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DNA Coiling.ppt

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DNA must be tightly packaged to fit inside cells. It is coiled around histone proteins to form nucleosomes, which are connected by linker DNA. Multiple nucleosomes then coil further to form the chromatin fiber. DNA is also supercoiled, winding and twisting upon itself, which allows it to condense even smaller. Supercoiling takes two forms - negative supercoiling unwinds the DNA slightly while positive supercoiling winds it more tightly. In cells, DNA is typically negatively supercoiled to favor processes like transcription and replication.

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DNA Coiling
DNA is a big molecule ? Ruptured viral particle (bacteriophage) X95 000 ? DNA about 1.7?m ? 2010 Paul Billiet ODWS
Supercoiling of topologically constrained DNA ? Topologically closed DNA can be circular (covalently closed circles) or loops that are constrained at the base ? The coiling (or wrapping) of duplex DNA around its own axis is called supercoiling.
Different topological forms of DNA
THE NUCLEOSOME ? Uncoiled the DNA of a human would stretch 2m ? The average diameter of a nucleus is 10?m ? The problem: To pack the DNA into the nucleus and yet have access to the genetic information. ? 2010 Paul Billiet ODWS
THE NUCLEOSOME ? Histones are made of a lot of basic amino acids ? Combined with acidic DNA they make a stable nucleoprotein called chromatin Histone core = an octomer (8 histone molecules) Histone molecules ? 2010 Paul Billiet ODWS
DNA wraps twice round the core DNA strand ? 2010 Paul Billiet ODWS
DNA held in place by another histone (H1) = the nucleosome H1 ? 2010 Paul Billiet ODWS
Nucleosomes are joined by linker DNA Linker DNA
DNA super coiling DNA double helix Nucleosome beads on a string 30-nm chromatin fibre
DNA super coiling 30-nm chromatin fibre Chromosome in extended form Condensed section of chromosome in mitosis ? 2010 Paul Billiet ODWS
DNA super coiling Condensed section of chromosome in mitosis Condensed chromosome ? 2010 Paul Billiet ODWS
Negative and positive supercoils ? Negative supercoils twist the DNA about its axis in the opposite direction from the clockwise turns of the right-handed (R-H) double helix. ¨C Underwound (favors unwinding of duplex). ¨C Has right-handed supercoil turns. ? Positive supercoils twist the DNA in the same direction as the turns of the R-H double helix. ¨C Overwound (helix is wound more tightly). ¨C Has left-handed supercoil turns.
Components of DNA Topology : Twist ? The clockwise turns of R-H double helix generate a positive Twist (T). ? The counterclockwise turns of L-H helix (Z form) generate a negative T. ? T = Twisting Number B form DNA: + (# bp/10 bp per twist) A form NA: + (# bp/11 bp per twist) Z DNA: - (# bp/12 bp per twist)
Components of DNA Topology : Writhe ? W = Writhing Number ? Refers to the turning of the axis of the DNA duplex in space ? Number of times the duplex DNA crosses over itself Relaxed molecule W=0 Negative supercoils, W is negative Positive supercoils, W is positive
Components of DNA Topology : Linking number ? L = Linking Number = total number of times one strand of the double helix (of a closed molecule) encircles (or links) the other. ? L = W + T
L cannot change unless one or both strands are broken and reformed ? A change in the linking number, DL, is partitioned between T and W, i.e. ? DL=DW+DT ? if DL = 0, then DW= -DT
Relationship between supercoiling and twisting
DNA in most cells is negatively supercoiled ? The superhelical density is simply the number of superhelical (S.H.) turns per turn (or twist) of double helix. ? Superhelical density = s = W/T = -0.05 for natural bacterial DNA ¨Ci.e., in bacterial DNA, there is 1 negative S.H. turn per 200 bp ? (calculated from 1 negative S.H. turn per 20 twists = 1 negative S.H. turn per 200 bp)
Negatively supercoiled DNA favors unwinding ? Negative supercoiled DNA has energy stored that favors unwinding, or a transition from B- form to Z DNA. ? For s = -0.05, DG=-9 Kcal/mole favoring unwinding Thus negative supercoiling could favor initiation of transcription and initiation of replication.

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DNA Coiling.ppt

  • 2. DNA is a big molecule ? Ruptured viral particle (bacteriophage) X95 000 ? DNA about 1.7?m ? 2010 Paul Billiet ODWS
  • 3. Supercoiling of topologically constrained DNA ? Topologically closed DNA can be circular (covalently closed circles) or loops that are constrained at the base ? The coiling (or wrapping) of duplex DNA around its own axis is called supercoiling.
  • 5. THE NUCLEOSOME ? Uncoiled the DNA of a human would stretch 2m ? The average diameter of a nucleus is 10?m ? The problem: To pack the DNA into the nucleus and yet have access to the genetic information. ? 2010 Paul Billiet ODWS
  • 6. THE NUCLEOSOME ? Histones are made of a lot of basic amino acids ? Combined with acidic DNA they make a stable nucleoprotein called chromatin Histone core = an octomer (8 histone molecules) Histone molecules ? 2010 Paul Billiet ODWS
  • 7. DNA wraps twice round the core DNA strand ? 2010 Paul Billiet ODWS
  • 8. DNA held in place by another histone (H1) = the nucleosome H1 ? 2010 Paul Billiet ODWS
  • 9. Nucleosomes are joined by linker DNA Linker DNA
  • 10. DNA super coiling DNA double helix Nucleosome beads on a string 30-nm chromatin fibre
  • 11. DNA super coiling 30-nm chromatin fibre Chromosome in extended form Condensed section of chromosome in mitosis ? 2010 Paul Billiet ODWS
  • 12. DNA super coiling Condensed section of chromosome in mitosis Condensed chromosome ? 2010 Paul Billiet ODWS
  • 13. Negative and positive supercoils ? Negative supercoils twist the DNA about its axis in the opposite direction from the clockwise turns of the right-handed (R-H) double helix. ¨C Underwound (favors unwinding of duplex). ¨C Has right-handed supercoil turns. ? Positive supercoils twist the DNA in the same direction as the turns of the R-H double helix. ¨C Overwound (helix is wound more tightly). ¨C Has left-handed supercoil turns.
  • 14. Components of DNA Topology : Twist ? The clockwise turns of R-H double helix generate a positive Twist (T). ? The counterclockwise turns of L-H helix (Z form) generate a negative T. ? T = Twisting Number B form DNA: + (# bp/10 bp per twist) A form NA: + (# bp/11 bp per twist) Z DNA: - (# bp/12 bp per twist)
  • 15. Components of DNA Topology : Writhe ? W = Writhing Number ? Refers to the turning of the axis of the DNA duplex in space ? Number of times the duplex DNA crosses over itself Relaxed molecule W=0 Negative supercoils, W is negative Positive supercoils, W is positive
  • 16. Components of DNA Topology : Linking number ? L = Linking Number = total number of times one strand of the double helix (of a closed molecule) encircles (or links) the other. ? L = W + T
  • 17. L cannot change unless one or both strands are broken and reformed ? A change in the linking number, DL, is partitioned between T and W, i.e. ? DL=DW+DT ? if DL = 0, then DW= -DT
  • 19. DNA in most cells is negatively supercoiled ? The superhelical density is simply the number of superhelical (S.H.) turns per turn (or twist) of double helix. ? Superhelical density = s = W/T = -0.05 for natural bacterial DNA ¨Ci.e., in bacterial DNA, there is 1 negative S.H. turn per 200 bp ? (calculated from 1 negative S.H. turn per 20 twists = 1 negative S.H. turn per 200 bp)
  • 20. Negatively supercoiled DNA favors unwinding ? Negative supercoiled DNA has energy stored that favors unwinding, or a transition from B- form to Z DNA. ? For s = -0.05, DG=-9 Kcal/mole favoring unwinding Thus negative supercoiling could favor initiation of transcription and initiation of replication.