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DNA TOPOLOGY

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Anu Sreejith

DNA topology studies the geometric properties and spatial relationships of DNA that are unaffected by changes in shape or size. It includes phenomena like supercoiling, knots, and catenanes that involve the linking and twisting of the two DNA strands. DNA topology is characterized by parameters like the linking number, which represents the number of times the two strands are twisted around each other. Enzymes called topoisomerases regulate DNA topology by introducing temporary breaks in the DNA strands to allow strand passage and control supercoiling levels.

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DNA TOPOLOGY DR. ANU P. ABHIMANNUE ASST. PROFESSOR, DEPARTMENT OF BIOTECHNOLOGY, ST.MARY’S COLLEGE, THRISSUR.
DNA TOPOLOGY • Dictionary explains topology as “The study of geometrical properties and spatial relations unaffected by the continuous change of shape or size of figures” • The topology of DNA, explains how the two complementary single strands are intertwined. • DNA topology encompasses supercoiling, knots, and catenanes. Dr. ANU P A, ST. MARY'S COLLEGE, THRISSUR 2
CHARACTERISTICS • The topology of closed circular DNA is characterized by the linking number (Lk), which is the number of links between two complementary single strands. • Linking number is demonstrated by Twist (Tw) - number of times the two strands are twisted around each other Writhe (Wr) - the geometric coiling of the double helix
KNOTS • Entanglement of flexible curves leads to knots
CATENANES • Topologically linked circular DNA molecules are called Catenanes. • Usually, they appear at the end of replication of circular DNA.
SUPERCOILING • Super coiling refers to the additional twisting of a DNA strand • Advantage of supercoiling – Reduce the space required for DNA packaging, allowing for more efficient storage of DNA • First observed by Jerome Vinograd at the California Institute of Technology in 1963. Vinograd: (February 9, 1913 – July 7, 1976), American biochemist
OBSERVATION • Jerome Vinograd and his colleagues observed two closed, circular DNA molecules of identical molecular mass exhibit very different rates of sedimentation during centrifugation. • Further analysis indicated that the DNA molecule sedimenting more rapidly had a more compact shape because the molecule was twisted upon itself and occupies a smaller volume and moves more rapidly
When same type of molecule in a supercoiled state and relaxed state is subjected to gel electrophoresis, the highly compact, supercoiled form moves rapidly. The same when subjected to ultra-centrifugation, supercoiled DNA settles at the bottom more faster. SUPER COILING
Overwound DNA • Positive supercoiling • Positive supercoiling of DNA occurs when it is twisted even tighter until the helix begins to distort and "knot.“ • Rarely DNA forms positive supercoiling eg: positive supercoils in front of the transcription site Underwound DNA • Negative supercoiling • Involves twisting against helical conformation which preferentially underwinds and "straightens" at low twisting stress, and knots the DNA into negative supercoils at high twisting stress. • Most DNA is negatively supercoiled. Eg: Circular DNAs like mitochondrial, viral, Bacterial and eukaryotic chromosome.
ENZYMES IN DNA TOPOLOGY • Topoisomerases – enzymes that change the topology of the DNA. • The first DNA topoisomerase was discovered by James Wang in 1971 • Cells contain a variety of topoisomerases • Broadly classified as • Type I topoisomerases • Type II topoisomerases Chinese-born American biochemist and biologist
Topoisomerases Type I topoisomerases • It create a transient break in one strand of DNA • Convert supercoiled DNA to relaxed form. • Plays significant role during DNA replication and transcription Type II topoisomerases • Transient break in both strands • It can supercoil and relax DNA, tie a DNA molecule into knots or untie; cause a population of independent DNA circles to become interlinked (catenated ) or vice versa. • Human topoisomerase II is a target for drugs (e.g., etoposide and doxorubicin) to prevent resealing of DNA in rapidly dividing cells and are therefore used in the treatment of cancer
Topoisomerases Type I topoisomerases • Mechanism : enzyme cleaves one strand and then allows the intact, complementary strand to undergo a controlled rotation, which relaxes the supercoiled molecule. Type II topoisomerases • Mechanism: Another segment of the DNA molecule is transported through the break, and the severed strands are resealed.
REFERENCES • Gerald Karp (2010). Cell and molecular biology: concepts and experiments (6th ed.). John Wiley & sons. ISBN-13 978-0-470-48337-4. • Neuman K.C., 2010. Single-molecule Measurements of DNA Topology and Topoisomerases. J Biol Chem. 285(25): 18967–18971. doi: 10.1074/jbc.R109.092437 • https://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/71-dna- structure-and-replic/supercoiling.html • http://earth.callutheran.edu/Academic_Programs/Departments/BioDev/o mm/topo1/frames/coil.htm#:~:text=Positive%20supercoiling%20of%20DN A%20occurs,twisting%20in%20a%20left%2Dhanded

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DNA TOPOLOGY

  • 1. DNA TOPOLOGY DR. ANU P. ABHIMANNUE ASST. PROFESSOR, DEPARTMENT OF BIOTECHNOLOGY, ST.MARY’S COLLEGE, THRISSUR.
  • 2. DNA TOPOLOGY • Dictionary explains topology as “The study of geometrical properties and spatial relations unaffected by the continuous change of shape or size of figures” • The topology of DNA, explains how the two complementary single strands are intertwined. • DNA topology encompasses supercoiling, knots, and catenanes. Dr. ANU P A, ST. MARY'S COLLEGE, THRISSUR 2
  • 3. CHARACTERISTICS • The topology of closed circular DNA is characterized by the linking number (Lk), which is the number of links between two complementary single strands. • Linking number is demonstrated by Twist (Tw) - number of times the two strands are twisted around each other Writhe (Wr) - the geometric coiling of the double helix
  • 4. KNOTS • Entanglement of flexible curves leads to knots
  • 5. CATENANES • Topologically linked circular DNA molecules are called Catenanes. • Usually, they appear at the end of replication of circular DNA.
  • 6. SUPERCOILING • Super coiling refers to the additional twisting of a DNA strand • Advantage of supercoiling – Reduce the space required for DNA packaging, allowing for more efficient storage of DNA • First observed by Jerome Vinograd at the California Institute of Technology in 1963. Vinograd: (February 9, 1913 – July 7, 1976), American biochemist
  • 7. OBSERVATION • Jerome Vinograd and his colleagues observed two closed, circular DNA molecules of identical molecular mass exhibit very different rates of sedimentation during centrifugation. • Further analysis indicated that the DNA molecule sedimenting more rapidly had a more compact shape because the molecule was twisted upon itself and occupies a smaller volume and moves more rapidly
  • 8. When same type of molecule in a supercoiled state and relaxed state is subjected to gel electrophoresis, the highly compact, supercoiled form moves rapidly. The same when subjected to ultra-centrifugation, supercoiled DNA settles at the bottom more faster. SUPER COILING
  • 9. Overwound DNA • Positive supercoiling • Positive supercoiling of DNA occurs when it is twisted even tighter until the helix begins to distort and "knot.“ • Rarely DNA forms positive supercoiling eg: positive supercoils in front of the transcription site Underwound DNA • Negative supercoiling • Involves twisting against helical conformation which preferentially underwinds and "straightens" at low twisting stress, and knots the DNA into negative supercoils at high twisting stress. • Most DNA is negatively supercoiled. Eg: Circular DNAs like mitochondrial, viral, Bacterial and eukaryotic chromosome.
  • 10. ENZYMES IN DNA TOPOLOGY • Topoisomerases – enzymes that change the topology of the DNA. • The first DNA topoisomerase was discovered by James Wang in 1971 • Cells contain a variety of topoisomerases • Broadly classified as • Type I topoisomerases • Type II topoisomerases Chinese-born American biochemist and biologist
  • 11. Topoisomerases Type I topoisomerases • It create a transient break in one strand of DNA • Convert supercoiled DNA to relaxed form. • Plays significant role during DNA replication and transcription Type II topoisomerases • Transient break in both strands • It can supercoil and relax DNA, tie a DNA molecule into knots or untie; cause a population of independent DNA circles to become interlinked (catenated ) or vice versa. • Human topoisomerase II is a target for drugs (e.g., etoposide and doxorubicin) to prevent resealing of DNA in rapidly dividing cells and are therefore used in the treatment of cancer
  • 12. Topoisomerases Type I topoisomerases • Mechanism : enzyme cleaves one strand and then allows the intact, complementary strand to undergo a controlled rotation, which relaxes the supercoiled molecule. Type II topoisomerases • Mechanism: Another segment of the DNA molecule is transported through the break, and the severed strands are resealed.
  • 13. REFERENCES • Gerald Karp (2010). Cell and molecular biology: concepts and experiments (6th ed.). John Wiley & sons. ISBN-13 978-0-470-48337-4. • Neuman K.C., 2010. Single-molecule Measurements of DNA Topology and Topoisomerases. J Biol Chem. 285(25): 18967–18971. doi: 10.1074/jbc.R109.092437 • https://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/71-dna- structure-and-replic/supercoiling.html • http://earth.callutheran.edu/Academic_Programs/Departments/BioDev/o mm/topo1/frames/coil.htm#:~:text=Positive%20supercoiling%20of%20DN A%20occurs,twisting%20in%20a%20left%2Dhanded