advanced course in molecular biology and...
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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
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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
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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
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Bergman cyclization
s radial not p radical
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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
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Formation of carbon racial from Calicheamycin and Neocarzinostatin
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4’ OH
4’ O2
H abstraction from deoxyribose backbone
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Science 1989, 245, 1396
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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
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Enzymatic Digestion of Oligonucleotides Containing
3’-Pyridazinylmethyl Termini
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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
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C-4’ hydroxylation is estimated to be a minimum of 17% of the total event (5.0μM/29.2μM)
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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
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Bithiazole(BT) Intercalation
DNAs superinposed
in the Presence and Absence of Co-BLM
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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
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Oxidation by TET preferentially occurs at linker DNA
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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.
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Metallo-Bleomycin Cleaves Parallel-Stranded DNA
Similarly to B-DNA. Ikeda, S.; Saito, I.; Sugiyama, H.
Tetrahedron Lett., 2000, 41, 3919-3922.