BIO 325 - Class notes - 102209

BIO 325 - Class notes - 102209 - (£11511 ~...

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H t I G t‘ l ' T t t l‘ - B‘ i M all i WEHJ Blotech aema 0 09y ofeggrfigr mrnumty ransp an 3 IOI1 IO OQY e G I'IE Centre ' teammate” WEHinV DNA Molecular Background & History . .- WEH'Revisted Animation Latest News Employment Opportunities institute Structure Management Supporting WEHI Make a Donation Annuai Report Research Cancer & Haematology Mo'ECU'aiGene‘mSO‘Ca'i‘tiltese molecular animations were created for a major immunoio . . . Infection g‘gfinmumty trans-national production effort to raise awareness, educate and Autoimmunityarranspianratormote DNA science to the wider community, coinciding with the Blowormalics 50th anniversary of the discovery of the double helix. Structural Biology Molecular Medicine . . . Conaborafive Research NOTE: The animations presented here do not have narration or text Education labels. Eg‘ifi’fli‘i‘siveswdems For versions with narration and labelling, contact WEHIJVLLyisit GeneTechnoEogyAccessmto View their versions, keep an eye out for the "DNA" (GTAC) documentary series by Windfait Films, or "DNA:The Secret of Life" Evenl5&Conferences . museum fiim available from the Morehead Planetarium Frequently ASK“ Quesm'ihtth/www.moreheadpianetariumcrg ). Resources WEHI-TV Contacts These animations need Quicktime 7 to View. You can download Finding WEHI . ‘ Quicktime player from Appte for Macintosh or Windows. Note, these 823:? WEH’ 8'0‘96" oeraii‘iimations are each about 1MB to 10MB in size. Intranet (Staff Only) Webmaster ©2008 -. . . Inifiauifiagaizgaan it Select an animatton from the table below l'lSi 80 e lCa esearc ”aimmne-WS‘E'“ About The Animator About The DNA Project Local [email protected]—tl: DNA DNA Unzip :y‘a-fjfgf’gggéay- DNA Chromosome Wrapping DNA Close Up The Centrat Dogma: Transcription Replication Initiation Complex The Central Dogma Transcription of The Central Dogma: Transtation of DNA to RNA RNA to Protein Recombinant DNA and Genetic Haemoglobin and Sickle Cell Anaemia Engineering C WWW. about. (Ni "/10“ am‘mot—A'CND i of 3 3/26/2009 10:02 AM combinatorial synthesis. which may well lead to greater diversity of integrated components. DNA—based commutation and algorithmic assembly is another active area of research. and one that is impossible to separate from DNA nanotechnology (see Box l). The field of DNA nanotechnology has attracted an influx of researchers overthe pastfewyears. A] l of thoseinvolved inthis area have benefited from the biotechnology enterprise that produces DNAw modifying enzymes and unusual components for synthetic DNA molecules.ltisiikelythatapplicationsinstructuralDNAnanotechnol— ogy ultimately will use variants on the theme of DNA (for example. peptide nucleic acids, containing an unconventional synthetic peptide backboneand nucleicacid bascsforsidechains),whosepropertiesmay be bettersuited to particulartypes ofapplications. For the past half-century, DNA has been almost exclusively the province of biologists and biologically oriented physical scientists, who have studied its biological impact and molecular properties. During the next 50 yeats, it is likely they will bejoined by materials scientists, nanotechnologlsts and computer engineers. who will exploit DNA’S chemical propertiesinanon~btological context. Ci doi:l0.1l}38’naturc-DHOS 1. Hoii‘mann. R. DNA asclay. Am. 5:182. W311 “994). 2. Cubans—s. M.T_ Schllttlc-r. RR_&Glmzmsid. J. K. Room-temperature repositioningol'indb ldualCefiG molecules at Cu steps: operationofa molcmlarcounting device. App}. Pins. Lett. 69. 3015401809916). Caruthers. M. HGcne synthesis machines: DNA chemistryano’ its uses. Sdence230. 231—285 (1985). Seaman. NC. Nucleic aridjunrtlons and lattices. }. "them. Biol 99. 2377251911982}. Seenlan. N. C. Molecular craftwork with DNA. Chem. Intel). L 38*17‘5995]. Jacgcr. L..h\k-sthol’. ER: teentis. N. B. TectoRNA: modular assemblyunits forthe constructional RNA nanorobjects. Nutlcinlcidrfles. 29.455463 (200i). '1‘. Zliang. X. Yan. H.,Shrn. 7. 8: Sccman. N. C. Paranernic cohesion of topologically-closed DNA molecule-5.}. Am. Chem.$or. 125.12940u129l1 (2002}. 8. Chem}. SrSeeman. N. C. 311:: synthesis from DNA olamolerule ulththeconnertbltyofacubev. Namreilifl. 631433i11991). 9. Set-man, N. C. Nucleic acid nanoslruclures and topology-Angeli; Chrm. Int. Ednfngl 37. 3220—3238 (1998). mu. X" Yang. X.. Q}. I. 8: Sccmarr. N. C. Antiparallcl DNA double crossover molecules as components i‘ornanoconstructlonJ Am. ChemSor. l l8.613176i40 {1996). il.Winimr. 5., Lin. F.. chzler. LA. 8; Seer-nan. NC. Design and selfvassernbly of too-dimensional DNA crystals. Nature-39!. 539-544 (1998). 12. Man. C- Sun. W. 8v Seaman. N. C.Designcd lwovdimensional DNA Holiidayguncllon arrays visualized by atomic force microscopy.].Anr.Ch£-m.50n12l. 5437—5 [43 “999). l3. iaBean. 3'. N a]. The construction. analysis. ligation and self-assembly ni’DNA triple Crossover romp!mcs.j.;l.rn. Chem. Soc. 122. 1843—1850 (2000). liMao. (2.. Sun. W. Siren. Z &Sctman.N.C. A DNA nanomechanlcaldhice based on thefiiz transition Naturt'397. 144—146 (199?). 15.8'urkr. B..Turbcrlicid. A. 1.. MillsA. Rh. Slmmri. EC. 8: Ne“ mannj. LADNAAfueiicd molecular machine made of DNA. Nature 106. 605—603 (2800). 16.5'an. il.,Zimng. X.. Shen.Z. 8rSeeman. N. C. A robust DNA mechanical device controlled by hybridization topology. Nature“ 5. 52£5 {2002). 1?. Nicmcycr. C. M. Kochicr. I. & Wucrdemann. C. DNAdlrrctcd assembly olbixnzymic complexes from in tfl‘nblolh'rylalcd NADPIHHMN oxidercdurtaseancllutift-me. Cherufi‘r'oChrmS,2~lZ~245 (2002). 13. Robinson. 13. H. g. Secrnan. N. C. The design ofa biochlp: a stile-assembling molecularesrale memory dm‘rc. Pmrrfni‘ng. 1295-300 (1987}. 19.1(ercn, K. stat. Sequence-specific moleculariithography on single DNA molecules. Science 297. 7245 {2002). ZilAlirisalos. A P. or al.01ganuation of ‘nanocrystal molecules' using DNA. Natty-e332. 6097611 {1996). 2 l. Tatan.A.. Muclc. RC- Miridn. C. A. & hub-gen R. 1. The DNAvmediated {omwlion ofsupramolecular mom and mululaycred nanoperticlestnicturrs}. rim. ChemSoc 122. Elli—G306 (2000). 22.Pcna. 5. R. N.. Raina.S.. Goodrich. G. l’" Fedorofl'. N. ‘18: Keating.C. D. Hybridization and enzymatic extension ofAu nanopartlcle-bound oligonurleol ides J. Arr}. Chem. 50512-1. 7314—7323 (2002). 23. Dekker.C. & Rather. M. FL Elrtt ronlc pmpcrlicsulDNA. P1531 “531“”. 29733 [200”- 24.Fahlrnan. R. P. 8: Sm. D. DNA ronformattonalsu ltches as sensitive electronic sensors ofanalytesJ. AurCthSoc124.4510—4515Umzl- 25.Socman. N. C. Ihc construction at 3D stick figures from branched DNA. DNA CeUBiol. ID. 4757536 {199i}. 26. Echarcil. L. H. eta]. Chemical copying of connectivity. Alston-1120. 285 {2002). 2?.Adleman, L Molecular computation ofsoiutlors to combinatorial problems. Science 266, lfiflielOZ‘i (1991). 28. Winfrre, E in DNA Based Computers Hocmo'ings ofa DIR-IA CS ll‘brkshtp. A pr i1 4'. 1395. Princeton Unit-cushy (och iipton. R] 8a Baum. E. B.) l99—219 (American Mathematical Society. Prm‘ldcnm. 1996}. 29.Wlnfree. E. Algorithmic self-assembly oFDNA‘. theoretical ruminations and 2D assembly experluwntgj, Biol. .‘l’IoI. StrucL Dynamic: (optimal. ”2. 2531270 [2000). St}. Mao. C.. Lchan.'E. ReifJ. H. &Scrnun. NC. logical computation using algorithmic self-assembly olDNA triple crossoier molecule: Mature-107.493—495 (3330) F’P‘W-P’ Acknowledgements This work has been supported by grants from the National Institute of General Medical Sciences. the Office of Naval Research. the National Science Foundation. and the Defense Advanced Research Projects Agency/Air Force Office ofScientific Research. NATURE [ VOL 421 l 23 JANUARY 2003 l \mwnalurecomfnature © 2003 Nature Publishing Group feature DNA replication and recombination Bruce Alherts National Academy of Sciences. 2101 Constitution Avenue. Washington DC 20418. USA Knowledge of the structure of DNA enabled scientists to undertake the difficult task of deciphering the detailed molecular mechanisms of two dynamic processes that are central to life: the copying of the genetic information by DNA replication. and its reassortment and repair by DNA recombination. Despite dramatic advances towards this goal over the past tive decades. many challenges remain for the next generation of molecular biologists. “Though factsare inherenrbrlesssatisfying than the intellectual condo" sions drawn from them. theirimportanceshouldneverbe questioned. " James D. Watson. 2002. '; NA carries all of the genetic information for life. One '. enormously long DNA molecule forms each of the chromosomes of an organism, 23 of them in a human. . The fundamental living unit is the single cell. A cell gives rise to many more cells through serial repetitions of a process known as cell division. Before each division, new copies must be made of each of the many molecules that form the cell. including the duplication of all DNA molecules. DNA replication is the name given to this duplication process. which enables an organism's genetic information — its genes — to be passed to the two daughter cells created when a cell divides. Only slightly less central to life is a process that requires dynamic DNA acrobatics. called homologous DNA recombination. which reshufiles the genes on chromosomes. In reactions closely linked to DNA replication. the recombination machinery also repairs damage that inevitably occurs to the long. fragile DNA molecules inside cells (see article in this issue by Friedberg. page 436). The model for the DNA double helix1 proposed by Iames Watson and Francis Crick is based on two paired DNA strands that are complementary in their nucleotide sequence. The model had striking implications forthe processesof DNA replication andDNA recombina tion. Before 1953, there had been no meaningful way of even speculat- ing about the molecular mechanisms of these two central genetic processes. But the proposal that each nucleotide in one strand of DNA was tightly base—paired with its complementary nucleotide on the opposite strand— either adenine (A) with thymine (T), or guanine (G) with cytosine (C) — meant that any part of the nucleotide sequence couldactasadirecttempiateforthecorrespondingportionoftheother strand.Asaresult.anypartofthesequencecanbeusedeithertocreateor to iecognize its partner nucleotide sequence —— the two functions that are central forDNA replication and DNA recombination, respectively. in this review. Idiscuss how the discoveryof the structure of DNA half a century ago opened new avenues for understanding the processes of DNA replicationand recombination. Ishall also emphaw size how. as our understanding of complex biological molecules and their interactions increased over the years. there have been profound changes in the way that biologists view the chemistry of life. Structural features of DNA The research that immediately followed the discovery of the double helix focused primarily on understanding the structural properties 431 feature Figural The DNA replication fork. a a. Nucleoside tnpirosphates serve as a substrate for DNA polymerase. according to the mechanism shown on the top strand. 5'; Each nocleoside tn'phosphate is made up of three phosphates (represented hereby yellow spheres). a deexyrihose sugar [beige rectangle) and one of four bases (differently coloured cylinders). The three phosphates arejeined to each other by high-energy bonds. and the cleavage oi these hands during the polymerization reaction releases the free energy needed to drive the incorporation ol each nucleotide into the growing DNA chain. The reaction shown on the bottom strand. vrhichwould cause DNA chain growth in the 3‘ to 5' chemical direction. does not occur in nature, b. DNA polymerases catalyse chain growth only in the 5' to 3' chemical direction. but both new daughter strands grow at Ute fork, so a dilemma oi the 1960s was how the bottom strand in this diagram was synthesized. The asymmetric nature of the replication lorkwas recognized by the early t 9163: the ‘leading strand' grows continuously. whereas the lagging strand' is syndtesized by a DNA polymerase through the backstitching mechanism illustrated. Thus, both strands are produced by DNA synthesis in the 5’ to 3' direction, [Redrawn from ref. 27. with permission.) Lagging strand with Okazaki fragments Most recently synthesized DNA of the molecule. DNA specifies RNA through the process of gene transcrlption. and the RNA molecules in turn specify all of the pro— teins Ola cell. This is the ‘centraldogma' of genetic informationtrans- fora. Any read-out of genetic information — whether it be during DNA replication or gene transcription —— requires access to the sequence of the bases buried in the interior ofthe double helix. DNA strand separation is therefore critical to DNA function. Thus, the WatsonuCrick mode] drove scientists to a search For conditions that would disrupt the hydrogen bonds joining the complementary base palrs.so asto separatethc two strands of the DNA double helix. Physical chemists found that heating a solution of DNA to temperatures near boiling (100 ”C). or subjecting it to extremes of pH, would cause the strands to separate —— a change termed ‘DNA douaturation'. The so—called ‘melting temperature {or Tm) of a stretch of DNA sequence depends on its nucleotide composition: those DNAS with a larger proportion of G—C base pairs exhibit a higher T," because of the three hydrogen bonds that Watson and Crick had predicted to hold a GAC base pair together, compared with only two for the A4" base pair. At physiological salt concentrations. the T", of mammalian DNA is nearly 90 °C. owing to the particular mix ofits base pairs (47% GeC and 53% A—T)3. initially it scented inconceivable that. once separated from its complementary partner. a DNA strand could reform a double helix again. In a complex mixture of DNA molecules, such a feat would require finding the one sequence match amongst millions during random collisions with other sequences, and then rapidly rewinding witltanewpartnerstrand.Thedramatic discoveryoftltis unexpected phenomenon‘. called ‘DNA renaturation', shed light on how sequences could be rearranged by DNA recombination. And it also provided a critical means by which DNA could be manipulated in the laboratory. Theannealingofcomplomentarynucleotidesequences, a process called hybridization, forms the basis of several DNA tecl1~ nologies that helped launch the biotechnology industry and modern genomics. These include gene cloning. genomic sequencing, and DNA copying by the polymerase chain reaction (see article by Hood and Galas on page 444). The arrangement of DNA molecules in chromosomes presented another mystery for scientists: a long, thin molecule would be highly sensitive to shear—induced breakage, and itwas hard to imagine that a mammalian chromosome might contain only a single DNA mole cule. This would require theta typicalchromosome be formed from a continuous DNA helix more than 100 million nucleotide pairs long 432 © 2003 NaturePubtishing Group # a massive molecule weighing more than 100 billion daltons. with an end—to—end distance of more than 3 cm. How could such a giant molecule be protected from accidental fragmentation in a cell only microns in diameter, while keeping it organized for efficient gene readout and other genetic functions? There was no precedent for such giant molecules outside the world of biology. But in the early 19603, autoradiographic studies revealed that the chromosome of the bacterium Escherichia call was in fact a single DNA molecule. more than 3 million nucleotide pairs in lengthf’. And when — more than a decade later — innovative physs ical techniques demonstrated that a single huge DNA molecule formed the basis for each mammalian chromosomes. the result was welcomed by scientists with little surprise. DNA replication forks How is the enormously long double-stranded DNA molecule that forms a chromosome accurately copied to producea second identical chromosome each time a cell divides? The template model for DNA replication, proposed by Watson and Crick in 1953 (ref. 7), gained universal acceptance after two discorrertes in the late 19505. One was an elegant experiment using density-labelled bacterial DNAS that confirmed the predicted templateianttrtemplate schemes. The other was the discovery of an enzyme called DNA polymerase. which uses one strand of DNA as a template to synthesize a new complementary strands. Four deoxyribonucleoside triphosphate nucleotides # dATP. dTTP. dGTP and dCTP f are the precursors to anew daughter DNA strand. each nucleotide selected by pairing with its comple— mentary nucleotide (T. A. C or G, respectivel...
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