Hybidization Technology Denaturing Nucleic Acids |
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Two major molecular interactions hold the double helix together: 1) H-Bonds between complementary bases 2) Stacking of the hydrophobic N-bases down the center of the helix In opposition to these stabilizing interactions is the electrostatic repulsion of There are two basic approaches to denaturing double-stranded DNA Chemical denaturants can be divided into three classes
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pH Bases like NaOH raise the pH until the H+ shared between the N-base electronegative centers ( N-H and O= ) is stripped from the H-bond. Loss of H-bonds between two complementary strands results in strand separation.
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Competitive Denaturants Compounds like urea and formaldehyde contain functional groups that can form H-bonds with the electronegative centers of the N-bases. At high concentrations (8M urea or 70% formamide) of the denaturant, the competition for H-bonds favors interactions between the denaturant and the N-bases rather than between complementary bases. As a result, the two strands separate.
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Covalent Modification Denaturants Reactive aldehydes like formaldehyde and glyoxal can covalently modify the electronegative centers of the N-bases and thereby block the formation of H-bonds between complementary bases. Covalent modification is reversible. |
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Before leaving the topic of DNA denaturation, lets look a little more closely at
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As the temperature rises, the kinetic motion of molecules in solution increases.
The initial A260 is stable until, over an interval of approximately 5 degrees C, the A260 suddenly increases by approximately 40%. This increase in absorbance is referred to as the The hyperchromic shift is due to the melting of the double helix into two single strands. The increased rotational freedom of the N-bases on strand separation accounts for the observed increase in absorbance. The melting temperature, or Tm, is the temperature at the midpoint of the hyperchormic shift as shown to the left.
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Three main factors affect the melting temperature. The GC content of the nucleic acid sample. [salt] DNA hybrid length
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The quantitative analyses of the melting behaviour of many naturally occuring DNAs is summarized in the formula (note: this formula describes the Tm of long DNA hybrids) | |||||||||||||||||||||||||||||
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note that the % GC term only holds over a limited range (45 to 75%) as does the salt term ( 0.01 to 0.4 M ). note that the salt term is negative in this range.
For short DNA hybrids, the 'zipper effect' alters the formula to
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Renaturation |
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