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Técnicas de Biologia Molecular em microbiologia Clínica Técnicas de Biologia Molecular em microbiologia Clínica

Polymerase Chain Reaction Polymerase Chain Reaction

DNA Sequencing Reactions • The DNA sequencing rxn is similar to the PCR rxn. DNA Sequencing Reactions • The DNA sequencing rxn is similar to the PCR rxn. • The rxn mix includes the template DNA, Taq polymerase, d. NTPs, dd. NTPs, and a primer: a small piece of single-stranded DNA 20 -30 nt long that hybridizes to one strand of the template DNA. • The rxn is intitiated by heating until the two strands of DNA separate, then the primers anneals to the complementary template strand, and DNA polymerase elongates the primer.

Dideoxynucleotides • In automated sequencing dd. NTPs are fluorescently tagged with 1 of 4 Dideoxynucleotides • In automated sequencing dd. NTPs are fluorescently tagged with 1 of 4 dyes that emit a specific wavelength of light when excited by a laser. • dd. NTPs are chain terminators because there is no 3’ hydroxy group to facilitate the elongation of the growing DNA strand. • In the sequencing rxn there is a higher concentration of d. NTPs than dd. NTPs.

DNA Replication in the Presence of dd. NTPs • DNA replication in the • DNA Replication in the Presence of dd. NTPs • DNA replication in the • • presence of both d. NTPs and dd. NTPs will terminate the growing DNA strand at each base. In the presence of 5% dd. TTPs and 95% d. TTPs Taq polymerase will incorporate a terminating dd. TTP at each ‘T’ position in the growing DNA strand. Note: DNA is replicated in the 5’ to 3’ direction.

Gel Electrophoresis DNA Fragment Size Determination • DNA is negatively charged because of the Gel Electrophoresis DNA Fragment Size Determination • DNA is negatively charged because of the Phosphate groups that make up the DNA Phosphate backbone. • Gel Electrophoresis separates DNA by fragment size. The larger the DNA piece the slower it will progress through the gel matrix toward the positive cathode. Conversely, the smaller the DNA fragment, the faster it will travel through the gel.

Putting It All Together • Using gel electrophoresis to separate each DNA fragment that Putting It All Together • Using gel electrophoresis to separate each DNA fragment that differs by a single nucleotide will band each fluorescently tagged terminating dd. NTP producing a sequencing read. • The gel is read from the bottom up, from 5’ to 3’, from smallest to largest DNA fragment.

Raw Automated Sequencing Data • A 5 lane example of raw automated sequencing data. Raw Automated Sequencing Data • A 5 lane example of raw automated sequencing data. Green: dd. ATP Red: dd. TTP Yellow: dd. GTP Blue: dd. CTP Animação Demo ABI

Analyzed Raw Data • In addition to nucleotide sequence text files the • • Analyzed Raw Data • In addition to nucleotide sequence text files the • • automated sequencer also provides trace diagrams. Trace diagrams are analyzed by base calling programs that use dynamic programming to match predicted and occurring peak intensity and peak location. Base calling programs predict nucleotide locations in sequencing reads where data anomalies occur. Such as multiple peaks at one nucleotide location, spread out peaks, low intensity peaks.

Pyrosequenciação • Incorporação sequencial de cada d. NTP • Quando ocorre há produção de Pyrosequenciação • Incorporação sequencial de cada d. NTP • Quando ocorre há produção de PPi • PPi é metabolizado originando luz • Só utilizável para pequenos fragmentos

Pyrosequencing Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001 Pyrosequencing Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001

Pyrosequencing - Solid Phase Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res Pyrosequencing - Solid Phase Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001

Pyrosequencing - Liquid Phase Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res Pyrosequencing - Liquid Phase Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001

Pyrogram Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001 Pyrogram Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001

PPi ATP PPi ATP

Sequenciação de Ácidos Nucleicos • Método de sangerelectroforese capilar • Pirosequenciação Sequenciação de Ácidos Nucleicos • Método de sangerelectroforese capilar • Pirosequenciação

Sequencing Strategies • Map-Based Assembly: • Create a detailed complete fragment map • Time-consuming Sequencing Strategies • Map-Based Assembly: • Create a detailed complete fragment map • Time-consuming and expensive • Provides scaffold for assembly • Original strategy of Human Genome Project • Shotgun: • Quick, highly redundant – requires 7 -9 X coverage for sequencing reads of • • • 500 -750 bp. This means that for the Human Genome of 3 billion bp, 21 -27 billion bases need to be sequence to provide adequate fragment overlap. Computationally intensive Troubles with repetitive DNA Original strategy of Celera Genomics

Genome Sequencing Approaches Genome Sequencing Approaches

Map-Based Assembly contigs Map-Based Assembly contigs

Shotgun Sequencing: Assembly of Random Sequence Fragments • To sequence a Bacterial Artificial Chromosome Shotgun Sequencing: Assembly of Random Sequence Fragments • To sequence a Bacterial Artificial Chromosome (100 -300 Kb), millions of copies are sheared randomly, inserted into plasmids, and then sequenced. If enough fragments are sequenced, it will be possible to reconstruct the BAC based on overlapping fragments.

Whole Genome Shotgun Sequencing genome cut many times at random • plasmids (2 – Whole Genome Shotgun Sequencing genome cut many times at random • plasmids (2 – 10 Kbp) • cosmids (40 Kbp) ~500 bp forward-reverse linked reads known dist ~500 bp

Challenges with Shotgun Sequencing • Sequencing errors ~1 -2% of bases are wrong • Challenges with Shotgun Sequencing • Sequencing errors ~1 -2% of bases are wrong • Repeats

ARACHNE: Whole Genome Shotgun Assembly 1. Find overlapping reads 2. Merge good pairs of ARACHNE: Whole Genome Shotgun Assembly 1. Find overlapping reads 2. Merge good pairs of reads into longer contigs 3. Link contigs to form supercontigs 4. Derive consensus sequence . . ACGATTACAATAGGTT. . http: //www-genome. wi. mit. edu/wga/

Gene Recognition • Predict the segments that code for protein • Predict the resulting Gene Recognition • Predict the segments that code for protein • Predict the resulting protein sequence

Cross-species Comparative Annotation • Ab initio prediction by looking at two orthologs simultaneously Cross-species Comparative Annotation • Ab initio prediction by looking at two orthologs simultaneously

Comparing Human and Mouse DNA • Most human genes have mouse orthologs • Coding Comparing Human and Mouse DNA • Most human genes have mouse orthologs • Coding exons usually correspond 1 -1 • Coding sequence similarity ~ 85%

GLASS: GLobal Alignment Sy. Stem • Fast global alignment of long sequences • Align GLASS: GLobal Alignment Sy. Stem • Fast global alignment of long sequences • Align divergent sequences with ordered islands of strong homology

The ROSETTA Method Input: orthologous human & mouse sequence • • Repeat masking GLASS The ROSETTA Method Input: orthologous human & mouse sequence • • Repeat masking GLASS global alignment Throw away regions of weak alignment Find genes in both sequences using coincidence of exon signals

Example: A Human/Mouse Ortholog Alignment: Human and mouse PCNA (Proliferating Cell Nuclear Antigene) genes Example: A Human/Mouse Ortholog Alignment: Human and mouse PCNA (Proliferating Cell Nuclear Antigene) genes Detection

Gene Transcriptional Regulation -300 GRE AP 2 MRE AP 2 AP 1 MRE SP Gene Transcriptional Regulation -300 GRE AP 2 MRE AP 2 AP 1 MRE SP 1 TATA 0 GENE promoter of methallothionein + enhancer promoter • Predict location of transcription factor binding sites, and composite regulatory elements

Genome Project (I) Genome Project (I)

Genome Project (II) Genome Project (II)