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Hiroshi Sugiyama Department of Chemistry, Graduate School of Science Institute for Integrated Cell-Material Sciences (iCeMS)
Kyoto University1
100 nm
生体分子機能論 2018-6水素引き抜き抗生物質
Advanced Course in Molecular Biology and Biochemistry
Basics1 Basic elements of nucleic acids and their synthesis
2 Sequencing of DNA
3 3D structure of DNA 1
4 3D structure of DNA 2
Chemistry 5) DNA alkylation
6) Hydrogen abstraction 1
7) Hydrogen abstraction 2
8) Charge transfer
Biology 9) Epigenetics 1
10) Epigenetics 2
11) ATRX
Hydrogen (H) atom abstraction:
H atom is abstracted from a substrate according to the general
reaction
X H-Y X-H+ Y+. .
Fe(V)-oxo Cytochrome p450
Tet protein
Carbon radical Calicheamicin g1
C-1027, Dynemicin A, Esperamicin A1
RH + O2 + NADPH + H+ → ROH + H2O +
NADP+
Bleomycin
Bergman cyclization
s radial not p radical
Antitumor antibiotics which induce DNA strand scission by H abstraction
Gemtuzumab ozogamicin:
(Mylotarg)
Calicheamycin analog CD33
monoclonal antibody
Conjugate
(acute myeloid leukemia)
used from 2000-2010
Increased patient death and no
benefit over conventional cancer
therapy
Formation of carbon racial from Calicheamycin and Neocarzinostatin
4’ OH
4’ O2
H abstraction from deoxyribose backbone
Science 1989, 245, 1396
Specific Detection of C-4’Hydroxylated
Abasic Sites Generated by Bleomycin and
Neocarzinostatin in DNA
Hiroshi Sugiyama, Hiroshi Kawabata, Tsuyoshi Fujiwara,
Yukihiro Dannoue, and Isao Saito*
Contribution from the Department of Synthetic Chemistry,
Faculty of Engineering, Kyoto University, Kyoto 606, Japan.
Received November 27, 1989
J. Am.Chem. Soc.1990,112,5252-5257
Enzymatic Digestion of Oligonucleotides Containing
3’-Pyridazinylmethyl Termini
Detection of Pyridazine Mononucleotide
from Co-PEM-Treated DNA
Co-PEM induces C-4‘ hydroxylation preferentially at GC and GT sites
and also mediates the release of A and T from poly(dT-dA).
Fe-PEM induces strand cleavage with the formation of glycolic acid termini at the 3’-end
C-4’ hydroxylation is estimated to be a minimum of 17% of the total event (5.0μM/29.2μM)
PDBID:2R2S
PDBID:1GJ2
Co(III) bleomycin : stable but it cleaves DNA under UV irradiation condition
Biochemistry (2001) 40, 5894-5905
Crystal structure of DNA-bound Co(III)bleomycin B2:
Insights on intercalation and minor groove bindingProc Natl Acad Sci USA,2008,105:5052-5056
Bithiazole(BT) Intercalation
DNAs superinposed
in the Presence and Absence of Co-BLM
20
DNMT TET
5-hydorxymethylcytosine(hmC)
5-formylcytosine(fC)
5-carboxylcytosine(caC)
TET TET
TDG and BER
cytosine(C)
5-methylcytosine(mC)
decarboxylase?
Demethylation by TET protein
• DNA repair protein, TDG (thymine DNA glycosylase) , has the activity to excise fC and caC
• Decarboxylation of caC to form C may occur, although the decarboxylase has not been discovered yet
21
Oxidation by TET preferentially occurs at linker DNA
Investigating Nucleosome Accessibility for MNase, FeII Peplomycin, and
Duocarmycin B2 by Using Capillary Electrophoresis
Zou, T.; Kizaki, S.; Sugiyama, H.
ChemBioChem. 2018, 19, 664-668.
Metallo-Bleomycin Cleaves Parallel-Stranded DNA
Similarly to B-DNA. Ikeda, S.; Saito, I.; Sugiyama, H.
Tetrahedron Lett., 2000, 41, 3919-3922.