DNA as an information storage system

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DNA as an information storage system

• Dan E. Krane
• Biological Sciences
• Wright State University, Dayton, OH 45435

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DNA is the genetic material

• Speculated about throughout human history
• First clear insight came from Watson and Crick in
  1953
• Genome the sum total of an organisms heritable
  information
• With knowledge comes power

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Levels of information organization in a genome

• Four nucleotides
• Genes
• Isochores
• Chromosomes
• Genomes

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Levels of information organization in a genome

• Four nucleotides (G, A, T, and C)
• Genes
• Isochores
• Chromosomes
• Genomes

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Levels of information organization in a genome

• Four nucleotides
• Genes (average length of 1,200 nts)
• Isochores
• Chromosomes
• Genomes

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Gene length and number

• Hundreds to tens of thousands of nts long
• Generally code for proteins
• Evolutionarily conserved
• Three to tens of thousands per genome

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Levels of information organization in a genome

• Four nucleotides
• Genes
• Isochores (millions of nts long)
• Chromosomes
• Genomes

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Isochores

• Long regions of homogenous base composition
• Integrated functional,evolutionary systems
• Associated with gene expression, organization and
  content

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Levels of information organization in a genome

• Four nucleotides
• Genes
• Isochores
• Chromosomes (tens of millions of nts)
• Genomes

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Chromosomes

• Circular or linear
• Visible with light microscope
• One or two copies per cell
• One to dozens make up a genome

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Levels of information organization in a genome

• Four nucleotides
• Genes
• Isochores
• Chromosomes
• Genomes (dozens to thousands of genes)

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Genomes

• Dozens to thousands of genes
• Organization (or lack thereof)
• C-value paradox
• Junk DNA

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Levels of information organization in a genome

• Four nucleotides (G, A, T, and C)
• Genes (average length of 1,200 nts)
• Isochores (millions of nts long)
• Chromosomes (tens of millions of nts)
• Genomes (dozens to thousands of genes)

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Tools of molecular biology

• Restriction enzymes
• Gel electrophoresis
• Hybridization
• Cloning
• Polymerase Chain Reaction (PCR)
• DNA sequencing

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DNA sequence data

• Watson and Crick Nobel Prize, 1956
• Maxam and Gilbert Nobel Prize, 1980
• 10,000 nts/person year in late 1980s
• 100,000 nts/person year in late 1990s
• Exponential increase in GenBank continues today

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LOCUS OCAGL1 551 bp mRNA
MAM 06-JUL-1989 DEFINITION Messenger RNA
for rabbit alpha-globin. ACCESSION V00875
J00658 VERSION V00875.1 GI1443 KEYWORDS
alpha-globin complementary DNA globin. SOURCE
rabbit. ORGANISM Oryctolagus cuniculus
Eukaryota Metazoa Chordata Craniata
Vertebrata Euteleostomi Mammalia
Eutheria Lagomorpha Leporidae
Oryctolagus. REFERENCE 1 (bases 1 to 551)
AUTHORS Heindell,H.C., Liu,A., Paddock,G.V.,
Studnicka,G.M. and Salser,W.A. TITLE The
primary sequence of rabbit alpha-globin mRNA
JOURNAL Cell 15 (1), 43-54 (1978) MEDLINE
79023071 COMMENT KST OCU.ALPGLOBIN. FEATURES
Location/Qualifiers source
1..551 /organism"Oryctolag
us cuniculus"
/db_xref"taxon9986" CDS
39..462 /note"reading
frame" /codon_start2
/protein_id"CAA24244.1"
/db_xref"GI1364228"
/db_xref"SWISS-PROTP01948"
/translation"VLSPADKTNIKTAWEKIGSHGGEYGAEAVERMF
LGFPTTKTYFP
HFDFTHGSEQIKAHGKKVSEALTKAVGHLDDLPGALSTLSDLHAHKLRVD
PVNFKLLS HCLLVTLANHHPSEFTPAVH
ASLDKFLANVSTVLTSKYR" BASE COUNT 112 a 198
c 144 g 97 t ORIGIN 1
acacttctgg tccagtccga ctgagaagga accaccatgg
tgctgtctcc cgctgacaag 61 accaacatca
agactgcctg ggaaaagatc ggcagccacg gtggcgagta
tggcgccgag 121 gccgtggaga ggatgttctt
gggcttcccc accaccaaga cctacttccc ccacttcgac
181 ttcacccacg gctctgagca gatcaaagcc cacggcaaga
aggtgtccga agccctgacc 241 aaggccgtgg
gccacctgga cgacctgccc ggcgccctgt ctactctcag
cgacctgcac 301 gcgcacaagc tgcgggtgga
cccggtgaat ttcaagctcc tgtcccactg cctgctggtg
361 accctggcca accaccaccc cagtgaattc acccctgcgg
tgcatgcctc cctggacaag 421 ttcctggcca
acgtgagcac cgtgctgacc tccaaatatc gttaagctgg
agcctgggag 481 ccggcctgcc ctccgccccc
cccatccccg cagcccaccc ctggtctttg aataaagtct
541 gagtgagtgg c //
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Analyses of DNA sequence data

• Gene prediction
• Phylogenetics
• Molecular evolution
• Gene expression/modification