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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. Primer is complementary to the region near the vector-insert junction. each reaction uses a specific ddNTPs (dideoxynucleotide) to terminate enzymatically the reaction. . • Based on premature termination of DNA synthesis.DNA Sequencing Sanger-Coulson method • ssDNA used as template. • Sequencing primer anneals to ssDNA. • Extension reaction is split into 4.
it can no longer be elongated. • This is just like regular nucleotides. . except it has no 3' hydroxyl group once it is added to the end of a DNA strand.DNA Sequencing • The reactions are run in the presence of ddNTPs.
• an enzyme (usually a variant of Taq polymerase) • a 'primer' . • free nucleotides.a small piece of single-stranded DNA about 20-30 nt long that can hybridize to one strand of the template DNA. .DNA Sequencing The reaction mix includes • the template DNA.
DNA Sequencing .
DNA Sequencing • 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). .
• The sequence of the DNA is determined by knowing the colour codes. G. • 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. and with “different” fluorescent colours on each. . C and T) present.
• An average of 500 nucleotides are read in each reaction. • DNA sequencing http://uk. the colours in one lane of a gel (one sample).com/watch?v=Mz4LSfecM4&feature=PlayList&p=BADA17575EBD7A76&playnext=1&index=8 .youtube.DNA Sequencing • The computer reads the sequence from the gel by scanning. from smallest fragment to largest. • The computer also produces a text file containing the nucleotide sequence.
DNA Sequencing .
. • This method involves base specific cleavages: . followed by high resolution acrylamide gel electrophoresis.DNA Sequencing Maxam and Gilbert method • Based on introduction of strand breaks at specific nucleotides by chemical degradation. • Not commonly used as it is slower than Sanger method.the sugar phosphate backbone of the DNA is then cleaved by piperidine at that site. • Used for sequencing of particular genes whose sequence is GC rich.base first modified using specific chemicals .
DNA Sequencing Maxam and Gilbert method .
. .pathogen/host relationships. organisms.protein function and cellular pathways.Genome Analysis • To know the sequence of the entire genome of an organism is useful for several reasons and it provides a better understanding of: . .gene interactions and the regulation of gene expression. . and hence.the evolution of gene/protein families.
and functions – Coordination of gene expression. information content. distribution. and computational scientists. chemists. and functions Gene regulation DNA sequence organization Chromosomal structure and organization Noncoding DNA types. amount. protein synthesis. engineers. among others. exact locations. and posttranslational events – Interaction of proteins in complex molecular machines . What we still do not know: – – – – – Gene number.Research challenges in genetics Deriving meaningful knowledge from DNA sequences will require the expertise and creativity of teams of biologists.
– – – – – – – – – 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. genomics . including microbial consortia useful for environmental restoration Developmental genetics.
3 x 109 High quality draft Partially sequenced 2. cerevisie E.8 x 109 3 billion .coli Human genome Mouse genome Dog genome Rat genome Human genome Size (bp) 5386 5243 4363 16600 49000 12500000 4600000 3.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.
and G). • The functions are unknown for over 50% of discovered genes.000 to 140. • Almost all (99. • The average gene consists of 3000 bases. .What Does the Human Genome Sequence Tell Us? By the Numbers • The human genome contains 3164. C.7 million chemical nucleotide bases (A.000.000. but sizes vary greatly • The total number of genes is estimated at 30. T. much lower than previous estimates of 80.9%) nucleotide bases are exactly the same in all people.
. • 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. • During the past 50 million years.• Less than 2% of the genome codes for proteins. a dramatic decrease seems to have occurred in the rate of accumulation of repeats in the human genome.
• Humans share most of the same protein families with worms. flies. and plants. 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.
4 million locations where single-base DNA differences (SNPs) occur in humans. 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. • The ratio of germline (sperm or egg cell) mutations is 2:1 in males vs females. including the greater number of cell divisions required for sperm formation than for eggs.Variations and Mutations • Scientists have identified about 1.
deafness. • Finding the DNA sequences underlying such common diseases as cardiovascular disease.Applications. for example. and blindness. • It will be possible to study all the genes in a genome. or all the transcripts in a particular tissue or organ. and cancers will provide focused targets for the development of effective new therapies. diabetes. . Future Challenges • The genome sequence will help on finding genes associated with disease. arthritis. • A number of genes have been associated with breast cancer. muscle disease.
proteomics. • These explorations will encompass studies in transcriptomics. new experimental methodologies. where.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. structural genomics. and under what conditions genes are expressed. . and comparative genomics. dynamic living systems. • Transcriptomics involves large-scale analysis of messenger RNAs transcribed from active genes to follow when.
• Structural genomics involves the generation of the 3-D structures of proteins. • Knock out studies will be used to understand the function of DNA sequences and the proteins they encode. offering clues to function and biological targets for drug design. • Comparative genomics involves the analysis of DNA sequence patterns of humans and well-studied model organisms for identifying human genes and interpreting their function.• Proteomics involves the study of protein expression and function. .
ornl.shtml#whatis .Human Genome Project Information http://www.gov/sci/techresources/Human_Genome/faq /seqfacts.