07BIS1012013ReplicLect_7

Lrodriguez 2013

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Unformatted text preview: e helix becomes more rigid or Writhing stiff. This promotes the stacking of the bases, one over the other. All of stacking this leads to greater stability of the helix. This phenomenon underscores the reasons NaCl is typically added to DNA solutions in the laboratory. the -- - -- -- - - - ---- - - - ---- BIS101­001, Spring 2013—Genes and Gene Expression R.L. Rodriguez ©2013 BIS101­001, Spring 2013—Genes and Gene Expression R.L. Rodriguez Na+ - - 17 DNA stability: Hydrophobicity ­ Hydrophobicity stabilizes DNA by forming ordered shells of water around each ordered base. This ordering of water molecules into shells decreases entropy (or the decreases tendency toward molecular randomness) and therefore is thermodynamically unfavorable. For this reason, shells tend to fuse together, thus reducing order or shells increasing entropy. Since fewer water molecules are ordered in fused shells as compared to shells around individual bases, a smaller number of water molecules remain in an ordered state. This increased entropy is thermodynamically favorable. favorable. = H 20 BIS101­001, Spring 2013—Genes and Gene Expression R.L. Rodriguez ©2013 BIS101­001, Spring 2013—Genes and Gene Expression R.L. Rodriguez 18 Base Stacking ­ Two views of base stacking in DNA. Figure 1 shows a van der Waal Two space filling model of single stranded DNA. The DNA backbone is shown as a yellow ribbon. On the right (Fig. 2), hydrogen bonding between between complementary base pairs and between stacked bases are shown (black arrow). shown BIS101­001, Spring 2013—Genes and Gene Expression R.L. Rodriguez ©2013 BIS101­001, Spring 2013—Genes and Gene Expression R.L. Rodriguez 19 DNA stability:van der Waals interactions ­ van der Waals forces also contribute to DNA structure. Because of van fluctuating charge distributions in atoms and molecules (dipole moments), they will attract each until they reach a point where the attractive force and the repulsive force balance out. This occurs when outer shell electrons in each atom begin to overlap. Half the distance between their respective nuclei is called Van der Waals radii. These forces are about Van These as strong as the weakest H bonds and therefore promote DNA stability. These forces are particularly important in DNA/protein interactions where a close fit between molecules is required. close s orbitals of Cl2 BIS101­001, Spring 2013—Genes and Gene Expression R.L. Rodriguez ©2013 BIS101­001, Spring 2013—Genes and Gene Expression R.L. Rodriguez 20 DNA stability: Hydrogen bonds ­ Hydrogen bonds are weak; only -0.3 to -3.0 kcal/mol* (Gibbs free energy of formation) above thermal noise. Hydrogen bonds are only second to the phosphodiester bonds in terms of contribution to DNA stability. The weakest hydrogen bond in DNA is -0.9 kcal/mol (AA), whereas thermal noise is about +0.6 kcal/...
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