Instructor: Dr. Natalia Tretyakova, Ph.D. «hyperlink ""»    -   6-3432
 PDB reference correction and design Dr.chem., Ph.D. Aris Kaksis, Associate Prof.
                                          DNA sequence specific binding Proteins
  C-Jun Proto Oncogene C-Fos Transcription Factor Ap-1 on 20 bp DNA
--> B chain 5'- T T C T CC T A T G A C T C A T CC A T -3'  chain  B -->
<--- A chain  3'-     A G A GG  A T A C T G A G T A GG T A A-5' chain  A <---
 Transcription Activation Myod Helix-Loop-Helix on double 14 bp DNA
---> E chaine 5'- T C  A A  C A GC T G T T G  A- T C A  A C A  GC T G T T G A-3' chaine H --->
<--- F chaine 3'-  A G T T G T CG A  C A A  C T -A G T T G T CG  A  C A A C T -5' chaine G <---
Dna Polymerase Beta E.C. Template-Primer 7 bp DNA fragment
                                                                                Mg2+ + 2',3'-DideoxyCytidine 5'-Triphosphate DdCTP
<--- P chaine 3'-   CCGCGGC-5' chaine P <---
---> T chaine 5'-GGGCGCCG-3' chaine T --->
9ICN.pdb 2 Na+ Tri PO4 
---> T chaine 5'-C  A T C T G-3' chaine T --->
<---  P chaine 3'-G T A  G A C-5' chaine P <---
1VAS.pdb EndoNuclease T4 on 13 bp DNA fragment

<--- C chaine     3'-A  gCgC     A CgCg  A T -5' chain C <---
 ---> B chaine 5'-A T CgCg     T gCgC T -3'  chain  B --->
Met Repressor-Operator METJ Biological Unit on 19 bp DNA one over
---> G chaine 5'- T T A  g A Cg T C T A g  A Cg T C T A-3' chain  D --->
   <--- H chaine    3'-A T C T gC A g A  T C T gC A  g A T T -5' chain C <---
Arc Repressor-Operator on 21 bp DNA one bp on 5' overhang
    <--- F chaine 3'- T A T C A T C T C A Cg  A A  g A T A  g T AA-5' chain C <---
---> E chaine 5'- T A T A g T A g  A g T gC T T C T A T C  A T -3' chain E --->
Purine Repressor Hypoxanthine on single stranded 17 bases DNA
ssDNA chaine 3'- T gC T T T T gCAAAAgCAA-5'
Operator Or1 Phage 434 Cro on 20 bp DNA fragment
---> A chaine 5'-A A g T A  C A  A A C T T T C T T g T A T -3'
<--- B chaine    3'- T C A T g T T T g  A A A  g A A  C A T A T -5'
Operator Or3 BacterioPhage 434 Cro on 20 bp DNA fragment
<--- B chaine   3'- T C  A T g T C  A  A  A A  A g A  A C A T A T -5'
---> A chaine 5'-A A g T A  C A  g T T T T T C T T g T A T -3'
Engrailed Homeodomain Complex With 20 bp DNA fragment of Fruit Fly

---> A chaine 5’- T T T T gCC  A T g T A  A T T A  CC T A  A-3' 
<--- B chaine       3’-A A  A Cgg T A  C A T T A  A T gg  A T T A-5'
Mouse Musculus c-Myb binding 16 bp DNA fragment
<--- A chaine 3'- T | A  C  A C A C  A g T C A  A T CC-5'
---> B chaine   5'-A | T g T g T g T C  A g T T A  gg-3'
Mat Alpha2 HomeoDomain two units on 19 bp DNA fragment
<--- A chaine         3’-CgC A  C A T T T A  C T T A  A T g T A  CA-5'
---> B chaine    5’- T gCg T g T A  A A T g  A A T T A  C A T g-3'
Telomere 24 bp DNA binding protein Rap1 two units
                          C|                                                       C|
---> E chaine 5'-CgCA CA CCCACAC ACC Ag   CTggTgTgTgggTgTgCg-3' D chaine
<--- F chaine 3'-gCgT gTgggTgTg TggTC   gACCACACACCC ACACgC-5' C chaine
                                                                              C|                                                      C|
Protein Prd paired 15 bp DNA fragment
<--- A chaine        3'-CAg T T ggC  A C T gCAA-5'
---> B chaine 5'- TTgTC A A  CCg T g A  Cg-3'
Antennapedia HomeoDomain binding 16 bp DNA fragment
---> A chaine 5'-g A A  A gCC  A T T A g  A g-3'
<--- B chaine 3'-C T T T Cgg T A  A T C T C-5'
Site Specific Recombinase g-d  Resolvase With 34 Bp DNA Cleavage Site
---> C chaine 5'-gC AgTgTCCgATAA TTTATAAA| T T A T Cgg A  C  A C T g-3' D chaine
   <--- F chaine  3'-g TCACAggCTATT|AAATATTT  A A T A  gCC T g T g  A C-5' E chaine
Binding HIN recombinase with DNA 13 bp fragment and minor groove

---> B chaine 5’T-g- T-T-T- T-T-g- A- T- A- A-g-A
<--- C chaine      3’C-A-A- A- A- A-C- T- A- T-T-C-T