Complex intragene deletion leads to oculocutaneous albinism in tanuki (Japanese raccoon dog)

Tanuki (Nyctereutes procyonoides viverrinus), or Japanese raccoon dog, is a canine native to Japan. Tanuki with complete oculocutaneous albinism are relatively frequent in mountainous areas of mainland Japan. Tyrosinase, which is encoded by the TYR gene, is an enzyme essential for the biosynthesis of melanin pigment. We examined the structure and nucleotide sequence of TYR in an albino tanuki and found that the third exon was removed due to a deletion of approximately 11 kb. In addition, two nonsynonymous nucleotide substitutions were found in the fifth exon. These mutations are possible causes of the albino phenotype; however, the order of occurrence is unclear. Even if the 11-kb deletion was not the first of these mutations, it is considered to cause a total loss of the tyrosinase function because the third exon carries codons for one of the two copper-binding sites of tyrosinase and these sites are essential for the enzyme function. Intriguingly, the deletion was not a simple removal of an 11-kb segment: an internal portion was retained as a segment in the reverse orientation. We propose possible formation processes for this mutation that involve multiple DNA scission events, or an inversion followed by a deletion.

The Novel Two-Metal-Ion Mechanism for Type II Topoisomerases by the QM/MM and Free Energy Study

Catalysis of Type II topoisomerase employs a combination of nucleobase and divalent metal ions with a long discussing two-metal-ion mechanism. High-level quantum mechanics/molecular mechanics (QM/MM) and thermodynamics cycle perturbation (QTCP) free energy calculations support an associative novel two-metal-ion mechanism and elucidate the catalytic roles of metal ion, in which one divalent metal ion stabilizes the phosphoric pentacovalent transition state and the 3’‒OH leaving group while the secondary one facilitates to reorganize the nearby hydrogen network and residues. The DNA scission is fast and exothermic that a stepwise pathway proceeds for the nucleophilic attack by Y805 following by the protonation of the ribose alkoxide, inducing the formation of a bending DNA strand. These findings advance the fundamental knowledge on topoisomerases and the development of targeting anticancer drugs.

The Novel Two-Metal-Ion Mechanism for Type II Topoisomerases by the QM/MM and Free Energy Study

Catalysis of Type II topoisomerase employs a combination of nucleobase and divalent metal ions with a long discussing two-metal-ion mechanism. High-level quantum mechanics/molecular mechanics (QM/MM) and thermodynamics cycle perturbation (QTCP) free energy calculations support an associative novel two-metal-ion mechanism and elucidate the catalytic roles of metal ion, in which one divalent metal ion stabilizes the phosphoric pentacovalent transition state and the 3’‒OH leaving group while the secondary one facilitates to reorganize the nearby hydrogen network and residues. The DNA scission is fast and exothermic that a stepwise pathway proceeds for the nucleophilic attack by Y805 following by the protonation of the ribose alkoxide, inducing the formation of a bending DNA strand. These findings advance the fundamental knowledge on topoisomerases and the development of targeting anticancer drugs.

The Novel Two-Metal-Ion Mechanism for Type II Topoisomerases by the QM/MM and Free Energy Study

Catalysis of Type II topoisomerase employs a combination of nucleobase and divalent metal ions with a long discussing two-metal-ion mechanism. High-level quantum mechanics/molecular mechanics (QM/MM) and thermodynamics cycle perturbation (QTCP) free energy calculations support an associative novel two-metal-ion mechanism and elucidate the catalytic roles of metal ion, in which one divalent metal ion stabilizes the phosphoric pentacovalent transition state and the 3’‒OH leaving group while the secondary one facilitates to reorganize the nearby hydrogen network and residues. The DNA scission is fast and exothermic that a stepwise pathway proceeds for the nucleophilic attack by Y805 following by the protonation of the ribose alkoxide, inducing the formation of a bending DNA strand. These findings advance the fundamental knowledge on topoisomerases and the development of targeting anticancer drugs.

DNA-binding, photocleavage and anti-cancer activity of tin(IV) corrole

A new tin(IV) corrole, 5,10,15-tris(4-methoxycarbonylphenyl) corrole tin(IV) (1-Sn) was synthesized and characterized. The DNA binding, photocleavage and anti-cancer activity were studied and compared with its free-base. The interaction of 1-Sn and its free-base 1 with calf thymus DNA had been investigated by spectroscopic methods, viscosity measurements and molecular docking analysis. The results revealed that 1-Sn and 1 could interact with calf thymus DNA via an outside groove binding mode. Furthermore, although 1 displayed no photonuclease activity, 1-Sn exhibited good photonuclease activity as indicated by agarose gel electrophoresis, and superoxide anion might be the active intermediate for the DNA scission. Finally, 1 was nontoxic but 1-Sn displayed cytotoxicity towards A549 tumor cell lines.

Dynamic control of strand excision during human DNA mismatch repair

Mismatch repair (MMR) is activated by evolutionarily conserved MutS homologs (MSH) and MutL homologs (MLH/PMS). MSH recognizes mismatched nucleotides and form extremely stable sliding clamps that may be bound by MLH/PMS to ultimately authorize strand-specific excision starting at a distant 3′- or 5′-DNA scission. The mechanical processes associated with a complete MMR reaction remain enigmatic. The purified human (Homo sapien or Hs) 5′-MMR excision reaction requires the HsMSH2–HsMSH6 heterodimer, the 5′ → 3′ exonuclease HsEXOI, and the single-stranded binding heterotrimer HsRPA. The HsMLH1–HsPMS2 heterodimer substantially influences 5′-MMR excision in cell extracts but is not required in the purified system. Using real-time single-molecule imaging, we show that HsRPA or Escherichia coli EcSSB restricts HsEXOI excision activity on nicked or gapped DNA. HsMSH2–HsMSH6 activates HsEXOI by overcoming HsRPA/EcSSB inhibition and exploits multiple dynamic sliding clamps to increase tract length. Conversely, HsMLH1–HsPMS2 regulates tract length by controlling the number of excision complexes, providing a link to 5′ MMR.