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Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays.

Keller A, Rackwitz J, Cauët E, Liévin J, Körzdörfer T, Rotaru A, Gothelf KV, Besenbacher F, Bald I - Sci Rep (2014)

Bottom Line: We investigated the DNA sequences 5'-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10(-14) cm(2) and 7.06 · 10(-14) cm(2).The highest cross section was found for 5'-TT(ATA)3TT and 5'-TT(ABrUA)3TT, respectively.Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy.

View Article: PubMed Central - PubMed

Affiliation: 1] Interdisciplinary Nanoscience Center (iNANO) and Danish National Research Foundation: Centre for DNA Nanotechnology (CDNA), Aarhus University, 8000 Aarhus C, Denmark [2] Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.

ABSTRACT
The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5'-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10(-14) cm(2) and 7.06 · 10(-14) cm(2). The highest cross section was found for 5'-TT(ATA)3TT and 5'-TT(ABrUA)3TT, respectively. BrU is a radiosensitizer, which was discussed to be used in cancer radiation therapy. The replacement of T by BrU into the investigated DNA sequences leads to a slight increase of the absolute strand break cross sections resulting in sequence-dependent enhancement factors between 1.14 and 1.66. Nevertheless, the variation of strand break cross sections due to the specific nucleotide sequence is considerably higher. Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy.

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The cross sections for DNA strand cleavage are determined by recording the fluence dependence of the relative number of strand breaks (left) upon irradiation with 18 eV electrons.On the right the sequence dependence of the strand break cross section is shown. The highest σSSB was observed with the TT(ATA)3TT nucleotide sequence.
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f2: The cross sections for DNA strand cleavage are determined by recording the fluence dependence of the relative number of strand breaks (left) upon irradiation with 18 eV electrons.On the right the sequence dependence of the strand break cross section is shown. The highest σSSB was observed with the TT(ATA)3TT nucleotide sequence.

Mentions: Fig. 1a shows a scheme of a triangular DNA origami platform carrying six target sequences, which represents the DNA nanoarray. Three biotinylated target sequences are situated in the center of the trapezoids, and three are located on the sides of the trapezoids. Basically, the nucleotide sequence of each of the six target oligonucleotides can be freely chosen. In the present study the three central target strands (green in Fig. 1a), and the three side positions (black in Fig. 1a) cannot be distinguished in the AFM images and are hence chosen to have the same sequence. Thus, two different target sequences are studied within one irradiation experiment, and the specific sequences and their positions are indicated in Fig. 1a. In Fig. 1b typical AFM images from DNA origami samples after incubation with streptavidin (SAv) which binds to biotin (Bt) are shown. The left image shows a control sample that was not irradiated while the image on the right was obtained from a sample irradiated with 18 eV electrons at a fluence of 5.0 × 1012 cm−2. The energy of 18 eV was chosen due to its relevance for the damage induced by secondary electrons originating from the ionization track of high-energy radiation. For secondary electrons the damage probability has a global maximum around 18 eV, i.e. the damage induced mainly by ionization and electronic excitation weighted by the LEE distribution in aqueous samples irradiated with high-energy radiation20. In the AFM image on the right-hand side of Fig. 1 the number of specifically bound SAv is reduced compared to the non-irradiated control sample indicating that a number of target sequences have been damaged by electron-induced strand breakage. To determine the absolute cross section for strand breakage (see Methods section), the relative number of SBs (NSB) was recorded as a function of the electron fluence. The fluence dependence of NSB for the target sequences TT(XTX)3TT with X = A, C, G is displayed in Fig. 2a. From the linear fit in the low-fluence regime σSSB is determined, which is shown in Fig. 2b. The oligonucleotide TT(GTG)3TT shows the lowest response to 18 eV electrons. To ensure for an accurate linear fit, a smaller fluence increment and thus more data points were chosen for TT(GTG)3TT.


Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays.

Keller A, Rackwitz J, Cauët E, Liévin J, Körzdörfer T, Rotaru A, Gothelf KV, Besenbacher F, Bald I - Sci Rep (2014)

The cross sections for DNA strand cleavage are determined by recording the fluence dependence of the relative number of strand breaks (left) upon irradiation with 18 eV electrons.On the right the sequence dependence of the strand break cross section is shown. The highest σSSB was observed with the TT(ATA)3TT nucleotide sequence.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4260214&req=5

f2: The cross sections for DNA strand cleavage are determined by recording the fluence dependence of the relative number of strand breaks (left) upon irradiation with 18 eV electrons.On the right the sequence dependence of the strand break cross section is shown. The highest σSSB was observed with the TT(ATA)3TT nucleotide sequence.
Mentions: Fig. 1a shows a scheme of a triangular DNA origami platform carrying six target sequences, which represents the DNA nanoarray. Three biotinylated target sequences are situated in the center of the trapezoids, and three are located on the sides of the trapezoids. Basically, the nucleotide sequence of each of the six target oligonucleotides can be freely chosen. In the present study the three central target strands (green in Fig. 1a), and the three side positions (black in Fig. 1a) cannot be distinguished in the AFM images and are hence chosen to have the same sequence. Thus, two different target sequences are studied within one irradiation experiment, and the specific sequences and their positions are indicated in Fig. 1a. In Fig. 1b typical AFM images from DNA origami samples after incubation with streptavidin (SAv) which binds to biotin (Bt) are shown. The left image shows a control sample that was not irradiated while the image on the right was obtained from a sample irradiated with 18 eV electrons at a fluence of 5.0 × 1012 cm−2. The energy of 18 eV was chosen due to its relevance for the damage induced by secondary electrons originating from the ionization track of high-energy radiation. For secondary electrons the damage probability has a global maximum around 18 eV, i.e. the damage induced mainly by ionization and electronic excitation weighted by the LEE distribution in aqueous samples irradiated with high-energy radiation20. In the AFM image on the right-hand side of Fig. 1 the number of specifically bound SAv is reduced compared to the non-irradiated control sample indicating that a number of target sequences have been damaged by electron-induced strand breakage. To determine the absolute cross section for strand breakage (see Methods section), the relative number of SBs (NSB) was recorded as a function of the electron fluence. The fluence dependence of NSB for the target sequences TT(XTX)3TT with X = A, C, G is displayed in Fig. 2a. From the linear fit in the low-fluence regime σSSB is determined, which is shown in Fig. 2b. The oligonucleotide TT(GTG)3TT shows the lowest response to 18 eV electrons. To ensure for an accurate linear fit, a smaller fluence increment and thus more data points were chosen for TT(GTG)3TT.

Bottom Line: We investigated the DNA sequences 5'-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10(-14) cm(2) and 7.06 · 10(-14) cm(2).The highest cross section was found for 5'-TT(ATA)3TT and 5'-TT(ABrUA)3TT, respectively.Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy.

View Article: PubMed Central - PubMed

Affiliation: 1] Interdisciplinary Nanoscience Center (iNANO) and Danish National Research Foundation: Centre for DNA Nanotechnology (CDNA), Aarhus University, 8000 Aarhus C, Denmark [2] Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.

ABSTRACT
The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5'-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10(-14) cm(2) and 7.06 · 10(-14) cm(2). The highest cross section was found for 5'-TT(ATA)3TT and 5'-TT(ABrUA)3TT, respectively. BrU is a radiosensitizer, which was discussed to be used in cancer radiation therapy. The replacement of T by BrU into the investigated DNA sequences leads to a slight increase of the absolute strand break cross sections resulting in sequence-dependent enhancement factors between 1.14 and 1.66. Nevertheless, the variation of strand break cross sections due to the specific nucleotide sequence is considerably higher. Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy.

Show MeSH
Related in: MedlinePlus