DNA Photo-Cross-Linking Using 3‑Cyanovinylcarbazole Modified Oligonucleotide with Threoninol Linker

3-Cyanovinylcarbazole modified d-threoninol (^CNVD) was incorporated in oligodeoxyribonucleotide and tested for a photo-cross-linking reaction with complementary oligodeoxyribonucleotide. The photoreactivity was 1.8- to 8-fold greater than that of 3-cyanovinylcarbazole modified deoxyribose (^CNVK) previously reported. From the results of melting analysis and circular dichroism spectroscopy of the duplexes, the relatively flexible structure of ^CNVD compared with ^CNVK might be advantageous for [2 + 2] photocycloaddition between the cyanovinyl group on the ^CNVD and pyrimidine base in the complementary strand

Critical Effect of Base Pairing of Target Pyrimidine on the Interstrand Photo-Cross-Linking of DNA via 3‑Cyanovinylcarbazole Nucleoside

To evaluate the effect of base pairing of the target pyrimidine on the interstrand photo-cross-linking reaction of DNA via 3-cyanovinylcarbazole nucleoside (^CNVK), a complementary base of target pyrimidine was substituted with noncanonical purine bases or 1,3-propandiol (S). As the decrease of the hydrogen bonds in the base pairing of target C accelerated the photo-cross-linking reaction markedly (3.6- to 7.7-fold), it can be concluded that the number of hydrogen bonds in the base pairing, i.e., the stability of base pairing, of the target pyrimidine plays a critical role in the interstrand photo-cross-linking reaction. In the case of G to S substitution, the highest photoreactivity toward C was observed, whose photoreaction rate constant (<i>k</i> = 2.0 s^–1) is comparable to that of ^CNVK toward T paired with A (<i>k</i> = 3.5 s^–1). This is the most reactive photo-cross-linking reaction toward C in the sequence specific interstrand photo-cross-linking. This might facilitate the design of the photo-cross-linkable oligodeoxyribonucleotides for various target sequences

Spatial discrepancies between the steel ball and CBCT corresponding to changes in CBCT imaging parameters between Tube 1 and Tube 2, or switching rotation direction between clockwise (CW) or counterclockwise (CCW).

<p>Spatial discrepancies between the steel ball and CBCT corresponding to changes in CBCT imaging parameters between Tube 1 and Tube 2, or switching rotation direction between clockwise (CW) or counterclockwise (CCW).</p

Histogram illustrating discrepancies in manual image matching with respect to image blurring for (a) the left-right (LR) direction, (b) the anterior-posterior (AP) direction, and (c) the superior-inferior (SI) direction.

<p>Histogram illustrating discrepancies in manual image matching with respect to image blurring for (a) the left-right (LR) direction, (b) the anterior-posterior (AP) direction, and (c) the superior-inferior (SI) direction.</p

The Vero4DRT system with dual implementation of the kV imaging system and electronic portal imaging device (EPID).

<p>Exposure by non-coplanar MV beams was enabled by gantry and ring rotation. Dynamic tumor motion tracking was conducted through exposure to the gimbaled MV X-ray head. The lock-on system was used to correct sagging by the X-ray beam axis.</p

Spatial discrepancy between the MV X-ray beam isocenter and CBCT center.

<p>The center of the MV beam and CBCT were calculated from the mean discrepancy between the MV beam or CBCT and the steel ball, respectively. The dotted line markings show the original data points of these discrepancies. The double arrows indicate the mean discrepancy of the MV beam isocenter and CBCT center.</p

Alignments conducted between the MV X-ray beam isocenter and the CBCT image-guidance system, and a comprehensive evaluation of the manual image matching accuracy.

<p>Alignments conducted between the MV X-ray beam isocenter and the CBCT image-guidance system, and a comprehensive evaluation of the manual image matching accuracy.</p

Tumor shadow consistency measurements showing a comparison between the theoretical tumor shadow size and averaged intensity (AI) and cone-beam computed tomography (CBCT) images.

<p>Tumor shadow consistency measurements showing a comparison between the theoretical tumor shadow size and averaged intensity (AI) and cone-beam computed tomography (CBCT) images.</p

The consistency of tumor shadow volumes between the theoretical volumes and the volumes in averaged intensity (AI)-CT and CBCT images.

<p>The consistency of tumor shadow volumes between the theoretical volumes and the volumes in averaged intensity (AI)-CT and CBCT images.</p

A phantom device with a centrally inserted steel ball was used to evaluate the reference point discrepancies between the MV beam and the CBCT system.

<p>Photographs of (a) the phantom exterior, (b) EPID image, and (c) CBCT image. The precision of manual image matching between the averaged intensity (AI)-CT and CBCT images was evaluated by the motion platform with the lung phantom. Photographs of (d) the phantom exterior, (e) the AI-CT image with contour information for the ITV and the PTV, and (f) the CBCT image.</p