Sunday, September 25, 2011

Dna's Molecular Structure

  

Erwin Chargaff, a biochemist at Columbia University, confirmed and refined Avery's conclusion that DNA was complex enough to carry genetic information. In 1950, Chargaff reported that DNA exhibited a phenomenon he dubbed a complementary relationship. The four DNA bases—adenine, cytosine, guanine, and thymine (A, C, G, T, identified earlier by Levene)—appeared to be paired. That is, any given sample of DNA contained equal amounts of G and C, and equal amounts of A and T; guanine was the complement to cytosine, as adenine was to thymine. Chargaff also discovered that the ratio of GC to AT differed widely among different organisms. Rather than Levene's short molecules, DNA could now be reconceived as a gigantic macromolecule, composed of varying ratios of the base complements strung together. Thus, the length of DNA differed between organisms.

 

Even as biochemists described DNA's chemistry, molecular physicists attempted to determine DNA's shape. Using a process called X-ray crystallography, chemist Rosalind Franklin and physicist Maurice Wilkins, working together at King's College London in the early 1950s, debated whether DNA had a helical shape. Initial measurements indicated a single helix, but later experiments left Franklin and Wilkins undecided between a double and a triple helix. Both Chargaff and Franklin were one step away from solving the riddle of DNA's structure. Chargaff understood base complementarity but not its relation to molecular structure; Franklin understood general structure but not how complementarity necessitated adouble helix.

 

In 1952, an iconoclastic research team composed of an American geneticist, James Watson, and a British physicist, Francis Crick, resolved the debate and unlocked DNA's secret. The men used scale-model atoms to construct a model of the DNA molecule. Watson and Crick initially posited a helical structure, but with the bases radiating outward from a dense central helix. After meeting with Chargaff, Watson and Crick learned that the GC and AT ratios could indicate chemical bonds; hydrogen atoms could bond the guanine and cytosine, but could not bond either base to adenine or thymine. The inverse also proved true, since hydrogen could bond adenine to thymine. Watson and Crick assumed these weak chemical links and made models of the nucleotide base pairs GC and AT. They then stacked the base-pair models one atop the other, and saw that the phosphate and sugar components of each nucleotide bonded to form two chains with one chain spinning "up" the molecule, the other spinning "down" the opposite side. The resulting DNA model resembled a spiral staircase—the famous double helix.

 

Watson and Crick described their findings in an epochal 1953 paper published in the journal Nature. Watson and Crick had actually solved two knotty problems simultaneously: the structure of DNA and how DNA replicated itself in cell division—an idea they elaborated in a second path breaking paper in Nature. If one split the long DNA molecule at the hydrogen bonds between the bases, then each half provided a framework for assembling its counterpart, creating two complete molecules—the doubling of chromosomes during cell division. Although it would take another thirty years for crystallographic confirmation of the double helix, Crick, Watson, and Rosalind Franklin's collaborator Maurice Wilkins shared the 1962 Nobel Prize in physiology or medicine (Franklin had died in 1958). The study of molecular genetics exploded in the wake of Watson and Crick's discovery.

 

Once scientists understood the structure of DNA molecules, they focused on decoding the DNA in chromosomes—determining which base combinations created structural genes (those genes responsible for manufacturing amino acids, the building blocks of life) and which combinations created regulator genes (those that trigger the operation of structural genes). Between 1961 and 1966, Marshall Nirenberg and Heinrich Matthaei, working at the National Institutes of Health, cracked the genetic code. By 1967, scientists had a complete listing of the sixty-four three-base variations that controlled the production of life's essential twenty amino acids. Researchers, however, still lacked a genetic map precisely locating specific genes on individual chromosomes. Using enzymes to break apart or splice together nucleic acids, American scientists, like David Baltimore, helped develop recombinant DNA or genetic engineering technology in the 1970s and 1980s.

 

Genetic engineering paved the way for genetic map-ping and increased genetic control, raising a host of political and ethical concerns. The contours of this debate have shifted with the expansion of genetic knowledge. In the 1970s, activists protested genetic engineering and scientists decried for-profit science; thirty years later, protesters organized to fight the marketing of genetically modified foods as scientists bickered over the ethics of cloning humans. Further knowledge about DNA offers both promises and problems that will only be resolved by the cooperative effort of people in many fields—medicine, law, ethics, social policy, and the humanities—not just molecular biology.



Gale Encyclopedia of US History - Discovering Dna

  

Dna (deoxyribonucleic acid) is a nucleic acid that carries genetic information. The study of DNA launched the science of Molecular Biology, transformed the study of genetics, and led to the cracking of the biochemical code of life. Understanding DNA has facilitated Genetic Engineering, the genetic manipulation of various organisms; has enabled cloning, the asexual reproduction of identical copies of genes and organisms; has allowed for genetic fingerprinting, the identification of an individual by the distinctive patterns of his or her DNA; and made possible the use of Genetics to predict, diagnose, prevent, and treat disease.

 

Discovering Dna

 

In the late nineteenth century, biologists noticed structural differences between the two main cellular regions, the nucleus and the cytoplasm. The nucleus attracted attention because short, stringy objects appeared, doubled, then disappeared during the process of cell division. Scientists began to suspect that these objects, dubbed chromosomes, might govern heredity. To understand the operation of the nucleus and the chromosomes, scientists needed to determine their chemical composition.

 

Swiss physiologist Friedrich Miescher first isolated "nuclein"—DNA—from the nuclei of human pus cells in 1869. Although he recognized nuclein as distinct from other well-known organic compounds like fats, proteins, and carbohydrates, Miescher remained unsure about its hereditary potential. Nuclein was renamed nucleic acid in 1889, and for the next forty years, biologists debated the purpose of the compound.

 

In 1929, Phoebus Aaron Levene, working with yeast at New York's Rockefeller Institute, described the basic chemistry of DNA. Levene noted that phosphorus bonded to a sugar (either ribose or deoxyribose, giving rise to the two major nucleic acids, RNA and DNA), and supported one of four chemical "bases" in a structure he called a nucleotide. Levene insisted that nucleotides only joined in four-unit-long chains, molecules too simple to transmit hereditary information.

 

Levene's conclusions remained axiomatic until 1944, when Oswald Avery, a scientist at the Rockefeller Institute, laid the groundwork for the field of molecular genetics. Avery continued the 1920s-era research of British biologist Fred Griffiths, who worked with pneumococci, the bacteria responsible for pneumonia. Griffiths had found that pneumococci occurred in two forms, the disease-causing S-pneumococci, and the harmless R-pneumococci. Griffiths mixed dead S-type bacteria with live R-type bacteria. When rats were inoculated with the mixture, they developed pneumonia. Apparently, Griffiths concluded, something had transformed the harmless R-type bacteria into their virulent cousin. Avery surmised that the transforming agent must be a molecule that contained genetic information. Avery shocked himself, and the scientific community, when he isolated the transforming agent and found that it was DNA, thereby establishing the molecular basis of heredity.

Discovering DNA - Houghton Mifflin Guide to Science & Technology

  

Discovering DNA

Today it is common knowledge that DNA, a nucleic acid, directs the development of cells. Scientists gradually learned about DNA in a curiously twisted fashion that is common in science. For one thing, the discovery of DNA required progress on three separate fronts: cytology (the study of cells through a microscope), genetics, and chemistry.

After Gregor Mendel's laws of heredity were rediscovered in 1900, considerable interest developed in what causes heredity. The fundamental structures involved -- the chromosomes -- had been discovered and studied by Walther Flemming in the 1880s, but no one knew that they were connected to heredity. They were just long thin structures that appeared when cells were stained during cell division. Also, Friederich Miescher had discovered nucleic acids in cell nuclei as early as 1869, but they were not connected either to heredity or to chromosomes -- although Miescher's later discovery that salmon sperm are almost entirely nucleic acid should have been a clue to the connection.

In 1907 Thomas Hunt Morgan, who was somewhat skeptical about genetics, began to use fruit flies in breeding experiments. Within a short time he found that Mendel's laws worked, but also that some inherited characteristics appeared to be linked together. These linkages behaved as if the units of heredity, the genes, lined up in long rows. A suitable long thin part of the cell that could physically contain the genes was the chromosome, as had earlier been suggested on other grounds by August Weismann. By 1911 Morgan was able to show that genes strung along the chromosomes are the agents of heredity.

While this development was occurring on the genetic front, there was also some progress being made in chemistry. In 1909 Phoebus Aaron Theodor Levene was the first to determine that nucleic acids contain a sugar, ribose. Twenty years later, he found that other nucleic acids contain a different sugar, deoxyribose. Hence, there are two types of nucleic acid: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Levene also worked out the other compounds that were in RNA and DNA. This chemistry was then explored in detail in the 1930s by Alexander Todd.

Chromosomes, like other cell structures, contain proteins. They also contain DNA. Proteins were known to be complex molecules that are biologically very active, so everyone thought that genes must be proteins -- until 1944 when Oswald Avery and coworkers showed that hereditary characteristics could be induced by pure DNA, without a protein involved.

By the early 1950s a few scientists from different fronts were tackling the problem of understanding DNA. Among these was Linus Pauling, who was at the time probably the most accomplished chemist. In 1951 Pauling, working with Robert Corey, determined that the structure of a class of proteins is a helix, which is a three-dimensional spiral. This was the first determination of the physical structure of a large biological molecule. At about this time, Pauling turned to the study of DNA, hoping to discover its structure as well.

In England, there were several scientists interested in the structure of DNA. Maurice Wilkins and Rosalind Franklin were doing X-ray diffraction studies of DNA in hopes of elucidating its structure. Diffraction studies had proved successful in analyzing crystal structures, and DNA could be crystallized.

Another English scientist interested in the subject was Francis Crick, a 35-year-old graduate student. With an undergraduate degree in physics, he too would have liked to do X-ray diffraction studies; but English custom kept him from competing with Wilkins and Franklin.

A fourth interested scientist was James Watson, an American. Watson was working as a postgraduate student, trying to learn about genetics from studying organisms. But he realized that the solution to the problem was more likely on the chemical front, so he abandoned what he was doing and applied for work in X-ray diffraction. He was lucky to be taken on at the same Cambridge laboratory where Francis Crick was pursuing his degree, not far from London, where Wilkins and Franklin worked.

News of Pauling's discovery of a helical structure in proteins set all the English group (except -- at first -- Franklin) thinking that DNA might be a helix as well. Alec Stokes, who was working with Wilkins, was the first to think DNA might be a helix, an idea he had developed when he first saw the diffraction studies. Wilkins thought it might be several helices twisted together.

Watson and Crick decided to try using the method by which Pauling had found the helix in proteins. He had stuck together models of the subunits of the molecule, rather as one puts a tinker toy set together. The models need to be constructed so that they fit together according to Pauling's theory of the chemical bond. Watson and Crick acquired a copy of Pauling's 1939 book on the chemical bond and came up with a model for DNA of three helices twisted together. But when they showed it to Wilkins and Franklin, Franklin pointed out that it disagreed with her diffraction data and had other deficiencies as well.

Watson gradually established to his and Crick's satisfaction that DNA does have a helical structure. Crick figured out that the bases in DNA are always paired in the same way. Franklin insisted on the correct location of the sugars.

Meanwhile, Pauling produced two versions of his model of DNA. It contained three twisted helices and was clearly wrong. One of the best chemists of the century had made a mistake in his chemistry.

After another false step, Watson finally built a model that incorporated two helices, paired bases, and the sugar structure recommended by Franklin. Crick did calculations that showed that this model was feasible. Wilkins and Franklin produced X-ray diffraction calculations that confirmed the structure. On a visit to Cambridge, Pauling agreed. The true nature of DNA had finally been discovered.

Curved Dna

  

Curved Dna

DNA containing tracts of (A)3-4•(T)3-4 (that is, runs of three or four bases of A in one strand and a similar run of T in the other) spaced at 10-base pair intervals can adopt a curved helix structure.

 In summary, DNA can exist in a very stable, right-handed double helix, in which the genetic information is very stable. Certain DNA sequences can also adopt alternative conformations, some of which are important regulatory signals involved in the genetic expression or replication of the DNA.


Left-Handed Z-Dna

  

Left-Handed Z-Dna

 Alternating runs of (CG)n•(CG)n or (TG)n•(CA)n dinucleotides in DNA, under superhelical tension or high salt (more than 3 M NaCl) (M, moles per liter) can adopt a left-handed helix called Z-DNA. In this form, the two DNA strands become wrapped in a left-handed helix, which is the opposite sense to that of canonical B-DNA. This can occur within a small region of a larger right-handed B-DNA molecule, creating two junctions at the B-Z transition region.

Quadruplex Dna

  

Quadruplex Dna

DNA sequences containing runs of G•C base pairs can form quadruplex, or four-stranded DNA, in which the four DNA strands are held together by Hoogsteen hydrogen bonds between all four guanines. The four guanines are aligned in a plane, and the successive rings of guanines are stacked one upon another.

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