Jena

InstituteofMolecular Biotechnology

Swetlana Nikolajewa, Andreas Beyer, Maik Friedel, Jens Hollunder, Thomas Wilhelm

Institute of Molecular Biotechnology, Jena Germany

Overview: Purine-Pyrimidine Patterns

Part 1 New Classification Scheme of the Genetic code

Part 2Type II Restriction Enzyme Binding Sites

Overview: Genetic Code

Part 1. The purine-pyrimidine scheme of the genetic codes shows

amino-acids patterns and regularities of codons

symmetry characteristics

possible predecessors of our contemporary quaternary triplet code

explanation for the number (22) of tRNA genes in mammalian mitochondrial genome

TC

PuRines vs. PYrimidines

A G

Purine pairs with Pyrimidine

3 H Bonds3 H Bonds 2 H Bonds2 H Bonds

3 nucleobases (triplets) of A, G, C, U code for 20 AAs

64 possible codons (4x4x4=43)

3 termination codons: UGA, UAG, UAA

Met (AUG) codon is also the start codon

2nd base

U C A G

1stbase

U

UUU Phe UUC Phe UUA Leu UUG Leu

UCU Ser UCC Ser UCA Ser UCG Ser

UAU Tyr UAC Tyr UAA StopUAG Stop

UGU Cys UGC Cys UGA StopUGG Trp

UCAG

3rd base

C

CUU Leu CUC Leu CUA Leu

CUG Leu

CCU Pro CCC Pro CCA Pro CCG Pro

CAU His CAC His CAA Gln CAG Gln

CGU Arg CGC Arg CGA Arg CGG Arg

UCAG

A

AUU Ile AUC Ile AUA Ile AUG Met

ACU Thr ACC Thr ACA Thr ACG Thr

AAU Asn AAC Asn AAA Lys AAG Lys

AGU Ser AGC Ser AGA Arg AGG Arg

UCAG

G

GUU Val GUC Val GUA Val GUG Val

GCU Ala GCC Ala GCA Ala GCG Ala

GAU Asp GAC Asp GAA Glu GAG Glu

GGU Gly GGC Gly GGA Gly GGG Gly

UCAG

The Common Genetic Code Table

The Common Genetic Code Table contains 64 fields…

Purine-Pyrimidine Classification Scheme of the Genetic Code

binary representation of nucleobases purines : A, G → 1pyrimidines: C, U → 0

C G binds via 3 hydrogen bonds in the complementary base pairing A U binds via 2 hydrogen bonds in the complementary base pairing

23 = 8 different binary triplets 000 , 001, … ,111each of these has again 8 possibilities, for instance: 000 stands for three pyrimidines: CCC, CCU, UUC, …, UUU 111 stands for three purines: GGG, GGA, GAA, …, AAA

Codon Strong codons6 H bonds

Mixed codons5 H bonds

Mixed codons5 H bonds

Weak codons4 H bonds

Pro CC (A/G)Proline

Ala GC (C/U)Alanine

Ala GC (A/G)Alanine

Leu CU (A/G)Leucine

Thr AC (C/U)Threonine

Thr AC (A/G)Threonine

Ser UC (C/U)Serine

Val GU (C/U)Valine

Val GU (A/G)Valine

Phe UU (C/U)Phenylalanine

Ile AU (C/U)Isoleucine

Ile/Met AU (A/G)Isoleucine/Methionine

000

001

100

101

Arg CG (C/U)Arginine

Cys UG (C/U)Cystein

His CA (C/U)Histidine

Tyr UA (C/U)Tyrosine

010

Arg CG (A/G)Arginine

Stop/Trp UG (A/G)Tryptophan

Gln CA (A/G)Glutamine

Stop UA (A/G)011

Gly GG (C/U)Glycine

Asp GA (C/U)Asparatic acid

Asn AA (C/U)Asparagine

110

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

Purine-Pyrimidine Table of the Genetic Code

…the new scheme contains the same information in only 32 fields.

Codon Strong 6 hydrogen bonds

Mixed 5 hydrogen bonds

Mixed5 hydrogen bonds

Weak4 hydrogen bonds

Pro CC (A/G)

Ala GC (C/U)

Ala GC (A/G)

Leu CU (A/G)

Thr AC (C/U)

Thr AC (A/G)

Ser UC (C/U)

Val GU (C/U)

Val GU (A/G)

Phe UU (C/U)

Ile AU (C/U)

Ile/Met AU (A/G)

000

001

100

101

Arg CG (C/U) Cys UG (C/U) His CA (C/U) Tyr UA (C/U)010

Arg CG (A/G) Stop/Trp UG (A/G) Gln CA (A/G) Stop UA (A/G)011

Gly GG (C/U) Asp GA (C/U)Asparatic acid

Asn AA (C/U)Asparagine

110

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

Amino Acid Patterns:Polar Requirement of NCN and NUN Codons

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

Codon Strong 6 H-bonds

Mixed 5 H-bonds

Mixed 5 H-bonds

Weak 4 H- bonds

Pro CC (A/G)

Ala GC (C/U)

Ala GC (A/G)

Leu CU (A/G)

Thr AC (C/U)

Thr AC (A/G)

Ser UC (C/U)

Val GU (C/U)

Val GU (A/G)

Phe UU (C/U)

Ile AU (C/U)

Ile/Met AU (A/G)

000

001

100

101

Arg CG (C/U) Cys UG (C/U) His CA (C/U) Tyr UA (C/U)010

Arg CG (A/G) Stop/Trp UG (A/G) Gln CA (A/G) Stop UA (A/G)011

Gly GG (C/U) Asp GA (C/U) Asn AA (C/U)110

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

Codon Strong 6 H-bonds

Mixed 5 H-bonds

Mixed 5 H-bonds

Weak 4 H-bonds

Pro CC (A/G)

Ala GC (C/U)

Ala GC (A/G)

Leu CU (A/G)

Thr AC (C/U)

Thr AC (A/G)

Val GU (C/U)

Val GU (A/G)

Ile AU (C/U)

Ile/Met AU (A/G)

001

100

101

Arg CG (C/U) Cys UG (C/U) His CA (C/U) Tyr UA (C/U)010

Arg CG (A/G) Stop/Trp UG (A/G) Gln CA (A/G) Stop UA (A/G)011

Gly GG (C/U) Asp GA (C/U) Asn AA (C/U)110

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)

Codon-Anticodon Symmetry

Ser UC (C/U) Phe UU (C/U)000 Leu CU (C/U)Pro CC (C/U)

Codon Strong 6 H-bonds

Mixed 5 H- bonds

Mixed 5 H-bonds

Weak 4 H-bonds

Pro CC (A/G)

Ala GC (C/U)

Ala GC (A/G)

Leu CU (A/G)

Thr AC (C/U)

Thr AC (A/G)

Ser UC (C/U)

Val GU (C/U)

Val GU (A/G)

Phe UU (C/U)

Ile AU (C/U)

Ile/Met AU (A/G)

000

001

100

101

Arg CG (C/U) Cys UG (C/U) His CA (C/U) Tyr UA (C/U)010

Arg CG (A/G) Stop/Trp UG (A/G) Gln CA (A/G) Stop UA (A/G)011

Gly GG (C/U) Asp GA (C/U) Asn AA (C/U)110

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)

Point Symmetry

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

Codon Strong 6 H-bonds

Mixed 5 H- bonds

Mixed 5 H-bonds

Weak 4 H-bonds

Pro CC (A/G)

Ala GC (C/U)

Ala GC (A/G)

Leu CU (A/G)

Thr AC (C/U)

Thr AC (A/G)

Ser UC (C/U)

Val GU (C/U)

Val GU (A/G)

Phe UU (C/U)

Ile AU (C/U)

Ile/Met AU (A/G)

000

001

100

101

Arg CG (C/U) Cys UG (C/U) His CA (C/U) Tyr UA (C/U)010

Arg CG (A/G) Stop/Trp UG (A/G) Gln CA (A/G) Stop UA (A/G)011

Gly GG (C/U) Asp GA (C/U) Asn AA (C/U)110

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)

Codon-Reverse Codon (XYZ↔ZYX) Symmetry

AUCCUA

GAUAsp

UAGSTOP

Asp

Codon-Reverse Codon (XYZ↔ZYX) Symmetry

Stop

AUC

Evolution of the Genetic Code

binary doublet: 41=4 fields

00 00 00 00

01 01 01 01

10 10 10 10

11 11 11 11

00* 00* 00* 00*

01* 01* 01* 01*

10* 10* 10* 10*

11* 11* 11* 11*

quaternary doublet code: 42=16 fields

our contemporary code is the quaternary triplet code: 43=64 fields

00

01

10

11

CGU, UAC,…

CGU, UAC,…

Codon Strong 6 H bonds

Mixed 5 H bonds

Mixed5 H bonds

Weak4 H bonds

Pro CC (A/G)Proline

Ala GC (C/U)Alanine

Ala GC (A/G)Alanine

Leu CU (A/G)Leucine

Thr AC (C/U)Threonine

Thr AC (A/G)Threonine

Ser UC (C/U)Serine

Val GU (C/U)Valine

Val GU (A/G)Valine

Phe UU (C/U)Phenylalanine

Ile AU (C/U)Isoleucine

Ile/Met AU (A/G)Isoleucine/Methionine

000

001

100

101

Arg CG (C/U)Arginine

Cys UG (C/U)Cystein

His CA (C/U)Histidine

Tyr UA (C/U)Tyrosine

010

Arg CG (A/G)Arginine

Stop/Trp UG (A/G)Tryptophan

Gln CA (A/G)Glutamine

Stop UA (A/G)011

Gly GG (C/U)Glycine

Asp GA (C/U)Asparatic acid

Asn AA (C/U)Asparagine

110

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 100 00 00 00

01 01 01 01

10 10 10 10

11 11 11 11

Codon Strong6 H bonds

Mixed5 H bonds

Mixed5 H bonds

Weak4 H bonds

Pro CC (A/G)Proline

Ala GC (C/U)Alanine

Ala GC (A/G)Alanine

Leu CU (A/G)Leucine

Thr AC (C/U)Threonine

Thr AC (A/G)Threonine

Ser UC (C/U)Serine

Val GU (C/U)Valine

Val GU (A/G)Valine

Phe UU (C/U)Phenylalanine

Ile AU (C/U)Isoleucine

Ile/Met AU (A/G)Isoleucine/Methionine

000

001

100

101

Arg CG (C/U)Arginine

Cys UG (C/U)Cystein

His CA (C/U)Histidine

Tyr UA (C/U)Tyrosine

010

Arg CG (A/G)Arginine

Stop/Trp UG (A/G)Tryptophan

Gln CA (A/G)Glutamine

Stop UA (A/G)011

Gly GG (C/U)Glycine

Asp GA (C/U)Asparatic acid

Asn AA (C/U)Asparagine

110

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 200 00 00 00

01 01 01 01

10 10 10 10

11 11 11 11

Mitochondrial genomes have several surprising features

genetic code of mitochondria

only 22 tRNAs are required for mammalian mitochondrial protein synthesis

?

Codon Strong6 H bonds

Mixed5 H bonds

Mixed5 H bonds

Weak4 H bonds

Pro CC (A/G)

Ala GC (C/U)

Ala GC (A/G)

Leu CU (A/G)

Thr AC (C/U)

Thr AC (A/G)

Val GU (C/U)

Val GU (A/G)

Ile AU (C/U)

Met/Met AU (A/G)

001

100

101

Arg CG (C/U) Cys UG (C/U) His CA (C/U) Tyr UA (C/U)010

Arg CG (A/G) Trp /Trp UG (A/G) Gln CA (A/G) Stop UA (A/G)011

Gly GG (C/U) Asp GA (C/U) Asn AA (C/U)110

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)

The Mammalian Mitochondrial Genetic Code

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

Codon Strong6 H bonds

Mixed5 H bonds

Mixed5 H bonds

Weak4 H bonds

tRNAIle AU (C/U)

tRNAMet AU (A/G)

001

100

101

tRNACys UG (C/U) tRNAHis CA (C/U) tRNATyr UA (C/U)010

tRNATrp UG (A/G) tRNAGln CA (A/G) STOP UA (A/G)011

tRNAAsp GA (C/U) tRNAAsn AA (C/U)110

tRNAGlu GA (A/G)111

tRNALeu2 UU (A/G)

tRNASer2 AG (C/U)

STOP AG (A/G) tRNALys AA (A/G)

The Mammalian Mitochondrial Code 8 tRNAs for family codons + 14 tRNAs for non-family codons = 22

tRNASer1 UC

tRNAPhe UU (C/U)000tRNALeu

1 CUtRNAPro CC

tRNAAla GC

tRNAArg CG

tRNAGly GG

tRNAThr AC tRNAVal GU

http://mamit-trna.u-strasbg.fr/2DStructures.html

Part 2. Common Patterns in Type II Restriction Enzyme Binding Sites

G A A T T C

Restriction Enzyme (Endonuclease)

Restriction enzymes recognize short specific DNA sequences enable bacteria to destroy foreign DNA are useful tools in biotechnology

G A A T T C

The most well studied class of REs is type II, which cleave DNA within their recognition sequences

Many recognition sequences are palindromic

Are REase similar in the binding sites?

Restriction Enzyme Source Recognition

SequencePur (1)–pyr (0)

pattern

AluI Arthrobacter luteus AG↓CT

HaeIII Haemophilus aegyptius GG↓CC

BamHI Bacillus amyloliquefaciens G↓GA TCC

HindIII Haemophilus influenzae A↓AG CTT

EcoRI Escherichia coli G↓AA TTC

11↓00

1↓11 000

11↓00

1↓11 000

1↓11 000

Examples from Kimball‘s Biology Pages

How significant is the Pattern RR/YY (11/00)?

Frequencies of dinucleotides trinucleotides tetranucleotides coded in three possible coding scheme:

R vs Y (G, A vs C, T) K vs M (G, T vs C, A) S vs W (G, C vs A, T)

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

Why is the Motif RR..YY preferred?

specific geometrical properties minimal slide values

strong tilt in the negative direction

positive roll

low stacking energy

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: stronger H-bond donor and acceptor

clusters

Outlook

Looking for binary patterns in the genomes

Additional information

Thank you for your attention !

http://www.imb-jena.de/tsb

Codon Strong 6 hydrogen bonds

Mixed 5 hydrogen bonds

Mixed 5 hydrogen bonds

Weak 4 hydrogen bonds

Pro CC (A/G)Proline

Ala GC (C/U)Alanine

Ala GC (A/G)Alanine

Leu CU (A/G)Leucine

Thr AC (C/U)Threonine

Thr AC (A/G)Threonine

Ser UC (C/U)Serine

Val GU (C/U)Valine

Val GU (A/G)Valine

Phe UU (C/U)Phenylalanine

Ile AU (C/U)Isoleucine

Ile/Met AU (A/G)Isoleucine/Methionine

000

001

100

101

Arg CG (C/U)Arginine

Cys UG (C/U)Cystein

His CA (C/U)Histidine

Tyr UA (C/U)Tyrosine

010

Arg CG (A/G)Arginine

Stop/Trp UG (A/G)Tryptophan

Gln CA (A/G)Glutamine

Stop UA (A/G)011

Gly GG (C/U)Glycine

Asp GA (C/U)Asparatic acid

Asn AA (C/U)Asparagine

110

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

Purine-Pyrimidine Scheme of the Genetic Code