Swetlana Nikolajewa, Andreas Beyer, Maik Friedel, Jens Hollunder, Thomas Wilhelm Institute of Molecular Biotechnology, Jen...
Overview: Purine-Pyrimidine Patterns  <ul><li>Part 1   New Classification Scheme of the Genetic code </li></ul><ul><li>Par...
Overview: Genetic Code <ul><li>Part 1.  The purine-pyrimidine scheme of the genetic codes shows  </li></ul><ul><ul><ul><li...
Pu R ines vs. P Y rimidines T C A G
Purine pairs with Pyrimidine 3 H Bonds 2 H Bonds
<ul><li>3 nucleobases (triplets)  of A, G, C, U code for 20 AAs </li></ul><ul><li>64 possible codons (4x4x4=4 3 ) </li></u...
Purine-Pyrimidine Classification Scheme  of the Genetic Code  <ul><li>binary representation of nucleobases  </li></ul><ul>...
Purine-Pyrimidine Table of the Genetic Code Codon Strong codons 6 H bonds Mixed codons 5 H bonds Mixed   codons 5 H bonds ...
Amino Acid Patterns: Polar Requirement of  NCN and NUN Codons Codon Strong   6 hydrogen bonds Mixed   5 hydrogen bonds Mix...
Codon Strong   6 H-bonds Mixed   5 H-bonds Mixed   5 H-bonds Weak   4 H- bonds Pro   CC   (A/G) Ala   G C   (C/U) Ala   G ...
Codon-Anticodon Symmetry  Codon Strong   6 H-bonds Mixed   5 H-bonds Mixed   5 H-bonds Weak   4 H-bonds Pro   CC   (A/G) A...
Point Symmetry  Codon Strong   6 H-bonds Mixed   5 H- bonds Mixed   5 H-bonds Weak   4 H-bonds Pro   CC   (A/G) Ala   G C ...
Codon-Reverse Codon   (XYZ ↔ ZYX)  Symmetry Codon Strong   6 H-bonds Mixed   5 H- bonds Mixed   5 H-bonds Weak   4 H-bonds...
CUA Asp Codon-Reverse Codon   (XYZ ↔ ZYX)  Symmetry AUC GAU Asp UAG STOP Stop AUC
Evolution of the Genetic Code   <ul><li>binary doublet:    4 1 =4 fields </li></ul><ul><li>quaternary doublet code:   4 2 ...
Evolution: Scenario 1 Codon Strong   6 H bonds Mixed   5 H bonds Mixed 5 H bonds Weak 4 H bonds Pro   CC   (A/G) Proline A...
Codon Strong 6 H bonds Mixed 5 H bonds Mixed 5 H bonds Weak 4 H bonds Pro   CC   (A/G) Proline Ala   G C   (C/U) Alanine A...
Deviations from the Standard Code   Codon Strong 6 H-bonds Mixed   5 H-bonds Mixed   5 H-bonds Weak   4 H-bonds Pro   CC  ...
Mitochondrial genomes   have several surprising features <ul><li>genetic code of mitochondria </li></ul><ul><li>only   22 ...
The Mammalian Mitochondrial Genetic Code Codon Strong 6 H bonds Mixed 5 H bonds Mixed 5 H bonds Weak 4 H bonds Pro   CC   ...
The  Mammalian  Mitochondrial Code   8  tRNAs for family codons +  14  tRNAs for non-family codons =  22 Codon Strong 6 H ...
Part 2. Common Patterns  in Type II Restriction Enzyme Binding Sites
Restriction Enzyme (Endonuclease) <ul><li>Restriction enzymes  </li></ul><ul><li>recognize  short specific  DNA  sequences...
Are REase similar in the binding sites?  11 ↓ 00 1 ↓ 11  000 11 ↓ 00 1 ↓ 11  000 1 ↓ 11  000 Examples from Kimball‘s Biolo...
How significant is the Pattern RR/YY (11/00)?  <ul><li>Frequencies of </li></ul><ul><ul><li>dinucleotides </li></ul></ul><...
Why is the Motif RR..YY preferred?  <ul><li>specific geometrical properties </li></ul><ul><ul><li>minimal slide values  </...
Outlook <ul><li>Looking for binary patterns  in the genomes </li></ul><ul><li>Additional information   </li></ul>Thank   y...
Purine-Pyrimidine Scheme of the Genetic Code Codon Strong 6 hydrogen bonds Mixed   5 hydrogen bonds Mixed   5 hydrogen bon...
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  1. 1. Swetlana Nikolajewa, Andreas Beyer, Maik Friedel, Jens Hollunder, Thomas Wilhelm Institute of Molecular Biotechnology, Jena Germany Purine-Pyrimidine Patterns in the Genetic Code and in Restriction Enzyme Recognition Sequences Jena Institute of Molecular Biotechnology
  2. 2. Overview: Purine-Pyrimidine Patterns <ul><li>Part 1 New Classification Scheme of the Genetic code </li></ul><ul><li>Part 2 Type II Restriction Enzyme Binding Sites </li></ul>
  3. 3. Overview: Genetic Code <ul><li>Part 1. The purine-pyrimidine scheme of the genetic codes shows </li></ul><ul><ul><ul><li>amino-acids patterns and regularities of codons </li></ul></ul></ul><ul><ul><ul><li>symmetry characteristics </li></ul></ul></ul><ul><ul><ul><li>possible predecessors of our contemporary quaternary triplet code </li></ul></ul></ul><ul><ul><ul><li>explanation for the number (22) of tRNA genes in mammalian mitochondrial genome </li></ul></ul></ul>
  4. 4. Pu R ines vs. P Y rimidines T C A G
  5. 5. Purine pairs with Pyrimidine 3 H Bonds 2 H Bonds
  6. 6. <ul><li>3 nucleobases (triplets) of A, G, C, U code for 20 AAs </li></ul><ul><li>64 possible codons (4x4x4=4 3 ) </li></ul><ul><ul><li>3 termination codons: UGA, UAG, UAA </li></ul></ul><ul><ul><li>Met (AUG) codon is also the start codon </li></ul></ul>The Common Genetic Code Table The Common Genetic Code Table contains 64 fields… U C A G GGU Gly GGC Gly GGA Gly GGG Gly GAU Asp GAC Asp GAA Glu GAG Glu GCU Ala GCC Ala GCA Ala GCG Ala GUU Val GUC Val GUA Val GUG Val G U C A G AGU Ser AGC Ser AGA Arg AGG Arg AAU Asn AAC Asn AAA Lys AAG Lys ACU Thr ACC Thr ACA Thr ACG Thr AUU Ile AUC Ile AUA Ile AUG Met A U C A G CGU Arg CGC Arg CGA Arg CGG Arg CAU His CAC His CAA Gln CAG Gln CCU Pro CCC Pro CCA Pro CCG Pro CUU Leu CUC Leu CUA Leu CUG Leu C 3rd base U C A G UGU Cys UGC Cys UGA Stop UGG Trp UAU Tyr UAC Tyr UAA Stop UAG Stop UCU Ser UCC Ser UCA Ser UCG Ser UUU Phe UUC Phe UUA Leu UUG Leu U 1st base G A C U 2nd base
  7. 7. Purine-Pyrimidine Classification Scheme of the Genetic Code <ul><li>binary representation of nucleobases </li></ul><ul><ul><ul><ul><ul><li>purines : A, G -> 1 </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>pyrimidines: C, U -> 0 </li></ul></ul></ul></ul></ul><ul><li>2 3 = 8 different binary triplets 000 , 00 1 , … , 111 each of these has again 8 possibilities, for instance: </li></ul><ul><ul><li>000 stands for three pyrimidines: CCC , CCU , UUC , …, UUU </li></ul></ul><ul><ul><li>111 stands for three purines: GGG, GGA, GAA, …, AAA </li></ul></ul>C G binds via 3 hydrogen bonds in the complementary base pairing A U binds via 2 hydrogen bonds in the complementary base pairing
  8. 8. Purine-Pyrimidine Table of the Genetic Code Codon Strong codons 6 H bonds Mixed codons 5 H bonds Mixed codons 5 H bonds Weak codons 4 H bonds Pro CC (A/G) Proline Ala G C (C/U) Alanine Ala G C (A/G) Alanine Leu CU (A/G) Leucine Thr A C (C/U) Threonine Thr A C (A/G) Threonine Ser UC (C/U) Serine Val G U (C/U) Valine Val G U (A/G) Valine Phe UU (C/U) Phenylalanine Ile A U (C/U) Isoleucine Ile /Met A U (A/G) Isoleucine/Methionine 000 00 1 1 00 1 0 1 Arg C G (C/U) Arginine Cys U G (C/U) Cystein His C A (C/U) Histidine Tyr U A (C/U) Tyrosine 0 1 0 Arg C G (A/G) Arginine Stop/Trp U G (A/G) Tryptophan Gln C A (A/G) Glutamine Stop U A (A/G) 0 11 Gly GG (C/U) Glycine Asp GA (C/U) Asparatic acid Asn AA (C/U) Asparagine 11 0 Gly GG (A/G) Glycine Glu GA (A/G) Glutamatic acid 111 Leu CU (C/U) Leucine Leu UU (A/G) Leucine Ser UC (A/G) Serine Ser AG (C/U) Serine Arg AG (A/G) Arginine Pro CC (C/U) Proline Lys AA (A/G) Lysine … the new scheme contains the same information in only 32 fields.
  9. 9. Amino Acid Patterns: Polar Requirement of NCN and NUN Codons Codon Strong 6 hydrogen bonds Mixed 5 hydrogen bonds Mixed 5 hydrogen bonds Weak 4 hydrogen bonds Pro CC (A/G) Ala G C (C/U) Ala G C (A/G) Leu CU (A/G) Thr A C (C/U) Thr A C (A/G) Ser UC (C/U) Val G U (C/U) Val G U (A/G) Phe UU (C/U) Ile A U (C/U) Ile /Met A U (A/G) 000 00 1 1 00 1 0 1 Arg C G (C/U) Cys U G (C/U) His C A (C/U) Tyr U A (C/U) 0 1 0 Arg C G (A/G) Stop/Trp U G (A/G) Gln C A (A/G) Stop U A (A/G) 0 11 Gly GG (C/U) Asp GA (C/U) Asparatic acid Asn AA (C/U) Asparagine 11 0 Gly GG (A/G) Glu GA (A/G) Glutamatic acid 111 Leu CU (C/U) Leu UU (A/G) Ser UC (A/G) Ser AG (C/U) Arg AG (A/G) Pro CC (C/U) Lys AA (A/G) Lysine C. R. Woese, G. J. Olsen, M. Ibba, D. Söll Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process. MMBR 2000(64) 202-236
  10. 10. Codon Strong 6 H-bonds Mixed 5 H-bonds Mixed 5 H-bonds Weak 4 H- bonds Pro CC (A/G) Ala G C (C/U) Ala G C (A/G) Leu CU (A/G) Thr A C (C/U) Thr A C (A/G) Ser UC (C/U) Val G U (C/U) Val G U (A/G) Phe UU (C/U) Ile A U (C/U) Ile /Met A U (A/G) 000 00 1 1 00 1 0 1 Arg C G (C/U) Cys U G (C/U) His C A (C/U) Tyr U A (C/U) 0 1 0 Arg C G (A/G) Stop/Trp U G (A/G) Gln C A (A/G) Stop U A (A/G) 0 11 Gly GG (C/U) Asp GA (C/U) Asn AA (C/U) 11 0 Gly GG (A/G) Glu GA (A/G) 111 Leu CU (C/U) Leu UU (A/G) Ser UC (A/G) Ser AG (C/U) Arg AG (A/G) Pro CC (C/U) Lys AA (A/G) Kyte&Doolittle, 1982, http:// biology-pages.info Amino Acid Patterns: Hydrophobicity
  11. 11. Codon-Anticodon Symmetry Codon Strong 6 H-bonds Mixed 5 H-bonds Mixed 5 H-bonds Weak 4 H-bonds Pro CC (A/G) Ala G C (C/U) Ala G C (A/G) Leu CU (A/G) Thr A C (C/U) Thr A C (A/G) Val G U (C/U) Val G U (A/G) Ile A U (C/U) Ile /Met A U (A/G) 00 1 1 00 1 0 1 Arg C G (C/U) Cys U G (C/U) His C A (C/U) Tyr U A (C/U) 0 1 0 Arg C G (A/G) Stop/Trp U G (A/G) Gln C A (A/G) Stop U A (A/G) 0 11 Gly GG (C/U) Asp GA (C/U) Asn AA (C/U) 11 0 Gly GG (A/G) Glu GA (A/G) 111 Leu UU (A/G) Ser UC (A/G) Ser AG (C/U) Arg AG (A/G) Lys AA (A/G) Ser UC (C/U) Phe UU (C/U) 000 Leu CU (C/U) Pro CC (C/U)
  12. 12. Point Symmetry Codon Strong 6 H-bonds Mixed 5 H- bonds Mixed 5 H-bonds Weak 4 H-bonds Pro CC (A/G) Ala G C (C/U) Ala G C (A/G) Leu CU (A/G) Thr A C (C/U) Thr A C (A/G) Ser UC (C/U) Val G U (C/U) Val G U (A/G) Phe UU (C/U) Ile A U (C/U) Ile /Met A U (A/G) 000 00 1 1 00 1 0 1 Arg C G (C/U) Cys U G (C/U) His C A (C/U) Tyr U A (C/U) 0 1 0 Arg C G (A/G) Stop/Trp U G (A/G) Gln C A (A/G) Stop U A (A/G) 0 11 Gly GG (C/U) Asp GA (C/U) Asn AA (C/U) 11 0 Gly GG (A/G) Glu GA (A/G) 111 Leu CU (C/U) Leu UU (A/G) Ser UC (A/G) Ser AG (C/U) Arg AG (A/G) Pro CC (C/U) Lys AA (A/G) D. Halitsky Extending the (Hexa-)Rhombic Dodecahedral Model of the Genetic Code: the Code's Four 6-fold Degeneracies and the Ten Orthogonal Projections of the 5-cube as 3-cube. Computer Systems Technology 2004
  13. 13. Codon-Reverse Codon (XYZ ↔ ZYX) Symmetry Codon Strong 6 H-bonds Mixed 5 H- bonds Mixed 5 H-bonds Weak 4 H-bonds Pro CC (A/G) Ala G C (C/U) Ala G C (A/G) Leu CU (A/G) Thr A C (C/U) Thr A C (A/G) Ser UC (C/U) Val G U (C/U) Val G U (A/G) Phe UU (C/U) Ile A U (C/U) Ile /Met A U (A/G) 000 00 1 1 00 1 0 1 Arg C G (C/U) Cys U G (C/U) His C A (C/U) Tyr U A (C/U) 0 1 0 Arg C G (A/G) Stop/Trp U G (A/G) Gln C A (A/G) Stop U A (A/G) 0 11 Gly GG (C/U) Asp GA (C/U) Asn AA (C/U) 11 0 Gly GG (A/G) Glu GA (A/G) 111 Leu CU (C/U) Leu UU (A/G) Ser UC (A/G) Ser AG (C/U) Arg AG (A/G) Pro CC (C/U) Lys AA (A/G)
  14. 14. CUA Asp Codon-Reverse Codon (XYZ ↔ ZYX) Symmetry AUC GAU Asp UAG STOP Stop AUC
  15. 15. Evolution of the Genetic Code <ul><li>binary doublet: 4 1 =4 fields </li></ul><ul><li>quaternary doublet code: 4 2 =16 fields </li></ul><ul><li>our contemporary code is the quaternary triplet code: 4 3 =64 fields </li></ul>C G U, U A C,… 11 11 11 11 1 0 1 0 1 0 1 0 0 1 0 1 0 1 0 1 00 00 00 00 11 * 11 * 11 * 11 * 1 0 * 1 0 * 1 0 * 1 0 * 0 1 * 0 1 * 0 1 * 0 1 * 00 * 00 * 00 * 00 * 11 1 0 0 1 00 C G U, U A C,…
  16. 16. Evolution: Scenario 1 Codon Strong 6 H bonds Mixed 5 H bonds Mixed 5 H bonds Weak 4 H bonds Pro CC (A/G) Proline Ala G C (C/U) Alanine Ala G C (A/G) Alanine Leu CU (A/G) Leucine Thr A C (C/U) Threonine Thr A C (A/G) Threonine Ser UC (C/U) Serine Val G U (C/U) Valine Val G U (A/G) Valine Phe UU (C/U) Phenylalanine Ile A U (C/U) Isoleucine Ile /Met A U (A/G) Isoleucine/Methionine 000 00 1 1 00 1 0 1 Arg C G (C/U) Arginine Cys U G (C/U) Cystein His C A (C/U) Histidine Tyr U A (C/U) Tyrosine 0 1 0 Arg C G (A/G) Arginine Stop/Trp U G (A/G) Tryptophan Gln C A (A/G) Glutamine Stop U A (A/G) 0 11 Gly GG (C/U) Glycine Asp GA (C/U) Asparatic acid Asn AA (C/U) Asparagine 11 0 Gly GG (A/G) Glycine Glu GA (A/G) Glutamatic acid 111 Leu CU (C/U) Leucine Leu UU (A/G) Leucine Ser UC (A/G) Serine Ser AG (C/U) Serine Arg AG (A/G) Arginine Pro CC (C/U) Proline Lys AA (A/G) Lysine 11 11 11 11 1 0 1 0 1 0 1 0 0 1 0 1 0 1 0 1 00 00 00 00
  17. 17. Codon Strong 6 H bonds Mixed 5 H bonds Mixed 5 H bonds Weak 4 H bonds Pro CC (A/G) Proline Ala G C (C/U) Alanine Ala G C (A/G) Alanine Leu CU (A/G) Leucine Thr A C (C/U) Threonine Thr A C (A/G) Threonine Ser UC (C/U) Serine Val G U (C/U) Valine Val G U (A/G) Valine Phe UU (C/U) Phenylalanine Ile A U (C/U) Isoleucine Ile /Met A U (A/G) Isoleucine/Methionine 000 00 1 1 00 1 0 1 Arg C G (C/U) Arginine Cys U G (C/U) Cystein His C A (C/U) Histidine Tyr U A (C/U) Tyrosine 0 1 0 Arg C G (A/G) Arginine Stop/Trp U G (A/G) Tryptophan Gln C A (A/G) Glutamine Stop U A (A/G) 0 11 Gly GG (C/U) Glycine Asp GA (C/U) Asparatic acid Asn AA (C/U) Asparagine 11 0 Gly GG (A/G) Glycine Glu GA (A/G) Glutamatic acid 111 Leu CU (C/U) Leucine Leu UU (A/G) Leucine Ser UC (A/G) Serine Ser AG (C/U) Serine Arg AG (A/G) Arginine Pro CC (C/U) Proline Lys AA (A/G) Lysine Evolution: Scenario 2 11 11 11 11 1 0 1 0 1 0 1 0 0 1 0 1 0 1 0 1 00 00 00 00
  18. 18. Deviations from the Standard Code Codon Strong 6 H-bonds Mixed 5 H-bonds Mixed 5 H-bonds Weak 4 H-bonds Pro CC (A/G) Ala G C (C/U) Ala G C (A/G) Leu CU (A/G) 1/2 Thr A C (C/U) Thr A C (A/G) Val G U (C/U) Val G U (A/G) Ile A U (C/U) Ile /Met A U (A/G) 5/0 00 1 1 00 1 0 1 Arg C G (C/U) Cys U G (C/U) His C A (C/U) Tyr U A (C/U) 0 1 0 Arg C G (A/G) Stop /Trp U G (A/G) 9/0 Gln C A (A/G) Stop U A (A/G) 2/4 0 11 Gly GG (C/U) Asp GA (C/U) Asn AA (C/U) 11 0 Gly GG (A/G) Glu GA (A/G) 111 Leu UU (A/G) 1/0 Ser UC (A/G) 1/0 Ser AG (C/U) Arg AG (A/G) 6/6 Lys AA (A/G) 3/0 Ser UC (C/U) Phe UU (C/U) 000 Leu CU (C/U) 1/1 Pro CC (C/U) http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
  19. 19. Mitochondrial genomes have several surprising features <ul><li>genetic code of mitochondria </li></ul><ul><li>only 22 tRNAs are required for mammalian mitochondrial protein synthesis </li></ul>?
  20. 20. The Mammalian Mitochondrial Genetic Code Codon Strong 6 H bonds Mixed 5 H bonds Mixed 5 H bonds Weak 4 H bonds Pro CC (A/G) Ala G C (C/U) Ala G C (A/G) Leu CU (A/G) Thr A C (C/U) Thr A C (A/G) Val G U (C/U) Val G U (A/G) Ile A U (C/U) Met/Met A U (A/G) 00 1 1 00 1 0 1 Arg C G (C/U) Cys U G (C/U) His C A (C/U) Tyr U A (C/U) 0 1 0 Arg C G (A/G) Trp /Trp U G (A/G) Gln C A (A/G) Stop U A (A/G) 0 11 Gly GG (C/U) Asp GA (C/U) Asn AA (C/U) 11 0 Gly GG (A/G) Glu GA (A/G) 111 Leu UU (A/G) Ser UC (A/G) Ser AG (C/U) STOP AG (A/G) Lys AA (A/G) Ser UC (C/U) Phe UU (C/U) 000 Leu CU (C/U) Pro CC (C/U) http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
  21. 21. The Mammalian Mitochondrial Code 8 tRNAs for family codons + 14 tRNAs for non-family codons = 22 Codon Strong 6 H bonds Mixed 5 H bonds Mixed 5 H bonds Weak 4 H bonds tRNA Ile A U (C/U) tRNA Met A U (A/G) 00 1 1 00 1 0 1 tRNA Cys U G (C/U) tRNA His C A (C/U) tRNA Tyr U A (C/U) 0 1 0 tRNA Trp U G (A/G) tRNA Gln C A (A/G) STOP U A (A/G) 0 11 tRNA Asp GA (C/U) tRNA Asn AA (C/U) 11 0 tRNA Glu GA (A/G) 111 tRNA Leu 2 UU (A/G) tRNA Ser 2 AG (C/U) STOP AG (A/G) tRNA Lys AA (A/G) tRNA Ser 1 UC tRNA Phe UU (C/U) 000 tRNA Leu 1 CU tRNA Pro CC tRNA Ala G C tRNA Arg C G tRNA Gly GG tRNA Thr A C tRNA Val G U http://mamit-trna.u-strasbg.fr/2DStructures.html
  22. 22. Part 2. Common Patterns in Type II Restriction Enzyme Binding Sites
  23. 23. Restriction Enzyme (Endonuclease) <ul><li>Restriction enzymes </li></ul><ul><li>recognize short specific DNA sequences </li></ul><ul><li>enable bacteria to destroy foreign DNA </li></ul><ul><li>are useful tools in biotechnology </li></ul>G A A T T C G A A T T C <ul><li>The most well studied class of REs is type II, which cleave DNA within their recognition sequences </li></ul><ul><li>Many recognition sequences are palindromic </li></ul>
  24. 24. Are REase similar in the binding sites? 11 ↓ 00 1 ↓ 11 000 11 ↓ 00 1 ↓ 11 000 1 ↓ 11 000 Examples from Kimball‘s Biology Pages G ↓ AA TTC Escherichia coli Eco RI A ↓ AG CTT Haemophilus influenzae Hind III G ↓ GA TCC Bacillus amyloliquefaciens Bam HI GG ↓ CC Haemophilus aegyptius Hae III AG ↓ CT Arthrobacter luteus Alu I Pur (1)–pyr (0) pattern Recognition Sequence Source Restriction Enzyme
  25. 25. How significant is the Pattern RR/YY (11/00)? <ul><li>Frequencies of </li></ul><ul><ul><li>dinucleotides </li></ul></ul><ul><ul><li>trinucleotides </li></ul></ul><ul><ul><li>tetranucleotides </li></ul></ul><ul><ul><li>coded in three possible coding scheme : </li></ul></ul><ul><ul><ul><ul><li>R vs Y (G, A vs C, T) </li></ul></ul></ul></ul><ul><ul><ul><ul><li>K vs M (G, T vs C, A) </li></ul></ul></ul></ul><ul><ul><ul><ul><li>S vs W (G, C vs A, T) </li></ul></ul></ul></ul>Type II 3726 In the symmetrical set the most significant dinucleotides are RR (or 11) (p-value <10 -63 ) and YY (or 00) (p-value <10 -29 ) In the asymmetric set RRR, YYY and YYYY are even more significant, but RR and YY also stand out. Symmetrical (98%) recognition sequences Asymmetrical (2%) recognition sequences
  26. 26. Why is the Motif RR..YY preferred? <ul><li>specific geometrical properties </li></ul><ul><ul><li>minimal slide values </li></ul></ul><ul><ul><li>strong tilt in the negative direction </li></ul></ul><ul><ul><li>positive roll </li></ul></ul><ul><ul><li>low stacking energy </li></ul></ul>Figure 1 Example of an interaction between an H-bond donor cluster (resulting from two adjacent purines AA) and an H-bond acceptor. Dinucleotides RR..YY are characterized by: <ul><li>stronger H-bond donor and acceptor clusters </li></ul>
  27. 27. Outlook <ul><li>Looking for binary patterns in the genomes </li></ul><ul><li>Additional information </li></ul>Thank you for your attention ! http://www.imb-jena.de/tsb
  28. 28. Purine-Pyrimidine Scheme of the Genetic Code Codon Strong 6 hydrogen bonds Mixed 5 hydrogen bonds Mixed 5 hydrogen bonds Weak 4 hydrogen bonds Pro CC (A/G) Proline Ala G C (C/U) Alanine Ala G C (A/G) Alanine Leu CU (A/G) Leucine Thr A C (C/U) Threonine Thr A C (A/G) Threonine Ser UC (C/U) Serine Val G U (C/U) Valine Val G U (A/G) Valine Phe UU (C/U) Phenylalanine Ile A U (C/U) Isoleucine Ile /Met A U (A/G) Isoleucine/Methionine 000 00 1 1 00 1 0 1 Arg C G (C/U) Arginine Cys U G (C/U) Cystein His C A (C/U) Histidine Tyr U A (C/U) Tyrosine 0 1 0 Arg C G (A/G) Arginine Stop/Trp U G (A/G) Tryptophan Gln C A (A/G) Glutamine Stop U A (A/G) 0 11 Gly GG (C/U) Glycine Asp GA (C/U) Asparatic acid Asn AA (C/U) Asparagine 11 0 Gly GG (A/G) Glycine Glu GA (A/G) Glutamatic acid 111 Leu CU (C/U) Leucine Leu UU (A/G) Leucine Ser UC (A/G) Serine Ser AG (C/U) Serine Arg AG (A/G) Arginine Pro CC (C/U) Proline Lys AA (A/G) Lysine
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