Chiral Selective Stacking of a Cationic Porphyrin along Z‑Form Poly[d(A-T)₂]

In this study, the binding mode of porphyrin-free single-stranded poly­[d­(AT)] and <i>trans</i>-BMPyP was observed in the Z-form <i>trans</i>-BMPyP–poly­[d­(A-T)₂] complex induced by extensive stacking depending on the temperature and concentration through circular dichroism (CD). The Z-form <i>trans</i>-BMPyP–poly­[d­(A-T)₂] complex (<i>R</i> = 0.30) retained the Z-form DNA structure at a low temperature (20 °C) by the <i>trans</i>-BMPyP molecules. When the temperature was increased to 60 °C, the DNA was almost unfolded as a single-stranded poly­[d­(AT)], but the extensive stacking binding mode of <i>trans</i>-BMPyP was maintained and the shape of the porphyrin Soret band was symmetrically changed in comparison with the shape of the Z-form DNA. However, when the temperature was raised to 80 °C, the extensive stacking binding mode of <i>trans</i>-BMPyP was also unfolded almost completely. The binding mode of the <i>trans</i>-BMPyP-single-stranded poly­[d­(AT)] complex was very similar to the already known binding mode of porphyrins and a double-stranded DNA. The binding mode was dependent on the concentration ratio ([porphyrin]/[DNA]): a monomeric binding mode at a concentration ratio of 0.04, a moderate groove binding mode at a concentration ratio between 0.08 and 0.16, and extensive stacking at a concentration ratio between 0.20 and 0.30. The same result was obtained when the temperature of the Z-form DNA (<i>R</i> = 0.30) was increased to 60 °C. However, those binding modes were not found in <i>cis</i>-BMPyP, which was because, in the extensive stacking of <i>trans</i>-BMPyP along the DNA skeleton, the distance between the two positive methylpyridine ions at the trans site and thymine, one of the DNA bases, is decreased, creating a much more hydrophobic environment. In addition, the poly AT sequences found from the CD spectra for the binding of <i>trans</i>-BMPyP–poly­[d­(A-T)₂] and <i>trans</i>-BMPyP–poly­[d­(AT)] (<i>R</i> = 0.30) showed that both of them underwent effective extensive stacking and that the chirality of extensive stacking was dependent on the form of DNA

Effect of periphery cationic substituents of porphyrin on the B-Z transition of poly[d(A-T)₂], poly[d(G-C)₂] and their binding modes

The binding mode of cationic porphyrin (trans-BMPyP) with poly[d(G-C)2] and poly[d(A-T)2] was examined according to the site of the periphery cationic methyl pyridine ion of the cationic porphyrin (o-, m-, p-) as well as the possibility of a B-Z transition depending on the binding modes by measuring the absorption spectrum and circular dichroism (CD). The negative band found in the soret region showed the intercalation mode of m- and p-trans-BMPyP-poly[d(G-C)2] to the DNA base pairs, but no B-Z transition was induced. On the other hand, the distinctive bisignate band found in the soret region of the CD spectrum for m- and p-trans-BMPyP-poly[d(A-T)2] suggests that m- and p-trans-BMPyP have an effective extensive stacking-based binding mode along with the skeleton of poly[d(A-T)2], wherein the B-Z transition was induced through extensive stacking. The difference in binding mode was attributed to the difference in the molecular structure depending on the site of the periphery cationic methyl pyridine ion in the cationic porphyrin. In other words, o-trans-BMPyP is nonplanar because of the steric hindrance of the cationic methyl pyridine ion at the o-site. In contrast, m- and p-trans-BMPyP are planar, but not all porphyrins with a planar structure undergo the B-Z transition. In conclusion, a B-Z transition is induced if the structure of a porphyrin is planar and the binding mode allows the porphyrins to be stacked effectively along the DNA skeleton, not in a binding mode where the porphyrin is intercalated to the DNA. Communicated by Ramaswamy H. Sarma</p

Binding mode of a cationic porphyrin to parallel and antiparallel thrombin binding aptamer G-quadruplex

The spectral properties of meso-tetrakis (N-methylpyridinium-4-yl)porphyrin (TMPyP) in the presence of parallel and antiparallel G-quadruplexes formed from a thrombin-binding aptamer G-quadruplex (5′-G3T2G3TGTG3T2G3) were investigated in this study. Red shift and hypochromism in the Soret absorption band of TMPyP were observed after binding to both parallel and antiparallel G-quadruplexes. The extent of changes in the absorption spectra were similar for both conformers. No circular dichroism spectrum was induced in the Soret region for both parallel and antiparallel G-quadruplexes. This is suggest that there is no or very weak interaction between electric transitions of nucleobases and porphyrin molecule. The accessibility of the neutral quencher I2 to the G-quadruplex-bound TMPyP was similar for both parallel and antiparallel G-quadruplexes. All these observations suggest that TMPyP was bound at the outside of the quadruplexes, and conceivably interacted with the phosphate group via a weak electrostatic interaction. Communicated by Ramaswamy H. Sarma</p

Photoinduced Reduction of Manganese(III) <i>meso</i>-Tetrakis(1-methylpyridinium-4-yl)porphyrin at AT and GC Base Pairs

The photoreduction of water-soluble cationic manganese­(III) <i>meso</i>-tetrakis­(1-methylpyridium-4-yl)­porphyrin (Mn^III(TMPyP)⁴⁺) bound to a synthetic polynucleotide, either poly­[d­(A-T)₂] or poly­[d­(G-C)₂], was examined by conventional absorption and circular dichroism (CD) spectroscopy, transient absorption, and transient Raman spectroscopy. Upon binding, Mn^III(TMPyP)⁴⁺ produced a positive CD signal for both polynucleotides, suggesting external binding. In the poly­[d­(A-T)₂]–Mn^III(TMPyP)⁴⁺ adduct case, an interaction between the bound porphyrin was suggested. The transient absorption spectral features of Mn^III(TMPyP)⁴⁺ in the presence of poly­[d­(A-T)₂] and poly­[d­(G-C)₂] were similar to those of the photoreduced products, Mn^II(TMPyP)⁴⁺, whereas Mn^III(TMPyP)⁴⁺ in the absence of polynucleotides retained its oxidation state. This indicated that both poly­[d­(A-T)₂] and poly­[d­(G-C)₂] act as electron donors, resulting in photo-oxidized G and A bases. The transient Raman bands (ν₂ and ν₄) that were assigned to porphyrin macrocycles exhibited a large downshift of ∼25 cm^–1, indicating the photoreduction of Mn^III to Mn^II porphyrins when bound to both polynucleotides. The transient Raman bands for pyridine were enhanced significantly, suggesting that the rotation of peripheral groups for binding with polynucleotides is the major change in the geometry expected in the photoreduction process. These photoinduced changes do not appear to be affected by the binding mode of porphyrin

Bioconjugation of l-3,4-Dihydroxyphenylalanine Containing Protein with a Polysaccharide

We describe the simple bioconjugation strategy in combination of periodate chemistry and unnatural amino acid incorporation. The residue specific incorporation of 3,4-dihydroxy-l-phenylalanine can alter the properties of protein to conjugate into the polymers. The homogeneously modified protein will yield quinone residues that are covalently conjugated to nucleophilic groups of the amino polysaccharide. This novel approach holds great promise for widespread use to prepare protein conjugates and synthetic biology applications

sj-docx-1-onc-10.1177_11795549231218082 – Supplemental material for A Phase II Study of 131I-rituximab for Patients With Relapsed or Refractory Marginal Zone Lymphoma

Supplemental material, sj-docx-1-onc-10.1177_11795549231218082 for A Phase II Study of 131I-rituximab for Patients With Relapsed or Refractory Marginal Zone Lymphoma by Yoon Jung Jang, Sang Moo Lim, Inki Lee, Byung Hyun Byun, Ilhan Lim, Byung Il Kim, Chang Woon Choi, Seung-Sook Lee, Sung Hyun Yang, Im Il Na, Hyo-Rak Lee, Dong-Yeop Shin and Hye Jin Kang in Clinical Medicine Insights: Oncology</p