Post on 11-Jul-2020
HiroshiSugiyamaDepartmentofChemistry,GraduateSchoolofScienceInstituteforIntegratedCell-MaterialSciences(iCeMS)
KyotoUniversity1
100nm
生体分子機能論 2018-2配列決定
Advanced Course in Molecular Biology and Biochemistry
Basics 1 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
Sequencing of DNA
1) In 1970s Maxam and Gilbert sequencing Sanger sequencing Slab gel electrophoresis (Nobel Prize Chemistry 1980) 2) In late 1990s to 2000s Capillary gel electrophoresis (Human Genome Project) 3) 2010- Next generation sequencing (NGS)
Maxam-Gilbert Chemical Sequencing
STEP1 Labeling A polynucleotide is labeled at either its 5’- or 3’-end with 32P.
STEP2 Chemical treatment Labeled polynucleotide is treated with a base-specific reagent and then the chemically modified polynucleotide causes strand breakage at each modified site.
STEP3 Electrophoresis Labeled fragments are electrophoresed side by side in denaturing acrylamide gels for size separation.
Maxam-Gilbert Chemical Sequencing
Maxam, A.; Gilbert, W. Methods in enzymology 1980, 65, 499–560.
Maxam-Gilbert Chemical Sequencing
type of modification reagent cleavage
A + G deprination 88 % formic acid (pH 2) 1 M piperidine (90 oC for 30 min)
G methylation dimethyl sulfate 1 M piperidine (90 oC for 30 min)
C base ring-opening hydrazine 1 M piperidine (90 oC for 30 min)
C + T base ring-opening hydrazine (1.5 M NaCl) 1 M piperidine (90 oC for 30 min)
Maxam-Gilbert Chemical Sequencing
A + G specific reaction
G specific reaction
Maxam-Gilbert Chemical SequencingC + T specific reaction
Maxam-Gilbert Chemical Sequencing
Maxam, M.; Gilbert, W. PNAS 1977, 74, 560–564.
10
Prof Teruo Matsuura Feb. 20th,1984
Organic Chemical Approaches to DNA Photochemistry -New Aspects of Thymine Photochemistry-
J. Am. Chem. Soc., 103, 1598 (1981), ibid 105, 698 (1983), ibid 105, 956 (1983)
Sequencing of DNA
1) In 1970s Maxam and Gilbert sequencing Sanger sequencing Slab gel electrophoresis (Nobel Prize Chemistry 1980) 2) In late 1990s to 2000s Capillary gel electrophoresis (Human Genome Project) 3) 2010- Next generation sequencing (NGS)
Fluorescent labeling ddNTP
The human genome project (HGP)
DNA sequence of the fragment
Sequence
Sequence
Sequence Sequence
Sequence
Sequence
(Bioinformatics)
Check for overlapping sequences
Genomic sequence
The human genome project (HGP)
Historical overview
The human genome project (HGP)
Sample of genomic DNA
Shotgun-method 1. step: Digestion of the genomic DNA
into smaller fragments (enzymes or shear).
2. step: Multiplication (cloning fragments in vector).
3. step: Sequencing (Sanger, dye terminator)
Laser induced fluorescence. Readout in capillary electrophoresis
The instrument: capillary electrophoresis
H3CO2C OH
NNN
N
NH2
O
NH
NO
H3C
CGTATpO
OpCG
OHO
NH
OCH3
OCH3OCH3
90 °C
(Tetrahedron Lett. 1990, 31, 7197)(Tetrahedron Lett. 1993, 34, 2179)
5 min
90 °C
DNA Cleavage
+
20 min(Chem. Res. Toxicol. 1994, 7, 677)
C A T A A A G
T G T A A A G
G G C A A A C
C A T T A A T H3CO2C
ON
NH
NNN
NHN
OHH3C
OCGTATpO
OpCG
O
NH
OCH3
OCH3OCH3
Duocarmycin A Alkylates Adenine N3 at the 3' End of AT Rich Sequences
5'-d(CGTATACG)-3'3'-d(GCATATGC)-5' 5'-d(CGTATACG)-3'
3'-d(GCATATGC)-5'
5'-d(CGTATACG)-3'
3'-d(GCATATGC)-5'
CO2CH3O
N
NHO
ONH
CH3O
CH3OOCH3
CH3
NO
HN
NO
NH
O
NH
N
N
O
HN
N
HN
O
N
N
O
NH
NO
NH
NO
NH
O
HN
O
NH
O N
OH
Cl
R
R = H (16S) , F (17) , Me (18), Br (19)
Figure 2. (a) Thermally induced strand cleavages of the 5'-Texas Red-labeled 208-bp DNA
fragment (6 nM) by conjugates 16S and 16–19 incubated for 1 h at 23 °C: lane 1 = DNA control;
lanes 2–5, 2.5, 5, 10, 20 nM of 16S; lanes 6–9, 2.5, 5, 10, 20 nM of 17; lanes 10–13, 2.5, 5, 10, 20
nM of 18; lanes 14–17, 2.5, 5, 10, 20 nM of 19; lanes 18–21, 2.5, 5, 10, 20 nM of 16. (b) A
schematic representation of sequence-specific alkylation by conjugates 16–19. Arrows indicate the
sites of adenine N3 alkylation. The alkylating base is shown in red bold.
Conformational analysis of CBI-vinyl moiety
To gain insight into the basis of the different reactivity of conjugates 16-19, we carried out
conformational analysis of CBI-vinyl moiety. Optimized structures using density functional theory
B3LYP calculation at the 6-31G (d,p) level (Gaussian 09 W) 21 are shown in Figure 4c. The results
clearly indicated that analogues of 16 and 17 mostly keep planer conformation. On the contrary,
analogues of 18 and 19 distort their conformation at the position of C2-C3 bond and cyclopropane
subunit far from the adenine N3, thus reduce their DNA alkylating activity. These results well
explain with the PAGE analysis for 16-19.
Figure 4. ������Figure 4 c, d Figure 5 a, b
Energy minimized structure of the d(CGCTTTGTCACGC) ODN1/ d (GCGTGACAAAGCG)
ODN2-16S′ complex. Vinyl linker is drawn in brown, cyclopropane unit of CBI is drawn in yellow
and ODN1 is drawn in purple, especially a reacting adenine is drawn in bold purple. (a) Overall
structure of conjugate 16 and ODN1/ODN2 complex. (b)Position and distance between the
CBI-vinyl moiety and adenine N3. (c)Chemical structures of AcPL(R)CBI moiety and dihedral
5'-CGCTTTGTCACGC-3'
3'-GCGAAACAGTCGC-5'
-β--β-
DNA alkylation at N3 of A can be evaluated by thermal DNA strand cleavageJ.Am.Chem.Soc.134,13074(2012)
PIPolyamideseco-CBIConjugateswithaVinylLinker
5'
5'
3'
3'
5'
3' 5'
3'
5' 3'
pUC18
378-827
Photoreaction of 5-Halouracil-Containing DNA Fragment
dXUTP ( X = Br or I )
PCR
302 nm
Sequencing Gel
top strand
bottom strand450 bp
TexasRed labeled primer
reverse primerXU
Reaction
Specific Cleavage at (G/C)AAXUXU and (G/C)AXUXU top strand
G C
T A
X =Br X = I reaction time
(sec) 0 15
30 45
60 0 45
90 135
180 G C
T A
X =Br X = I
0 15
30 45
60 0 45
90 135
180
site 1
site 2
site 3
site 4
site 5
site 6
site 7
site 8
site 13
site 12
site 11
site 10
site 9
bottom strand 5’-N80 TCGAATTCGT AATCATGGTC ATAGCTGTTT 3’-N80 AGCTTAAGCA TTAGTACCAG TATCGACAAA CCTGTGTGAA ATTGTTATCC GCTCACAATT GGACACACTT TAACAATAGG CGAGTGTTAA CCACACAACA TACGAGCCGG AAGCATAAAG GGTGTGTTGT ATGCTCGGCC TTCGTATTTC TGTAAAGCCT GGGGTGCCTA ATGAGTGAGC ACATTTCGGA CCCCACGGAT TACTCACTCG TAACTCACAT TAATTGCGTT GCGCTCACTG ATTGAGTGTA ATTAACGCAA CGCGAGTGAC CCCGCTTTCC AGTCGGGAAA CCTGTCGTGC GGGCGAAAGG TCAGCCCTTT GGACAGCACG CAGCTGCATT AATGAATCGG CCAACGCGCG GTCGACGTAA TTACTTAGCC GGTTGCGCGC GGGAGAGGCG GTTTGCGAAT TGGGCGCTCT N140-3’ CCCTCTCCGC CAAACGCTTA ACCCGCGAGA N140-5’
site 1
site 2 site 3
site 4
site 5
site 6 site 7
site 8
site 13
site 12
site 11
site 10
site 9
top strand
bottom strand
(G/C)AAXUXU or (G/C)AXUXU
T = XU
Sequencing of DNA
1) In 1970s Maxam and Gilbert sequencing Sanger sequencing Slab gel electrophoresis (Nobel Prize Chemistry 1980) 2) In late 1990s to 2000s Capillary gel electrophoresis (Human Genome Project) 3) 2010- Next generation sequencing (NGS)
Sanger sequencing Next generation sequencing
PCR vs emulsion PCR
DNA sequencing by Ion Torrent Personal Genome Machine
Genomic Fragment
Adapters
DNA sequencing by Ion Torrent Personal Genome Machine
Genomic Fragment
Barcode
DNA sequencing by Ion Torrent Personal Genome Machine
DNA sequencing by Ion Torrent Personal Genome Machine
Bead/ISP
Adapter Complement Sequences
The idea is that each bead should be amplified all over with a SINGLE library fragment.
DNA sequencing by Ion Torrent Personal Genome Machine
Problem: How do I do PCR to amplify the fragments without having to use 1 tube for each reaction?
DNA sequencing by Ion Torrent Personal Genome Machine
DNA sequencing by Ion Torrent Personal Genome Machine
Shotgun sequencing by PGM/454
DNA sequencing by Ion Torrent Personal Genome Machine
DNA sequencing by Ion Torrent Personal Genome Machine
DNA sequencing by Ion Torrent Personal Genome Machine
DNA sequencing by Ion Torrent Personal Genome Machine
DNA sequencing by Ion Torrent Personal Genome Machine
DNA sequencing by Ion Torrent Personal Genome Machine
Shotgun sequencing by PGM/454
DNA sequencing by Ion Torrent Personal Genome Machine
~3.5 µm for Ion Torrent, ~30 µm for 454
DNA sequencing by Ion Torrent Personal Genome Machine
JM Rothberg et al. Nature 475, 348-352 (2011)
Sensor, well and chip architecture.
Data collection and base calling.
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1 2 3 4 5
T T T
T T
DNA sequencing by Ion Torrent Personal Genome Machine
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1 2 3 4 5
A A A
A A
DNA sequencing by Ion Torrent Personal Genome Machine
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1 2 3 4 5
G G G
G G G
DNA sequencing by Ion Torrent Personal Genome Machine
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1 2 3 4 5
G
T T T
T T T
DNA sequencing by Ion Torrent Personal Genome Machine
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1 2 3 4 5
G T
C C C
C C C
DNA sequencing by Ion Torrent Personal Genome Machine
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1 2 3 4 5
G T C
A A A
A A
DNA sequencing by Ion Torrent Personal Genome Machine
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1 2 3 4 5
G T C
T T T
T T T T
DNA sequencing by Ion Torrent Personal Genome Machine
A C G C G C C G G G T C A G A A C C C G A T C G C G 5’3’
5’T G C G C G G C C C A
Primer
Only give polymerase one nucleotide at a time:
If that nucleotide is incorporated, enzymes turn by-products into light:
T C A G T C A G T C A G
1 2 3 4 5
G T C T T
G G G
G G G G G
The real power of this method is that it can take place in millions of tiny wells in a single plate at once.
DNA sequencing by Ion Torrent Personal Genome Machine
Nat. Rev.Genet. 2010, 11, 31–46
Nature 2005, 437, 376–380
Fluor
Science 2009, 323, 133-138
Future: Nanopore sequencing
Chromatin Immunoprecipitation (ChIP) is a type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or other DNA binding sites, and possibly defining cistromes. ChIP also aims to determine the specific location in the genome that various histone modifications are associated with, indicating the target of the histone modifiers.
Wikipedia, Chromatin Immunoprecipitation
RNA-seq analysis of small molecule-regulated RNA.
Sequencing
RNA seq
SPI-seq
Cross linking IP-seq
ChIP-seq TAmC-seq
Mapping of non-B DNA
DNA strand breakage mapping
Protein-DNA interaction study
Transcriptome profiling
DNA epigenetic modification
NGS
Applications of high-throughput sequencing technologies in PIP design
Dervan et al. J. Am. Chem. Soc. 2012, 134, 17814–17822 Dervan et al. J. Am. Chem. Soc. 2014, 136, 3687-3694
ChemBioChem 2014, 15, 2647-2651
IdentificationoftargetsiteforalkylatingPIPinthehumangenome
Genome-wide alkylating PIP’s high affinity binding site
ParallelSequencing
Nucleus
Micrococcalnuclease(MNase)digestion
AffinityPurification
NAR 2016, 44, 4014