Extended Elective Studies DNA analysis, Proteomics and Metabolomics ASM013 - 2009/10 Dr Giovanna Bermano – firstname.lastname@example.org - Room A35a
• Important to know the precise order of nucleotides in DNA as: - gives clues about function of gene product responsible for disease; - allows comparison of gene sequence with sequences of genes in databanks and possible discovery of cause of disease; - allows comparison of a newly discovered gene to previously discovered genes in other organisms which may reflect common functions for the protein products. • Two methods: - Enzymatic method of Sanger-Coulson (commonly used) - Chemical degradation method of Maxam and Gilbert
• Taq or T7 DNA polymerase extend the primer using dNTPs.DNA Sequencing
Sanger-Coulson method • ssDNA used as template. • Sequencing primer anneals to ssDNA. • Extension reaction is split into 4. Primer is complementary to the region near the vector-insert junction.
. • Based on premature termination of DNA synthesis. each reaction uses a specific ddNTPs (dideoxynucleotide) to terminate enzymatically the reaction.
. • This is just like regular nucleotides. except it has no 3' hydroxyl group once it is added to the end of a DNA strand. it can no longer be elongated.DNA Sequencing
• The reactions are run in the presence of ddNTPs.
• free nucleotides.DNA Sequencing
The reaction mix includes • the template DNA.
.a small piece of single-stranded DNA about 20-30 nt long that can hybridize to one strand of the template DNA. • an enzyme (usually a variant of Taq polymerase) • a 'primer' .
• Gel electrophoresis can be used to separate the fragments by size. • This can be repeated for all four ddNTPs. • This diagram shows the results of a sequencing reaction run in the presence of dideoxyCytidine (ddCTP).
and with “different” fluorescent colours on each. G.
. C and T) present. • The sequence of the DNA is determined by knowing the colour codes. • The gel is read from bottom to top: TGCGTCCA-(etc).DNA Sequencing
• All four reactions can be run in a single tube with “all four” of the ddNTPs (A.
the colours in one lane of a gel (one sample).com/watch?v=Mz4LSfecM4&feature=PlayList&p=BADA17575EBD7A76&playnext=1&index=8
. from smallest fragment to largest. • An average of 500 nucleotides are read in each reaction. • The computer also produces a text file containing the nucleotide sequence. • DNA sequencing
• The computer reads the sequence from the gel by scanning.youtube.
• Not commonly used as it is slower than Sanger method. • Used for sequencing of particular genes whose sequence is GC rich. • This method involves base specific cleavages: .base first modified using specific chemicals . followed by high resolution acrylamide gel electrophoresis.
.the sugar phosphate backbone of the DNA is then cleaved by piperidine at that site.DNA Sequencing
Maxam and Gilbert method • Based on introduction of strand breaks at specific nucleotides by chemical degradation.
Maxam and Gilbert method
• To know the sequence of the entire genome of an organism is useful for several reasons and it provides a better understanding of: . .pathogen/host relationships.
. .gene interactions and the regulation of gene expression.the evolution of gene/protein families. organisms. . and hence.protein function and cellular pathways.
and posttranslational events – Interaction of proteins in complex molecular machines
. and computational scientists. and functions Gene regulation DNA sequence organization Chromosomal structure and organization Noncoding DNA types. information content. chemists. and functions – Coordination of gene expression. among others. What we still do not know: – – – – – Gene number. exact locations. engineers. protein synthesis. distribution.Research challenges in genetics
Deriving meaningful knowledge from DNA sequences will require the expertise and creativity of teams of biologists. amount.
– – – – – – – – –
Predicted vs experimentally determined gene function Evolutionary conservation among organisms Protein conservation (structure and function) Proteomes (total protein content and function) in organisms Correlation of SNPs (single-base DNA variations among individuals) with health and disease Disease-susceptibility prediction based on gene sequence variation Genes involved in complex traits and multigene diseases Complex systems biology. including microbial consortia useful for environmental restoration Developmental genetics. genomics
coli Human genome Mouse genome Dog genome Rat genome Human genome Size (bp) 5386 5243 4363 16600 49000 12500000 4600000 3.8 x 109 3 billion
.3 x 109 High quality draft Partially sequenced 2. cerevisie E.Genome Analysis
Year 1975 1977 1978 1981 1982 1996 1997 2001 2002 2003 2004 2006 Organism Bacteriophage ФX174 SV40 pBR322 Human mitochondria Bacteriophage λ S.
T.000.000. C. and G).
. • The functions are unknown for over 50% of discovered genes. • The average gene consists of 3000 bases. • Almost all (99.9%) nucleotide bases are exactly the same in all people.000 to 140. but sizes vary greatly • The total number of genes is estimated at 30.7 million chemical nucleotide bases (A. much lower than previous estimates of 80.What Does the Human Genome Sequence Tell Us?
By the Numbers • The human genome contains 3164.
• During the past 50 million years.
. a dramatic decrease seems to have occurred in the rate of accumulation of repeats in the human genome.• Less than 2% of the genome codes for proteins. • Repetitive sequences are thought to have no direct functions. • Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome. but they shed light on chromosome structure and dynamics.
• Humans share most of the same protein families with worms. but the number of gene family members has expanded in humans.How the Human Compares with Other Organisms
• Humans have on average three times as many kinds of proteins as the fly or worm because of mRNA transcript "alternative splicing" and chemical modifications to the proteins. flies. and plants.
Researchers point to several reasons for the higher mutation rate in the male germline.
. • This information promises to revolutionize the processes of finding disease-associated sequences. including the greater number of cell divisions required for sperm formation than for eggs.Variations and Mutations
• Scientists have identified about 1.4 million locations where single-base DNA differences (SNPs) occur in humans. • The ratio of germline (sperm or egg cell) mutations is 2:1 in males vs females.
and blindness. • Finding the DNA sequences underlying such common diseases as cardiovascular disease. • It will be possible to study all the genes in a genome.
. arthritis. Future Challenges • The genome sequence will help on finding genes associated with disease. and cancers will provide focused targets for the development of effective new therapies. • A number of genes have been associated with breast cancer.Applications. muscle disease. deafness. for example. diabetes. or all the transcripts in a particular tissue or organ.
new experimental methodologies. and under what conditions genes are expressed. where. • Transcriptomics involves large-scale analysis of messenger RNAs transcribed from active genes to follow when. structural genomics. • These explorations will encompass studies in transcriptomics. dynamic living systems. proteomics. and comparative genomics.
.The Next Step: Functional Genomics
• To use this vast reservoir of data to explore how DNA and proteins work with each other and the environment to create complex.
• Knock out studies will be used to understand the function of DNA sequences and the proteins they encode. • Comparative genomics involves the analysis of DNA sequence patterns of humans and well-studied model organisms for identifying human genes and interpreting their function. offering clues to function and biological targets for drug design.• Proteomics involves the study of protein expression and function. • Structural genomics involves the generation of the 3-D structures of proteins.
.Human Genome Project Information