Some say that DNA is denatured only at basic pH. And some say at both acidic and basic pH. So I want to know clearly why and how if DNA is also denatured by basic pH.
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2 Answers
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Alkaline denaturation neutralize the charge of acids but also cause hydrolysis of bases upon prolonged treatment. Strong bases will raise pH until the H+ shared between the N-base electronegative centers (N-H and O=) is stripped from the H-bond, effectively breaking them.
Organic solvents such as dimethyl sulfoxide and formamide, or high pH, could break the hydrogen bonding between DNA strands too. Low salt concentration could also denature DNA double-strands by removing ions that stabilize the negative charges on the two strands from each other.
Low pH (less than pH 1): both RNA and DNA hydrolyze (phosphodiester bonds break and the bases break off).
High pH (greater than pH 11): RNA hydrolyzes, DNA will denature but the phosphodieser backbone remains intact.
[salt] Tm is sensitive to Na+ concentration. Na+ acts to shield the negative charges of the sugar-phosophate backbone from interacting with one another. The repulsion between the negatively charged phosphate backbones is the major force destabilizing the double helix, therefore increasing Na+ concentration increases helix stability and decreasing Na+ concentration decreases helix stability.
References:
http://faculty.tru.ca/dnelson/courses/biol335/335notes/3recdna/4-hybrization/recDNA3a.html
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1367631/pdf/biophysj00681-0002.pdf
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$\begingroup$ So could u please explain how denaturation differs from hydrolysis? $\endgroup$– Aung TCommented Feb 8, 2016 at 15:36
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2$\begingroup$ @AungT As far as i know with the term denaturation is related to the change from a double strand DNA (dsDNA) to a single strand DNA (ssDNA) due to breakage of hydrogen bonds (it could be caused by heat), while in hydrolysis there is a degradation of the strands backbone eg phosphodiesterases enzymes hydrolyse the phosphodiester bond between different nucleotides. $\endgroup$– MauroMCommented Feb 9, 2016 at 9:57
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Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure and secondary structure which is present in their native state, by application of some external stress or compound such as a strong acid or base, a concentrated inorganic salt, an organic solvent (e.g., alcohol or chloroform), radiation or heat
The denaturation of nucleic acids such as DNA due to high temperatures is the separation of a double strand into two single strands, which occurs when the hydrogen bonds between the strands are broken.
DNA Hydrolysis is a chemical method of DNA denaturation.DNA hydrolysis is the breaking of DNA through the addition of water. It can be done in several fashions; enzymatic (exonucleases)or chemicals (acid).
In general, hydrolysis is defined as the cleavage of chemical bonds by the addition of water
References:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806061/
file:///C:/Users/user/Downloads/9783540201120-c1.pdf
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$\begingroup$ So hydrolysis is also a kind of denaturation? The difference is just the method used? $\endgroup$– Aung TCommented Feb 9, 2016 at 2:19