Concept


Dogma and logic dictated that the mRNA code is a faithful representation of the DNA from which it is transcribed. This exact correspondence between mRNA sequence and DNA sequence was generally upheld in experiments with bacterial cells (prokaryotes). However, inconsistencies surfaced as recombinant-DNA techniques allowed researchers to explore the genes of higher cells (eukaryotes). Then, it was found that mRNA transcripts appeared to be shorter than their corresponding genes. This difference became obvious in electron micrographs of mRNA bound to its complementary DNA template — where regions of DNA without corresponding mRNA form loops. In fact, the protein coding information in genes is interrupted by non-coding sequences called introns, which results in "split genes." The entire DNA code is faithfully transcribed into a temporary form of RNA (pre-mRNA), but this is edited in the nucleus to yield a mature mRNA. The process of RNA splicing involves removing non-coding regions, introns, and splicing together adjacent coding regions, exons.

Animation


Hi, I'm Rich Roberts … and I'm Phil Sharp. In the 70's, while at Cold Spring Harbor Laboratory, we developed a number of important tools and techniques which led to our amazing discovery of interrupted genes. The first 'tool' we developed is a class of enzymes called restriction endonucleases — or simply restriction enzymes. In 1971, Hamilton Smith and Dan Nathans first used restriction enzymes to cut and analyze DNA. Restriction enzymes recognize and cut a specific sequence of DNA by breaking the sugar-phosphate backbone. Both Phil and I identified new restriction enzymes with different cutting specificities. Using these restriction enzymes, a large piece of DNA can be cut into smaller gene-size pieces. This was important, because to study and characterize a gene, we needed a way to reproducibly generate gene-size DNA. Restriction sites are specific, cutting a piece of DNA with the same enzyme will always give the same DNA fragments. Depending on the frequency of the recognition sequence in a target DNA, a restriction enzyme can cut a DNA molecule many times or not at all. In the late 70s and early 80s, my lab at Cold Spring Harbor isolated and identified over 3/4 of the known restriction enzymes. Both Rich and I were also working on the DNA of simple viruses like adenovirus, which has 35,000 base pairs of DNA. We used restriction enzymes to cut adenovirus DNA into smaller pieces. For example, a restriction enzyme called EcoRI cuts DNA anywhere the sequence GAATTC is found, and breaks the backbone between the G and A. Having cut adenovirus DNA into small pieces, the DNA fragments needed to be separated so they could be analyzed. Ultracentrifugation, like that used by Meselson and Stahl, could work but was expensive and time consuming. Gel electrophoresis — earlier used to separate proteins — was the ideal technique to separate DNA fragments. Electrophoresis uses an electric current to separate different-sized molecules in a porous, sponge-like matrix. Smaller molecules move more easily through the gel pores than larger molecules. For proteins, a polyacrylamide gel was used. However, polyacrylamide gels only separate small molecules and can't separate gene-sized fragments of DNA. While at Cold Spring Harbor, I worked with Joe Sambrook and Bill Sugden and developed an agarose gel, made from highly purified seaweed. This separated DNA molecules ranging from several hundred nucleotides in length to over 10,000 nucleotides. The gel is submersed in a tank filled with a salt solution that conducts electricity. Using a pipette, DNA samples are loaded into slots made in the agarose gel. The DNA samples are colorless, but we add a blue "tracking" dye. This makes it easier to load the samples and we can visually track the DNA migration through the gel. Remember that the phosphate groups in the DNA backbone carry negatively-charged oxygens — giving a DNA molecule an overall negative charge. In an electric current, negatively-charged DNA moves toward the positive pole of the electrophoresis chamber. The DNA molecules move through the gel by "reptation" — a reptile-like snaking through the pores of the agarose matrix. Smaller DNA fragments migrate faster and further over a given period of time than do larger fragments. This is how DNA fragments can be separated by size in an agarose gel. We also introduced the use of the fluorescent dye, ethidium bromide, to stain DNA. Ethidium bromide binds tightly to the double helix, and glows when illuminated with ultraviolet light. This lets us see where the separated DNA fragments ended up. A photo is taken of the gel for later analysis. The size of any DNA restriction fragment can be determined by comparing it to "markers" — DNA fragments of known sizes. A "map" of restriction enzyme sites can be generated by cutting a piece of DNA with different combinations of restriction enzymes. Let's go through an example. Suppose we had a 15,000 base-pair (15 kb) piece of DNA. When cut with EcoRI and run on a gel, we see two bands. We can size the bands by comparing them to 'marker' DNA — fragments of known sizes. As you can see, one is 8 kilobases (kb) and the other is 7kb. So, EcoRI cuts this 15 kb DNA only once. As you can see, one is 8 kilobases (kb) and the other is 7kb. So, EcoRI cuts this 15 kb DNA only once. But, since we don't know the relative order of the BamHI to the EcoRI sites, the BamHI sites can be arranged to give two maps. To figure out which BamHI map is correct, we can perform a "double digest" using both EcoRI and BamHI to cut the DNA. This lets us map the restriction sites relative to each other. Doing the double digest with our DNA gives bands whose lengths are 7, 5, and 3 kb. When we compare the double-digest data to the EcoRI and BamHI single digests, we see that the 8 kb EcoRI fragment is missing, and is "replaced" by fragments that are 5 and 3 kb long. This tells us that there is a single BamHI site within the 8 kb EcoRI fragment. The final EcoRI/BamHI map fits all the data from the double and the single enzyme digests. This strategy of restriction enzyme mapping was and is used to map DNA genomes. These maps are extremely useful because with them we can correlate the genetic map with a physical map of DNA segments. We can locate genes on pieces of DNA. By the 1970s, the details of transcription — making messenger RNA molecules from DNA coding regions — had been worked out for bacterial cells. In particular, we knew that bacterial mRNA molecules and their DNA counterparts were "colinear." That is, if aligned next to each other, the mRNA and DNA matched up along their entire length. However, when we did the same experiment with eukaryotic mRNA and DNA, we saw distinct "loops" of DNA between the matched RNA/DNA segments. We called these R-loops. These R-loops must be non-coding sequences. Working with Rich Gelinas, a post-doc, we started looking at the differences between mRNA and DNA. Based on the information from the adenovirus restriction map that Phil Sharp and I made, I cut the adenovirus DNA and isolated specific fragments. I used a single-stranded BamHI DNA fragment ... ... and I mixed it with adenovirus messenger RNA. With help from Louise Chow and Tom Broker, we used the electron microscope to see what, if any, DNA/RNA hybrids and R-loops were made. We saw that one end of the mRNA hybridized to three points on the BamHI DNA fragment. This gave the 2 R-loops seen in the electron micrograph. The DNA loops out because the sequences are not present in the mRNA. It was obvious that RNA and DNA weren't colinear as we had assumed. The gene on the DNA was split compared to the mRNA sequence. By using the 'right' restricted DNA fragment and comparing the results, I determined the start of the mRNA on the DNA, and which DNA segments coded for the rest of the mRNA. We used this electron micrograph in our 1977 Cell paper: An Amazing Sequence Arrangement at the 5' Ends of Adenovirus 2 Messenger RNA. While Rich was doing his work at Cold Spring Harbor, I was getting similar results from my experiments at MIT. The discovery of split genes revolutionized our thinking of how genes are organized.

Gallery


Rich Roberts in his lab at Cold Spring Harbor, 1975.
Rich Roberts in his office at New England Biolabs, 1999.
Louise Chow and Thom Broker.
Electron micrograph of RNA/DNA hybrid. This was one of the original photos that Roberts and his group used for analyzing their results.
Rich Roberts as Dr. December in the 1997 Studmuffins of Science Calendar.
The Sambrook lab at Cold Spring Harbor Laboratory around 1971 where Phil Sharp was a post-doc. (L-R) Arlene Jackson, Phil Sharp and C. Mulder.

Audio/Video


Audio Glossary

Adenovirus, Electrophoresis, Exon, Gene, Messenger RNA (mRNA), Ribonucleic acid (RNA)

Video Interviews

Richard Roberts

Rich Roberts is Director of Research for New England Biolabs, one of the first commercial sources for restriction enzymes that is today a leading supplier of molecular biology reagents.

Clip 1 (0:33)
How he first became interested in restriction enzymes - hearing a talk by Dan Nathans.

Clip 2 (0:58)
Describing the early work purifying restriction enzymes.

Clip 3 (0:57)
Describing the early experimental evidence for "interrupted" RNA transcripts that went on to suggest the subsequent electron micrograph studies.

Clip 4 (1:31)
Describing the set up of the electron micrograph experiments.

Clip 5 (1:29)
Performing the electron micrograph DNA/RNA hybridizations, and seeing the results.

Clip 6 (1:09)
Should an aspiring student pursue a career in science? -- finding and developing your passion.

Phil Sharp

Phil Sharp is the Salvador E. Luria Professor of Biology at the Massachusetts Institute of Technology. His laboratory studies both the catalytic processes responsible for splicing and the nature of the factors conferring specificity.

Clip 1 (1:02)
Recounting how he came to Cold Spring Harbor Laboratory to study viruses.

Clip 2 (0:55)
Describing long nuclear versus short cytoplasmic message RNA, and what the differences suggested.

Clip 3 (1:10)
Interpreting the electron micrographs that led to the discovery of the split gene.

Clip 4 (0:52)
Developing the experimental technologies used to study DNA fragments: agarose gel electrophoresis and restriction enzymes.

Clip 5 (1:20)
Commenting on how the real excitement of science comes when you don't know what's going on, and you get to be part of "the chase."

Biography


 

Richard Roberts and Phil Sharp shared the 1993 Nobel Prize for the discovery of the split gene theory.

RICHARD JOHN ROBERTS (1943-)

Richard (Rich) Roberts was born in Derby, England. His family moved to Bath when he was four. His father was a mechanic and his mother was a homemaker. His father was very supportive of Roberts' inquisitive nature. He helped him build a chemistry lab in the basement where Roberts made and studied fireworks and other chemicals.

This interest in chemistry plus a fascination with games and puzzles led him to pursue a research career. It was a chance to be a detective and solve chemical puzzles in the world of science. He graduated from Sheffield University in 1965 and stayed to do graduate work with his organic chemistry professor - one of the few who used problem solving to emphasize the challenge and not the chore of learning.

While finishing his Ph.D., Roberts read John Kendrew's book, Thread of Life: An Introduction to Molecular Biology. This introduction to the early history of crystallography and molecular biology fascinated Roberts. He decided to switch fields and chose a lab that would allow him to go into molecular biology. For a post-doctoral tenure, Roberts went to Harvard to work in Jack Strominger's lab.

At Harvard, Roberts learned the jargon of biochemistry. His project involved sequencing a tRNA involved in bacterial cell wall biosynthesis. Based on his readings he decided that the radioactive method of sequencing being developed by Fred Sanger in Cambridge was the best. In 1970, he went to Cambridge, learned the technique and when he came back, Roberts taught many of the area scientists how to sequence the Sanger way.

In 1972, after a 10-minute interview, James Watson offered Roberts a position at Cold Spring Harbor Laboratory. Watson wanted him to sequence the DNA of SV40, a virus. Roberts accepted the position and started investigating the enzyme Endonuclease R which he heard about from Dan Nathans. The enzyme cut DNA into specific pieces. Roberts realized that if there were more of these enzymes, he could use them to cut DNA into manageable sizes and thus use them in sequencing. Soon Roberts and his lab had a whole collection of restriction enzymes. During the '70s and early '80s, about 75 out of 100 known enzymes were isolated in Roberts' lab.

Some of these restriction enzymes were used to map adenovirus DNA, a project in which Phil Sharp, in Joe Sambrook's lab, was also involved. In 1974, Roberts and Richard Gelinas started working with the adenovirus mRNA. They reasoned they could identify the DNA promoter region by sequencing the 5' end of the mRNA and then mapping it to the DNA. The promoter would be upstream of the 5' end of the mRNA. Through the course of their experiments, they discovered biochemical proof that the genes in adenovirus were split. Roberts then devised the electron microscope experiments that proved visually that this was true. In 1993, Roberts shared the Nobel Prize in Physiology or Medicine with Phil Sharp for the discovery of the split gene.

Roberts also helped develop one of the first computer programs that maps and analyzes DNA restriction enzyme fragments. He was an early advocate of computer use in molecular biology.

In 1992, Roberts moved to New England Biolabs - a company where he is now one of two Research Directors. In addition to basic research, the company makes and sells research reagents and is noted for its production of restriction enzymes.

Roberts is still fascinated by puzzles and games. His favorite is croquet, which he says combines the skill of snooker with the strategy of chess. His problem-solving nature is tempered with a dry sense of humor as evidenced by his appearance in "The Stud Muffins of Science 1997 Calendar," and his annual trip to the Ig Nobel Awards (the "opposite" of the Nobels) at Harvard University.

PHILLIP ALLEN SHARP (1944-)

Phillip (Phil) Sharp was born in rural Kentucky. He grew up on a farm, and while not particularly interested in biology, Sharp did enjoy his science and math classes in school. His parents encouraged him to go to college, and Sharp earned his tuition by raising cattle and growing tobacco.

Sharp went to Union College, a small liberal arts school. He majored in chemistry and math and went on to the University of Illinois for graduate school. His thesis project was on the description of DNA. It was more physical chemistry as opposed to experimental molecular biology.

In 1966, Cold Spring Harbor Laboratory held a symposium on The Genetic Code. Sharp read the symposium volume and became interested in molecular biology and genetics. When he started looking for a post-doc in 1969, Sharp applied and was accepted to work with Norman Davidson at the California Institute of Technology - a lab working on problems relating to the phage and bacterial genomes. Sharp learned how to use techniques like electron microscopy to experiment and test theories. Sharp worked with and studied bacterial plasmids, and figured out that plasmids that confer sex or drug resistance have transposable elements.

In 1971, Sharp did another post-doc at Cold Spring Harbor Laboratory. James Watson was his supervisor, but because he was still at Harvard, Sharp worked more closely with Joe Sambrook. Sharp was interested in gene expression and worked with simple viruses, like SV40 and adenovirus. Using restriction enzymes, which had just been discovered, and an adapted gel electrophoresis technique, Sharp mapped the adenovirus genome. He and his colleagues then mapped the adenoviral mRNAs and linked them to function.

These experiments were started at Cold Spring Harbor and continued at Massachusetts Institute of Technology where in 1974, Sharp was offered a job at the Center for Cancer Research. Sharp and his colleagues noticed that long nuclear RNA did not exist in the cytoplasm. They speculated that these long nuclear RNAs were processed into shorter mRNAs. Using RNA/DNA hybrids, they showed that cytoplasmic mRNA was processed and edited. This led to the split gene theory for which Sharp shared the 1993 Nobel Prize for Physiology or Medicine.

In 1978, Sharp and a group of other scientists, including Walter Gilbert, founded Biogen Inc., one of the first biotech companies. It is now centered in Boston and is currently the only non-conglomerated biotech company. Sharp is the Chairman of the Scientific Board at Biogen and a member of its Board of Directors.

In 1985, Sharp became the director of the Center for Cancer Research after Salvador Luria retired. In 1991, he stepped down as director and became the head of the Department of Biology at MIT. His tenure as head of the department ended in 1999 and he is currently Institute Professor.

In addition to the Nobel, Sharp has won numerous prizes for his work. Until 1995, Sharp was on the editorial board for the journal Cell and is a member of many scientific organizations like the National Academy and the American Philosophical Society. He has served as a member of the President's Advisory Council on Science and Technology and on a number of search committees and peer-review government granting agencies like the NIH.

Factoid

Links


 

Links

Webcutter

This site allows you to input any nucleotide sequence and it will give you a map that tells you where and which restriction enzymes will cut the sequence.

Rebase: The Restriction Enzyme Database

Maintained by Dr. Rich Roberts and Dana Macelis at the New England Biolabs, Rebase is a searchable database of all the known restriction enzymes. You can find information about the enzymes, their cutting specificities and journal references.

Bibliography

  • Alberts, Bruce et al., 1983, Molecular Biology of the Cell, Garland Publishing Inc., New York.

  • Dunn, L.C., 1991, A Short History of Genetics: The Development of Some of the Main Lines of Thought: 1864-1939, Iowa State University Press, Ames.

  • Griffiths, Anthony, et al., 1996, An Introduction to Genetic Analysis, W. H. Freeman and Company, New York.

  • Judson, Horace Freeland, 1979, The Eighth Day of Creation: Makers of the Revolution in Biology, Simon and Schuster, New York.

  • Lagerkvist, Ulf, 1998, DNA Pioneers and Their Legacy, Yale University Press, New Haven.

  • Lewin, Benjamin, 1990, Genes IV, Oxford University Press, New York.

  • Micklos, David A., and Freyer, Greg A., 1990, DNA Science: A First Course in Recombinant DNA Technology, Cold Spring Harbor Laboratory Press, New York.

  • Rosenfield, Israel, Ziff, Edward, and Van Loon, Borin, 1983, DNA for Beginners, Writers and Readers Publishing, Inc.

  • Watson, James D., Gilman, Michael, Witkowski, Jan, and Zoller, Mark, 1982, Recombinant DNA, 2nd edition, W. H. Freeman and Company, New York.

  • Witkowski, J. A., 1988, The Discovery of "Split" Genes: a Scientific Revolution, Trends in Biochemical Sciences, 13: 110-113.

Glossary


Adenovirus - A group of DNA containing viruses which cause respiratory disease, including one form of the common cold. Adenoviruses can also be genetically modified and used in gene therapy to treat cystic fibrosis, cancer, and potentially other diseases.
Electrophoresis - The process in which molecules (such as proteins, DNA, or RNA fragments) can be separated according to size and electrical charge by applying an electric current to them. The current forces the molecules through pores in a thin layer of gel, a firm jelly-like substance. The gel can be made so that its pores are just the right dimensions for separating molecules within a specific range of sizes and shapes. Smaller fragments usually travel further than large ones. The process is sometimes called gel electrophoresis.
Exon - The region of a gene that contains the code for producing the gene's protein. Each exon codes for a specific portion of the complete protein. In some species (including humans), a gene's exons are separated by long regions of DNA (called introns or sometimes "junk DNA") that have no apparent function.
Gene - The functional and physical unit of heredity passed from parent to offpsring. Genes are pieces of DNA, and most genes contain the information for making a specific protein.
Messenger RNA (mRNA) -
Ribonucleic acid (RNA) -

Children resemble their parents.
Genes come in pairs.
Genes don't blend.
Some genes are dominant.
Genetic inheritance follows rules.
Genes are real things.
All cells arise from pre-existing cells.
Sex cells have one set of chromosomes; body cells have two.
Specialized chromosomes determine gender.
Chromosomes carry genes.
Genes get shuffled when chromosomes exchange pieces.
Evolution begins with the inheritance of gene variation.
Mendelian laws apply to human beings.
Mendelian genetics cannot fully explain human health and behavior.
DNA and proteins are the molecules of the cell nucleus.
One gene makes one protein.
A gene is made of DNA.
Bacteria and viruses have DNA too.
The DNA molecule is shaped like a twisted ladder.
A half DNA ladder is a template for copying the whole.
RNA is an intermediary between DNA and protein.
DNA words are three letters long.
A gene is a discrete sequence of DNA nucleotides.
Some viruses store genetic information in RNA.
RNA was the first genetic molecule.
Mutations are changes in genetic information.
Some types of mutations are automatically repaired.
A chromosome is a package for DNA.
Higher cells incorporate an ancient chromosome.
Some DNA does not encode protein.
Some DNA can jump.
Genes can be turned on and off.
Genes can be moved between species.
DNA responds to signals from outside the cell.
Different genes are active in different kinds of cells.
Master genes control basic body plans.
Development balances cell growth and death.
A genome is an entire set of genes.
Living things share common genes.
DNA is only the starting point for understanding human biology.
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