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2010
1)
Structure
A) Primary
Chain A (Protein)
1KKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGP
V F A P P Y E P LYS LYS PRO LYS ASN LYS ASP LYS ASP LYS LYS VAL PRO GLU PRO ASP ASN LYS LYS LYS
LYS PRO LYS LYS GLU GLU GLU GLN LYS TRP LYS TRP TRP GLU GLU GLU ARG TYR PRO GLU GLY ILE LYS
TRP LYS PHE LEU GLU HIS LYS GLY PRO VAL PHE ALA PRO PRO TYR GLU PRO K K P K N K D K D K K V P
E P D N K K K K P K K E E E Q K W K W W E E E R Y P E G I K W K F L E H K G P V F A P P Y E P 174 61 L P
ENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTN
E E K N I LEU PRO GLU ASN VAL LYS PHE TYR TYR ASP GLY LYS VAL MET LYS LEU SER PRO LYS ALA GLU
GLU VAL ALA THR PHE PHE ALA LYS MET LEU ASP HIS GLU TYR THR THR LYS GLU ILE PHE ARG LYS ASN
PHE PHE LYS ASP TRP ARG LYS GLU MET THR ASN GLU GLU LYS ASN ILE L P E N V K F Y Y D G K V M K L
S P K A E E V A T F F A K M L D H E Y T T K E I F R K N F F K D W R K E M T N E E K N I 121 I T N L S K C D
F T Q M S Q Y F K A Q T E A R K Q M S K E E K L K I K E E N E K L L K E Y G F C I M D N H K E R I A N F ILE
THR ASN LEU SER LYS CYS ASP PHE THR GLN MET SER GLN TYR PHE LYS ALA GLN THR GLU ALA ARG
LYS GLN MET SER LYS GLU GLU LYS LEU LYS ILE LYS GLU GLU ASN GLU LYS LEU LEU LYS GLU TYR GLY
PHE CYS ILE MET ASP ASN HIS LYS GLU ARG ILE ALA ASN PHE I T N L S K C D F T Q M S Q Y F K A Q T E
A R K Q M S K E E K L K I K E E N E K L L K E Y G F C I M D N H K E R I A N F 181 K I E P P G L F R G R G N
H P K M G M L K R R I M P E D I I I N C S K D A K V P S P P P G H K W K E V R H D N K V T W L LYS ILE
GLU PRO PRO GLY LEU PHE ARG GLY ARG GLY ASN HIS PRO LYS MET GLY MET LEU LYS ARG ARG ILE
MET PRO GLU ASP ILE ILE ILE ASN CYS SER LYS ASP ALA LYS VAL PRO SER PRO PRO PRO GLY HIS LYS
TRP LYS GLU VAL ARG HIS ASP ASN LYS VAL THR TRP LEU K I E P P G L F R G R G N H P K M G M L K R R
I M P E D I I I N C S K D A K V P S P P P G H K W K E V R H D N K V T W L 241 V S W T E N I Q G S I K Y I M
L N P S S R I K G E K D W Q K Y E T A R R L K K C V D K I R N Q Y R E D W K S K E M K V R VAL SER TRP
THR GLU ASN ILE GLN GLY SER ILE LYS TYR ILE MET LEU ASN PRO SER SER ARG ILE LYS GLY GLU LYS
ASP TRP GLN LYS TYR GLU THR ALA ARG ARG LEU LYS LYS CYS VAL ASP LYS ILE ARG ASN GLN TYR ARG
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Biophysics K. Banu Kö se (50091012) 22.10.2010
GLU ASP TRP LYS SER LYS GLU MET LYS VAL ARG V S W T E N I Q G S I K Y I M L N P S S R I K G E K D W
Q K Y E T A R R L K K C V D K I R N Q Y R E D W K S K E M K V R 301 Q R A V A L Y F I D K L A L R A G N E
K E E G E T A D T V G C C S L R V E H I N L H P E L D G Q E Y V V E F D F L G K D GLN ARG ALA VAL ALA
LEU TYR PHE ILE ASP LYS LEU ALA LEU ARG ALA GLY ASN GLU LYS GLU GLU GLY GLU THR ALA ASP THR
VAL GLY CYS CYS SER LEU ARG VAL GLU HIS ILE ASN LEU HIS PRO GLU LEU ASP GLY GLN GLU TYR VAL
VAL GLU PHE ASP PHE LEU GLY LYS ASP Q R A V A L Y F I D K L A L R A G N E K E E G E T A D T V G C C S
L R V E H I N L H P E L D G Q E Y V V E F D F L G K D 361 S I R Y Y N K V P V E K R V F K N L Q L F M E N K
Q P E D D L F D R L N T G I L N K H L Q D L M E G L T A K V F R T Y N SER ILE ARG TYR TYR ASN LYS VAL
PRO VAL GLU LYS ARG VAL PHE LYS ASN LEU GLN LEU PHE MET GLU ASN LYS GLN PRO GLU ASP ASP
LEU PHE ASP ARG LEU ASN THR GLY ILE LEU ASN LYS HIS LEU GLN ASP LEU MET GLU GLY LEU THR ALA
LYS VAL PHE ARG THR TYR ASN S I R Y Y N K V P V E K R V F K N L Q L F M E N K Q P E D D L F D R L N T
G I L N K H L Q D L M E G L T A K V F R T Y N 421 A S I T L Q Q Q L K E L T A P D E N I P A K I L S Y N R A N
R A V A I L C N H Q R A P P K T F E K S M M N L Q T K I D A ALA SER ILE THR LEU GLN GLN GLN LEU LYS
GLU LEU THR ALA PRO ASP GLU ASN ILE PRO ALA LYS ILE LEU SER TYR ASN ARG ALA ASN ARG ALA
VAL ALA ILE LEU CYS ASN HIS GLN ARG ALA PRO PRO LYS THR PHE GLU LYS SER MET MET ASN LEU
GLN THR LYS ILE ASP ALA A S I T L Q Q Q L K E L T A P D E N I P A K I L S Y N R A N R A V A I L C N H Q R
A P P K T F E K S M M N L Q T K I D A 481 K K E Q L A D A R R D L K S A K A D A K V M K D A K T K K V V E
S K K K A V Q R L E E Q L M K L E V Q A T D R E E N K Q LYS LYS GLU GLN LEU ALA ASP ALA ARG ARG
ASP LEU LYS SER ALA LYS ALA ASP ALA LYS VAL MET LYS ASP ALA LYS THR LYS LYS VAL VAL GLU SER
LYS LYS LYS ALA VAL GLN ARG LEU GLU GLU GLN LEU MET LYS LEU GLU VAL GLN ALA THR ASP ARG
GLU GLU ASN LYS GLN K K E Q L A D A R R D L K S A K A D A K V M K D A K T K K V V E S K K K A V Q R L
E E Q L M K L E V Q A T D R E E N K Q 541 I A L G T S K L N Y L D P R I T V A W C K K W G V P I E K I Y N K
T Q R E K F A W A I D M A D E D Y E F ILE ALA LEU GLY THR SER LYS LEU ASN PTR LEU ASP PRO ARG ILE
THR VAL ALA TRP CYS LYS LYS TRP GLY VAL PRO ILE GLU LYS ILE TYR ASN LYS THR GLN ARG GLU LYS
PHE ALA TRP ALA ILE ASP MET ALA ASP GLU ASP TYR GLU PHE I A L G T S K L N Y L D P R I T V A W C K
KWGVPIEKIYNKTQREKFAWAIDMADEDYEF
Chain B (DNA)
1AAAAAGACTT
Chain C (DNA)
1CGAAAAATTTTT
Chain D (DNA)
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Biophysics K. Banu Kö se (50091012) 22.10.2010
1AAAAATTTTT CGAAGTCTTT TT
b) Secondary
Chain A (Protein)
1KKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGP
V F A P P Y E P LYS LYS PRO LYS ASN LYS ASP LYS ASP LYS LYS VAL PRO GLU PRO ASP ASN LYS LYS LYS
LYS PRO LYS LYS GLU GLU GLU GLN LYS TRP LYS TRP TRP GLU GLU GLU ARG TYR PRO GLU GLY ILE LYS
TRP LYS PHE LEU GLU HIS LYS GLY PRO VAL PHE ALA PRO PRO TYR GLU PRO K K P K N K D K D K K V P
E P D N K K K K P K K E E E Q K W K W W E E E R Y P E G I K W K F L E H K G P V F A P P Y E P 174 61 L P
ENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTN
E E K N I LEU PRO GLU ASN VAL LYS PHE TYR TYR ASP GLY LYS VAL MET LYS LEU SER PRO LYS ALA GLU
GLU VAL ALA THR PHE PHE ALA LYS MET LEU ASP HIS GLU TYR THR THR LYS GLU ILE PHE ARG LYS ASN
PHE PHE LYS ASP TRP ARG LYS GLU MET THR ASN GLU GLU LYS ASN ILE L P E N V K F Y Y D G K V M K L
S P K A E E V A T F F A K M L D H E Y T T K E I F R K N F F K D W R K E M T N E E K N I 121 I T N L S K C D
F T Q M S Q Y F K A Q T E A R K Q M S K E E K L K I K E E N E K L L K E Y G F C I M D N H K E R I A N F ILE
THR ASN LEU SER LYS CYS ASP PHE THR GLN MET SER GLN TYR PHE LYS ALA GLN THR GLU ALA ARG
LYS GLN MET SER LYS GLU GLU LYS LEU LYS ILE LYS GLU GLU ASN GLU LYS LEU LEU LYS GLU TYR GLY
PHE CYS ILE MET ASP ASN HIS LYS GLU ARG ILE ALA ASN PHE I T N L S K C D F T Q M S Q Y F K A Q T E
A R K Q M S K E E K L K I K E E N E K L L K E Y G F C I M D N H K E R I A N F 181 K I E P P G L F R G R G N
H P K M G M L K R R I M P E D I I I N C S K D A K V P S P P P G H K W K E V R H D N K V T W L LYS ILE
GLU PRO PRO GLY LEU PHE ARG GLY ARG GLY ASN HIS PRO LYS MET GLY MET LEU LYS ARG ARG ILE
MET PRO GLU ASP ILE ILE ILE ASN CYS SER LYS ASP ALA LYS VAL PRO SER PRO PRO PRO GLY HIS LYS
TRP LYS GLU VAL ARG HIS ASP ASN LYS VAL THR TRP LEU K I E P P G L F R G R G N H P K M G M L K R R
I M P E D I I I N C S K D A K V P S P P P G H K W K E V R H D N K V T W L 241 V S W T E N I Q G S I K Y I M
L N P S S R I K G E K D W Q K Y E T A R R L K K C V D K I R N Q Y R E D W K S K E M K V R VAL SER TRP
THR GLU ASN ILE GLN GLY SER ILE LYS TYR ILE MET LEU ASN PRO SER SER ARG ILE LYS GLY GLU LYS
ASP TRP GLN LYS TYR GLU THR ALA ARG ARG LEU LYS LYS CYS VAL ASP LYS ILE ARG ASN GLN TYR ARG
GLU ASP TRP LYS SER LYS GLU MET LYS VAL ARG V S W T E N I Q G S I K Y I M L N P S S R I K G E K D W
Q K Y E T A R R L K K C V D K I R N Q Y R E D W K S K E M K V R 301 Q R A V A L Y F I D K L A L R A G N E
K E E G E T A D T V G C C S L R V E H I N L H P E L D G Q E Y V V E F D F L G K D GLN ARG ALA VAL ALA
LEU TYR PHE ILE ASP LYS LEU ALA LEU ARG ALA GLY ASN GLU LYS GLU GLU GLY GLU THR ALA ASP THR
VAL GLY CYS CYS SER LEU ARG VAL GLU HIS ILE ASN LEU HIS PRO GLU LEU ASP GLY GLN GLU TYR VAL
VAL GLU PHE ASP PHE LEU GLY LYS ASP Q R A V A L Y F I D K L A L R A G N E K E E G E T A D T V G C C S
L R V E H I N L H P E L D G Q E Y V V E F D F L G K D 361 S I R Y Y N K V P V E K R V F K N L Q L F M E N K
Q P E D D L F D R L N T G I L N K H L Q D L M E G L T A K V F R T Y N SER ILE ARG TYR TYR ASN LYS VAL
PRO VAL GLU LYS ARG VAL PHE LYS ASN LEU GLN LEU PHE MET GLU ASN LYS GLN PRO GLU ASP ASP
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Biophysics K. Banu Kö se (50091012) 22.10.2010
LEU PHE ASP ARG LEU ASN THR GLY ILE LEU ASN LYS HIS LEU GLN ASP LEU MET GLU GLY LEU THR ALA
LYS VAL PHE ARG THR TYR ASN S I R Y Y N K V P V E K R V F K N L Q L F M E N K Q P E D D L F D R L N T
G I L N K H L Q D L M E G L T A K V F R T Y N 421 A S I T L Q Q Q L K E L T A P D E N I P A K I L S Y N R A N
R A V A I L C N H Q R A P P K T F E K S M M N L Q T K I D A ALA SER ILE THR LEU GLN GLN GLN LEU LYS
GLU LEU THR ALA PRO ASP GLU ASN ILE PRO ALA LYS ILE LEU SER TYR ASN ARG ALA ASN ARG ALA
VAL ALA ILE LEU CYS ASN HIS GLN ARG ALA PRO PRO LYS THR PHE GLU LYS SER MET MET ASN LEU
GLN THR LYS ILE ASP ALA A S I T L Q Q Q L K E L T A P D E N I P A K I L S Y N R A N R A V A I L C N H Q R
A P P K T F E K S M M N L Q T K I D A 481 K K E Q L A D A R R D L K S A K A D A K V M K D A K T K K V V E
S K K K A V Q R L E E Q L M K L E V Q A T D R E E N K Q LYS LYS GLU GLN LEU ALA ASP ALA ARG ARG
ASP LEU LYS SER ALA LYS ALA ASP ALA LYS VAL MET LYS ASP ALA LYS THR LYS LYS VAL VAL GLU SER
LYS LYS LYS ALA VAL GLN ARG LEU GLU GLU GLN LEU MET LYS LEU GLU VAL GLN ALA THR ASP ARG
GLU GLU ASN LYS GLN K K E Q L A D A R R D L K S A K A D A K V M K D A K T K K V V E S K K K A V Q R L
E E Q L M K L E V Q A T D R E E N K Q 541 I A L G T S K L N Y L D P R I T V A W C K K W G V P I E K I Y N K
TQREKFAWAIDMADEDYEF
Chain B (DNA)
1AAAAAGACTT
Chain C (DNA)
1CGAAAAATTTTT
Chain D (DNA)
1AAAAATTTTTCGAAGTCTTTTT
c) Tertiary
Chain A (Protein)
1KKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGP
V F A P P Y E P LYS LYS PRO LYS ASN LYS ASP LYS ASP LYS LYS VAL PRO GLU PRO ASP ASN LYS LYS LYS
LYS PRO LYS LYS GLU GLU GLU GLN LYS TRP LYS TRP TRP GLU GLU GLU ARG TYR PRO GLU GLY ILE LYS
TRP LYS PHE LEU GLU HIS LYS GLY PRO VAL PHE ALA PRO PRO TYR GLU PRO K K P K N K D K D K K V P
E P D N K K K K P K K E E E Q K W K W W E E E R Y P E G I K W K F L E H K G P V F A P P Y E P 174 61 L P
ENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTN
E E K N I LEU PRO GLU ASN VAL LYS PHE TYR TYR ASP GLY LYS VAL MET LYS LEU SER PRO LYS ALA GLU
GLU VAL ALA THR PHE PHE ALA LYS MET LEU ASP HIS GLU TYR THR THR LYS GLU ILE PHE ARG LYS ASN
PHE PHE LYS ASP TRP ARG LYS GLU MET THR ASN GLU GLU LYS ASN ILE L P E N V K F Y Y D G K V M K L
S P K A E E V A T F F A K M L D H E Y T T K E I F R K N F F K D W R K E M T N E E K N I 121 I T N L S K C D
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F T Q M S Q Y F K A Q T E A R K Q M S K E E K L K I K E E N E K L L K E Y G F C I M D N H K E R I A N F ILE
THR ASN LEU SER LYS CYS ASP PHE THR GLN MET SER GLN TYR PHE LYS ALA GLN THR GLU ALA ARG
LYS GLN MET SER LYS GLU GLU LYS LEU LYS ILE LYS GLU GLU ASN GLU LYS LEU LEU LYS GLU TYR GLY
PHE CYS ILE MET ASP ASN HIS LYS GLU ARG ILE ALA ASN PHE I T N L S K C D F T Q M S Q Y F K A Q T E
A R K Q M S K E E K L K I K E E N E K L L K E Y G F C I M D N H K E R I A N F 181 K I E P P G L F R G R G N
H P K M G M L K R R I M P E D I I I N C S K D A K V P S P P P G H K W K E V R H D N K V T W L LYS ILE
GLU PRO PRO GLY LEU PHE ARG GLY ARG GLY ASN HIS PRO LYS MET GLY MET LEU LYS ARG ARG ILE
MET PRO GLU ASP ILE ILE ILE ASN CYS SER LYS ASP ALA LYS VAL PRO SER PRO PRO PRO GLY HIS LYS
TRP LYS GLU VAL ARG HIS ASP ASN LYS VAL THR TRP LEU K I E P P G L F R G R G N H P K M G M L K R R
I M P E D I I I N C S K D A K V P S P P P G H K W K E V R H D N K V T W L 241 V S W T E N I Q G S I K Y I M
L N P S S R I K G E K D W Q K Y E T A R R L K K C V D K I R N Q Y R E D W K S K E M K V R VAL SER TRP
THR GLU ASN ILE GLN GLY SER ILE LYS TYR ILE MET LEU ASN PRO SER SER ARG ILE LYS GLY GLU LYS
ASP TRP GLN LYS TYR GLU THR ALA ARG ARG LEU LYS LYS CYS VAL ASP LYS ILE ARG ASN GLN TYR ARG
GLU ASP TRP LYS SER LYS GLU MET LYS VAL ARG V S W T E N I Q G S I K Y I M L N P S S R I K G E K D W
Q K Y E T A R R L K K C V D K I R N Q Y R E D W K S K E M K V R 301 Q R A V A L Y F I D K L A L R A G N E
K E E G E T A D T V G C C S L R V E H I N L H P E L D G Q E Y V V E F D F L G K D GLN ARG ALA VAL ALA
LEU TYR PHE ILE ASP LYS LEU ALA LEU ARG ALA GLY ASN GLU LYS GLU GLU GLY GLU THR ALA ASP THR
VAL GLY CYS CYS SER LEU ARG VAL GLU HIS ILE ASN LEU HIS PRO GLU LEU ASP GLY GLN GLU TYR VAL
VAL GLU PHE ASP PHE LEU GLY LYS ASP Q R A V A L Y F I D K L A L R A G N E K E E G E T A D T V G C C S
L R V E H I N L H P E L D G Q E Y V V E F D F L G K D 361 S I R Y Y N K V P V E K R V F K N L Q L F M E N K
Q P E D D L F D R L N T G I L N K H L Q D L M E G L T A K V F R T Y N SER ILE ARG TYR TYR ASN LYS VAL
PRO VAL GLU LYS ARG VAL PHE LYS ASN LEU GLN LEU PHE MET GLU ASN LYS GLN PRO GLU ASP ASP
LEU PHE ASP ARG LEU ASN THR GLY ILE LEU ASN LYS HIS LEU GLN ASP LEU MET GLU GLY LEU THR ALA
LYS VAL PHE ARG THR TYR ASN S I R Y Y N K V P V E K R V F K N L Q L F M E N K Q P E D D L F D R L N T
G I L N K H L Q D L M E G L T A K V F R T Y N 421 A S I T L Q Q Q L K E L T A P D E N I P A K I L S Y N R A N
R A V A I L C N H Q R A P P K T F E K S M M N L Q T K I D A ALA SER ILE THR LEU GLN GLN GLN LEU LYS
GLU LEU THR ALA PRO ASP GLU ASN ILE PRO ALA LYS ILE LEU SER TYR ASN ARG ALA ASN ARG ALA
VAL ALA ILE LEU CYS ASN HIS GLN ARG ALA PRO PRO LYS THR PHE GLU LYS SER MET MET ASN LEU
GLN THR LYS ILE ASP ALA A S I T L Q Q Q L K E L T A P D E N I P A K I L S Y N R A N R A V A I L C N H Q R
A P P K T F E K S M M N L Q T K I D A 481 K K E Q L A D A R R D L K S A K A D A K V M K D A K T K K V V E
S K K K A V Q R L E E Q L M K L E V Q A T D R E E N K Q LYS LYS GLU GLN LEU ALA ASP ALA ARG ARG
ASP LEU LYS SER ALA LYS ALA ASP ALA LYS VAL MET LYS ASP ALA LYS THR LYS LYS VAL VAL GLU SER
LYS LYS LYS ALA VAL GLN ARG LEU GLU GLU GLN LEU MET LYS LEU GLU VAL GLN ALA THR ASP ARG
GLU GLU ASN LYS GLN K K E Q L A D A R R D L K S A K A D A K V M K D A K T K K V V E S K K K A V Q R L
E E Q L M K L E V Q A T D R E E N K Q 541 I A L G T S K L N Y L D P R I T V A W C K K W G V P I E K I Y N K
T Q R E K F A W A I D M A D E D Y E F ILE ALA LEU GLY THR SER LYS LEU ASN PTR LEU ASP PRO ARG ILE
THR VAL ALA TRP CYS LYS LYS TRP GLY VAL PRO ILE GLU LYS ILE TYR ASN LYS THR GLN ARG GLU LYS
PHE ALA TRP ALA ILE ASP MET ALA ASP GLU ASP TYR GLU PHE I A L G T S K L N Y L D P R I T V A W C K
K W G V P I E K I Y N K T Q R E K F A W A I D M A D E D Y E F 765
Chain B (DNA)
1AAAAAGACTT
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Chain C (DNA)
1CGAAAAATTTTT
Chain D (DNA)
1AAAAATTTTTCGAAGTCTTTTT
Quaternary
Hetero Tetrametric
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This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of
DNA during transcription. This enzyme catalyzes the transient breaking and rejoining of a single
strand of DNA which allows the strands to pass through one another, thus altering the topology of
DNA. This gene is localized to chromosome 20 and has pseudogenes which reside on chromosomes 1
and 22.
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conformational states results in uncompetitive inhibition and exemplifies the relevance of screening
for ligands and drugs that stabilize (“trap”) these macromolecular complexes
(DNA Topoisomerase I Inhibitors: Chemistry, Biology, and Interfacial Inhibition/ Yves Pommiera/Laboratory of Molecular
Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
Chem. Rev., 2009)
e)
Crystallization Experiments
Method VAPOR DIFFUSION, SITTING DROP pH 6.4 Temperature 289.0 Details PEG 8000, MES,
Ammonium Sulfate, pH 6.40, VAPOR DIFFUSION, SITTING DROP, temperature 289K
a= 56.95 α = 90
b= 114.14 β = 94.18
c= 73.5 γ= 90
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2) DNA TOPOLOGY
This supercoiling or writhing of circular DNAs was a result of the DNAs being
underwound with respect to the relaxed form of DNA. There are actually fewer turns in the
DNA helix than one would expect given the natural pitch of DNA in solution
(10.4 base pairs per turn).
When a linear DNA is free in solution it assumes a pitch which contains 10.4
base pairs per turn. This is less tightly wound than the 10.0 base pairs per turn in the
Watson and Crick B-form DNA.
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Biophysics K. Banu Kö se (50091012) 22.10.2010
The total number of times one strand of the DNA helix is linked with the other
in a covalently closed circular molecule is known as the linking number Lk.
1. The linking number is only defined for covalently closed DNA and its value is
fixed as long as the molecule remains covalently closed.
2. The linking number does not change whether the covalently closed circle is
forced to lie in a plane in a stressed conformation or whether it is allowed to
supercoil about itself freely in space.
Lk = Tw + Wr
The twists Tw are the number of times that the two strands are twisted about
each other while the writhes Wr is the number of times that the DNA helix is coiled
about itself in three-dimensional space.
Unlike the Twist and the Linking number, the writhe of DNA only depends on
the path the helix axis takes in space, not on the fact that the DNA his two strands. If
the path of the DNA is in a plane, the Wr is always zero. Also if the path of the DNA
helix were on the surface of a sphere (like the seams of a tennis ball or base ball) then
the total Writhe can also be shown to be zero.
Writhes
DNA GEOMETRY
A-DNA / B-DNA
When DNA fibres are formed at low humidity DNA assumes a less hydrated form. (A-form)
This structure was determined at the same time as the B-form. This too is a double helix
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structure, but is formed at a lower hydration than B-DNA (i.e.<75% humidity). Once again
this structure was the result of X-ray difractioin from DNA fibres so the position of the base
pairs is an average over the whole fibre.
The helix is wider, flatter and more compressed than the B-DNA helix. If synthetic RNA
molecules which are complementary in sequence form a double helix they form an A-type
double helix. This is due to the fact that the -OH group in the 2' position of the ribose would
be sterically hindered in the B-form helix. However remember that naturally occuring RNA
molecules are not normally complementary. (Why?)
A-DNA B-DNA
pitch=2.8nm pitch=3.6nm
11 base pairs/turn 10 base pairs/turn
sugar=C3'-endo sugar=C2'-endo
The planes of the bases are tilted 20 degrees to the helix axis, and there is a very deep major
groove, and a very shallow minor groove.
The physiological relevance of the A-form of DNA is not established. Most of the DNA in
chromatin is thought to be in the B-form.
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Biophysics K. Banu Kö se (50091012) 22.10.2010
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Oligonucleotide Structures
More recently small, self-complimentary pieces of DNA have been co-crystallised and their
stuctures determined by X-ray crystallography. These are true crystalls and the positions of
each individual atom and base-pair can be determined. This contrasts with the fibre difraction
patterns which only give an average picture for all base pairs. Analysis of these crystalls has
shown that DNA can have quite large local deviations from the canonical Watson and Crick
structure and that these deviations appear to be dependent on the sequence of base pairs. The
crystal structure of the B-DNA decamer:
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Biophysics K. Banu Kö se (50091012) 22.10.2010
These average values are quite close to the values for those for B-DNA determined from fibre
difraction. However there are large variations from these average values for individual base
pairs in the sequence, such that:
The variations in geometry appear to be sequence specific, purines favouring the C2'-endo
sugars, and pyrimidines the C3'-endo sugars. The conformation of a residue is also affected by
what it's neighbours conformation is (i.e. the AT pairs in the middle have a slightly different
conformation to those next to the GC's).
Use the mouse to rotate and zoom the image and convince yourself of the changes in propeller
twist and dihedral angle. The changes in sugar conformation are not quite so easy to spot.
The helix is curved by approximately 19o and not straight. (This is not easy to spot either if
you have not had a lot of experience looking at structures of this type.) DNA helices are
reasonably flexible to bending about small angles, so it is not known whether the curve seen is
due to natural conditions or an artifact of the crystallisation process.
There is a row of tightly bonded water molecules in the major groove in the AT-rich region. It
is not possible to say if these water molecules are present in native DNA as fibre difraction
does not enable water molecules to be identified. It is thought these water molecules may
provide a "spine of hydration" which stabilises the structure in the B-form and may be lost in
the transition to A-form. This is speculation however.
DNA is easily deformed, and does not have a precisely regular structure. Geometric variations
apear to be sequence specific...
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Biophysics K. Banu Kö se (50091012) 22.10.2010
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Biophysics K. Banu Kö se (50091012) 22.10.2010
Z-DNA
The third and final geometry of DNA is that of the so-called Z-DNA.
This is sometimes seen when the sequence is of alternating purines and pyrimidines and was
first seen in the structure of the alternating deoxynucleotide dCpGpCpGpCpG.
If this structure displays the hydrogens-white dots- use the pull down menu to turn them off.
(OPTIONS submenu)
The Z structure was first shown in oligonucleotides, and an anti-parallel double helix forms ...
Left handed
12 base pairs/turn
BUT the helix is: Pitch is 4.5nm per turn
Deep minor groove
Little or no major groove
This structure is formed by rotating the N-glycosyl bonds of G residues 180o with respect to
their conformation in B-DNA. In Z DNA all of the purines are in the "syn" conformation and
all the pyrimidines are in the "anti" conformation. Because the purines are "flipped" because
of the 180o rotation the pyrimidines must also "flip" to keep the base pairing intact. However
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Biophysics K. Banu Kö se (50091012) 22.10.2010
pyrimidine nucleotides do not readily assume the "syn" configuration because of steric
hinderance between the oxy group at position 2 of the pyrimidine and the atoms of the sugar.
In order to keep the base pairs intact the whole nucleoside (base plus sugar) has to flip 180o.
Despite these quite drastic conformational changes it is topologically possible for the G bases
to go syn and the C nucleosides to rotate 180o without breaking and reforming the hydrogen
bonds. This means that the B to Z structural transition can occur without any separation of the
helix.
Sources:
1- http://www.pdb.org/pdb/explore/explore.do?structureId=1TL8
2- http://pubs.acs.org/doi/abs/10.1021/cr900097c
3- http://www.ebi.ac.uk/pdbsum/1tl8
4- http://books.google.com.tr/books?
id=WGBAGyzvQOUC&pg=PA25&dq=DNA+TOPOLOGY+AND+GEOMETRY&source=gbs_toc_r&cad=4#v
=onepage&q=DNA%20TOPOLOGY%20AND%20GEOMETRY&f=false
5- http://www.ima.umn.edu/2007-2008/T9.15.07/activities/Olson-Wilma/IMA_tutorial_1.pdf
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