investigation of the SE-induced damage to large biomolecules allows direct comparison of the yield of products induced by high energy photons and LEEs under identical experimental conditions.     

Low energy electron and O- reactions in films of O2 coadsorbed with benzene or toluene

A detailed understanding of nascent reactive events leading to DNA damage is required to describe ionizing radiation effects on living cells. These early, sub-picosecond events involve mainly low energy (E < 20 eV) secondary electrons (SE), and low energy (E < 5 eV) secondary ion (and neutral) fragments; the latter are created either by the primary radiation, or by SE via dissociative electron attachment (DEA). While recent work has shown that SE initiate DNA strand break formation via DEA, the subsequent damage induced by the DEA ion fragments in DNA, or its basic components is unknown. Here, we report 0-20 eV electron impact measurements of anion desorption from condensed films containing O2 and either benzene (C6H6), or toluene (C6H5CH3); these molecules represent the most fundamental structural analogs of pyrimidine bases. Our experiments show that all of the observed OH- yields are the result of reactive scattering of 1-5 eV O- fragments produced initially by DEA to O2. These O- reactions involve hydrogen abstraction from benzene or toluene, and result in the formation of benzyl radicals, or toluene radicals centered on either the ring or exocyclic methyl group. O- scatters over nm distances comparable to DNA dimensions, and reactions involve a transient anion collision complex. Anion desorption is found to depend on both, the temperature of hydrocarbon film formation (morphology), and the order of overlayer adsorption, e.g. O2 on benzene, or benzene on O2. Our measurements support the notion that in irradiated DNA similar secondary-ion reactions can be initiated by the abundant secondary electrons, and may lead to clustered damage.     

Synthesis and characterization of new low band‐gap polymers containing electron‐accepting acenaphtho[1,2‐c]thiophene‐S,S‐dioxide groups

Two donor–acceptor conjugated polymers, PTSSO‐TT and PTSSO‐BDT, composed of acenaphtho[1,2‐c]thiophene ‐ S,S‐dioxide (TSSO) as a new electron acceptor and thienothiophene (TT) or benzo[1,2‐b:4,5‐b']dithiophene (BDT) as electron donors, were synthesized with Stille cross‐coupling reactions. The number‐averaged molecular weights (M_n) of PTSSO‐TT and PTSSO‐BDT were found to be 15100 and 26000 Da, with dispersity of 1.8 and 2.4, respectively. The band‐gap energies of PTSSO‐TT and PTSSO‐BDT are 1.56 and 1.59 eV, respectively. The HOMO levels of PTSSO‐TT and PTSSO‐BDT are ?5.4 and ?5.5 eV, respectively. These results indicate that the inclusion of TSSO accepting units into polymers is a very effective method for lowering their HOMO energy levels. The field‐effect mobilities of PTSSO‐TT and PTSSO‐BDT were determined to be 1.5 × 10^?3 and 4.5 × 10^?4 cm² V^?1 s^?1, respectively. A polymer solar cell device prepared with PTSSO‐TT as the active layer was found to exhibit a power conversion efficiency (PCE) of 3.79% with an open circuit voltage of 0.71 V under AM 1.5 G (100 mW cm^?2) conditions. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 498–506     

Synthesis and Characterization of Acetylene‐Linked Bisphenalenyl and Metallic‐Like Behavior in Its Charge‐Transfer Complex

We prepared and isolated a phenalenyl‐based neutral hydrocarbon ( 1 b ) with a biradical index of 14 %, as well as its charge‐transfer (CT) complex 1 b –F₄‐TCNQ. The crystal structure and the small HOMO–LUMO gap assessed by electrochemical and optical methods support the singlet‐biradical contribution to the ground state of the neutral 1 b . This biradical character suggests that 1 b has the electronic structure of phenalenyl radicals coupled weakly through an acetylene linker, that is, some independence of the two phenalenyl moieties. The monocationic species 1 b^{. +} was obtained by reaction with the organic electron acceptor F₄‐TCNQ. The cationic species has a small disproportionation energy ΔE for the reaction 2× 1 b^{. +}? 1 b + 1 b ²⁺, which presumably originates from the independence of the phenalenyl moieties. The small ΔE led to a small on‐site Coulombic repulsion U_eff=0.61 eV in the CT complex. Moreover, a very effective orbital overlap of the phenalenyl rings between molecules afforded a relatively large transfer integral t=0.09 eV. The small U_eff/4t ratio (=1.7) resulted in a metallic‐like conductive behavior at around room temperature. Below 280 K, the CT complex showed a transition into a semiconductive state as a result of bond formation between phenalenyl and F₄‐TCNQ carbon atoms.     

Intelligent,Biodegradable, and Self‐Healing Hydrogels Utilizing DNA Quadruplexes

A new class of hydrogels utilizing DNA (DNA quadruplex gel) has been constructed by directly and symmetrically coupling deoxynucleotide phosphoramidite monomers to the ends of polyethylene glycols (PEGs) in liquid phase, and using the resulting DNA‐PEG‐DNA triblock copolymers as macromonomers. Elongation of merely four deoxyguanosine residues on PEG, which produces typically ≈10 grams of desired DNA‐PEG conjugates in one synthesis, resulted in intelligent and biodegradable hydrogels utilizing DNA quadruplex formation, which are responsive to various input signals such as Na⁺, K⁺, and complementary DNA strand. Gelation of DNA quadruplex gels takes place within a few seconds upon the addition of a trigger, enabling free formation just like Ca⁺‐alginate hydrogels or possible application as an injectable polymer (IP) gel. The obtained hydrogels show good thermal stability and rheological properties, and even display self‐healing ability.     

Diazido Mixed‐Amine Platinum(IV) Anticancer Complexes Activatable by Visible‐Light Form Novel DNA Adducts

Platinum diam(m)ine complexes, such as cisplatin, are successful anticancer drugs, but suffer from problems of resistance and side‐effects. Photoactivatable Pt^IV prodrugs offer the potential of targeted drug release and new mechanisms of action. We report the synthesis, X‐ray crystallographic and spectroscopic properties of photoactivatable diazido complexes trans,trans,trans‐[Pt(N₃)₂(OH)₂(MA)(Py)] ( 1 ; MA=methylamine, Py=pyridine) and trans,trans,trans‐[Pt(N₃)₂(OH)₂(MA)(Tz)] ( 2 ; Tz=thiazole), and interpret their photophysical properties by TD‐DFT modelling. The orientation of the azido groups is highly dependent on H bonding and crystal packing, as shown by polymorphs 1 p and 1 q . Complexes 1 and 2 are stable in the dark towards hydrolysis and glutathione reduction, but undergo rapid photoreduction with UVA or blue light with minimal amine photodissociation. They are over an order of magnitude more potent towards HaCaT keratinocytes, A2780 ovarian, and OE19 oesophageal carcinoma cells than cisplatin and show particular potency towards cisplatin‐resistant human ovarian cancer cells (A2780cis). Analysis of binding to calf‐thymus (CT), plasmids, oligonucleotide DNA and individual nucleotides reveals that photoactivated 1 and 2 form both mono‐ and bifunctional DNA lesions, with preference for G and C, similar to transplatin, but with significantly larger unwinding angles and a higher percentage of interstrand cross‐links, with evidence for DNA strand cross‐linking further supported by a comet assay. DNA lesions of 1 and 2 on a 50 bp duplex were not recognised by HMGB1 protein, in contrast to cisplatin‐type lesions. The photo‐induced platination reactions of DNA by 1 and 2 show similarities with the products of the dark reactions of the Pt^II compounds trans‐[PtCl₂(MA)(Py)] ( 5 ) and trans‐[PtCl₂(MA)(Tz)] ( 6 ). Following photoactivation, complex 2 reacted most rapidly with CT DNA, followed by 1 , whereas the dark reactions of 5 and 6 with DNA were comparatively slow. Complexes 1 and 2 can therefore give rapid potent photocytotoxicity and novel DNA lesions in cancer cells, with no activity in the absence of irradiation.     

Targeting of Single‐Stranded Oligonucleotides through Metal‐Induced Cyclization of Short Complementary Strands

A new strategy to cyclize short synthetic oligonucleotides on DNA or RNA target strands is described. The approach is based on metal‐templated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2′ : 6′,2′′‐terpyridine (Tpy) moieties at their 3′‐ and 5′‐ends. Cyclization after metal addition (Zn²⁺, Fe²⁺) was demonstrated by means of thermal‐denaturation experiments, MALDI‐Q‐TOF‐MS, and gel electrophoresis (PAGE). 1D‐ and 2D‐NMR Experiments were performed to analyze the association of complementary strands after metal‐mediated cyclization. Our protocol allows the efficient circularization of synthetic oligonucleotides. Thereby, the hybridization on a complementary strand was more efficient with an RNA target strand and a 2′‐O‐methylated circularized oligomer.     

Single‐Molecule Visualization of the Activity of a Zn2+‐Dependent DNAzyme

We demonstrate the single‐molecule imaging of the catalytic reaction of a Zn²⁺‐dependent DNAzyme in a DNA origami nanostructure. The single‐molecule catalytic activity of the DNAzyme was examined in the designed nanostructure, a DNA frame. The DNAzyme and a substrate strand attached to two supported dsDNA molecules were assembled in the DNA frame in two different configurations. The reaction was monitored by observing the configurational changes of the incorporated DNA strands in the DNA frame. This configurational changes were clearly observed in accordance with the progress of the reaction. The separation processes of the dsDNA molecules, as induced by the cleavage by the DNAzyme, were directly visualized by high‐speed atomic force microscopy (AFM). This nanostructure‐based AFM imaging technique is suitable for the monitoring of various chemical and biochemical catalytic reactions at the single‐molecule level.     

Solution‐Processable n‐Type Semiconductors Based on Unsymmetrical Naphthalene Imides: Synthesis,Characterization, and Applications in Field‐Effect Transistors

A series of unsymmetrical naphthalene imide derivatives ( 1a , 1b , 2 , 3 , 4 , 5 ) with high electron affinity was synthesized and used in n‐channel organic field‐effect transistors (OFETs). They have very good solubility in common organic solvents and good thermal stability up to 320 °C. Their photophysical, electrochemical, and thermal properties were investigated in detail. They showed low‐lying LUMO energy levels from ?3.90 to ?4.15 eV owing to a strong electron‐withdrawing character. Solution‐processed thin‐film OFETs based on 1a , 1b , 2 , 3 , 4 were measured in both N₂ and air. They all showed n‐type FET behavior. The liquid‐crystalline compounds 1a , 1b , and 3 showed good performance owing to the self‐healing properties of the film in the liquid‐crystal phase. Compound 3 has an electron mobility of up to 0.016 cm² V^?1 s^?1 and current on/off ratios of 10⁴–10⁵.     

Single,double, and multiple double strand breaks induced in DNA by 3-100 eV electrons

Nonthermal secondary electrons with initial kinetic energies below 100 eV are an abundant transient species created in irradiated cells and thermalize within picoseconds through successive multiple energy loss events. Here we show that below 15 eV such low-energy electrons induce single (SSB) and double (DSB) strand breaks in plasmid DNA exclusively via formation and decay of molecular resonances involving DNA components (base, sugar, hydration water, etc.). Furthermore, the strand break quantum yields (per incident electron) due to resonances occur with intensities similar to those that appear between 25 and 100 eV electron energy, where nonresonant mechanisms related to excitation/ionizations/dissociations are shown to dominate the yields, although with some contribution from multiple scattering electron energy loss events. We also present the first measurements of the electron energy dependence of multiple double strand breaks (MDSB) induced in DNA by electrons with energies below 100 eV. Unlike the SSB and DSB yields, which remain relatively constant above 25 eV, the MDSB yields show a strong monotonic increase above 30 eV, however with intensities at least 1 order of magnitude smaller than the combined SSB and DSB yields. The observation of MDSB above 30 eV is attributed to strand break clusters (nano-tracks) involving multiple successive interactions of one single electron at sites that are distant in primary sequence along the DNA double strand, but are in close contact; such regions exist in supercoiled DNA (as well as cellular DNA) where the double helix crosses itself or is in close proximity to another part of the same DNA molecule.     

Studies on the Extension of Sequence‐independence and the Enhancement of DNA Triplex Formation

A more elaborate sequence‐independent triple‐helix formation viability study was carried out and extended from a recombination‐like triple‐helical DNA motif of a previous study (J. Mol. Recognition 14, 122–139 (2001)). The intended triple‐helix was formed by mixing one part of a DNA hairpin duplex and one part of a single (or third) strand identical to one of the duplex strands and complementary to the other strand. In contrast to the common purine and pyrimidine motifs in triple‐stranded DNA, the strands of the recombination‐like motif are not monotonously built from pyrimidine only, or purine only, in the sequence. The stability of the recombination‐like motif triplexes with varying sequences was monitored by UV thermal melting curves. The results showed that the order of the stability of the R‐form DNA base triads (J. Mol. Biol., 239, 181–200 (1994)) is G*(G ○ C) > C*(C ○ G) > A*(A ○ T) >T*(T ○ A) (the Watson‐Crick base pair is denoted in the parentheses) in 200 mM NaCl, at pH 7. In an attempt to increase the stability of the triplex in the recombination‐like motif, we replaced cytidine by 5‐methylcytidine (^mC) of the third strand. There is a general trend that ^mC modification stabilizes the complex (<2 °C per ^mC). The complex is furthermore stabilized by Mg²⁺ ion. The Tm increases from 7 to 2 °C from less stable to highly stable triplex by 20 mM Mg²⁺ ion in solution.