Editing Denaturation (biochemistry) (section)

=== Denaturation due to chemical agents ===
[[File:DNA Denaturation by Formamide.png|thumb|Formamide denatures DNA by disrupting the hydrogen bonds between base pairs. Orange, blue, green, and purple lines represent adenine, thymine, guanine, and cytosine respectively. The three short black lines between the bases and the formamide molecules represent newly formed hydrogen bonds.]]
With [[polymerase chain reaction]] (PCR) being among the most popular contexts in which DNA denaturation is desired, heating is the most frequent method of denaturation.<ref name=":02">{{cite journal|date=2014|title=Characterization of denaturation and renaturation of DNA for DNA hybridization|journal=Environmental Health and Toxicology|volume=29|doi=10.5620/eht.2014.29.e2014007|pmid=25234413|pmc=4168728|last1=Wang|first1=X|page=e2014007}}</ref> Other than denaturation by heat, nucleic acids can undergo the denaturation process through various chemical agents such as [[formamide]], [[guanidine]], [[sodium salicylate]], [[dimethyl sulfoxide]] (DMSO), [[propylene glycol]], and [[urea]].<ref name="ReferenceA">{{cite journal|date=1961|title=Denaturation of deoxyribonucleic acid by formamide|volume=51|issue=1|pages=91013–7|last1=Marmur|first1=J|journal=Biochimica et Biophysica Acta|doi=10.1016/0006-3002(61)91013-7|pmid=13767022}}</ref> These chemical denaturing agents lower the melting temperature (T<sub>m</sub>) by competing for hydrogen bond donors and acceptors with pre-existing [[nitrogenous base]] pairs. Some agents are even able to induce denaturation at room temperature. For example, [[Alkalinity|alkaline]] agents (e.g. NaOH) have been shown to denature DNA by changing [[pH]] and removing hydrogen-bond contributing protons.<ref name=":02"/> These denaturants have been employed to make [[Temperature gradient gel electrophoresis|Denaturing Gradient Gel Electrophoresis gel]] (DGGE), which promotes denaturation of nucleic acids in order to eliminate the influence of nucleic acid shape on their [[Gel electrophoresis of nucleic acids|electrophoretic]] mobility.<ref>{{cite web|url=https://www.nationaldiagnostics.com/electrophoresis/article/denaturing-polyacrylamide-gel-electrophoresis-dna-rna|title=Denaturing Polyacrylamide Gel Electrophoresis of DNA & RNA|website=Electrophoresis|date=15 August 2011 |publisher=National Diagnostics|access-date=13 October 2016}}</ref>

==== Chemical denaturation as an alternative ====
The [[Optical rotation|optical activity]] (absorption and scattering of light) and hydrodynamic properties ([[Rotational diffusion|translational diffusion]], [[sedimentation coefficient]]s, and [[rotational correlation time]]s) of [[formamide]] denatured nucleic acids are similar to those of heat-denatured nucleic acids.<ref name="ReferenceA"/><ref>{{cite journal|last2=Bustamante|first2=C|last3=Maestre|first3=M|date=1980|title=The Optical Activity of Nucleic Acids and their Aggregates|journal=Annual Review of Biophysics and Bioengineering|volume=9|issue=1|pages=107–141|doi=10.1146/annurev.bb.09.060180.000543|pmid=6156638|last1=Tinoco|first1=I}}</ref><ref>{{cite journal|date=2002|title=Calculation of hydrodynamic properties of small nucleic acids from their atomic structure|journal=Nucleic Acids Research|volume=30|issue=8|pages=1782–8|doi=10.1093/nar/30.8.1782|pmid=11937632|pmc=113193|last1=Fernandes|first1=M}}</ref> Therefore, depending on the desired effect, chemically denaturing DNA can provide a gentler procedure for denaturing nucleic acids than denaturation induced by heat. Studies comparing different denaturation methods such as heating, beads mill of different bead sizes, probe [[sonication]], and chemical denaturation show that chemical denaturation can provide quicker denaturation compared to the other physical denaturation methods described.<ref name=":02"/> Particularly in cases where rapid renaturation is desired, chemical denaturation agents can provide an ideal alternative to heating. For example, DNA strands denatured with [[Alkalinity|alkaline agents]] such as [[Sodium hydroxide|NaOH]] renature as soon as [[Phosphate-buffered saline|phosphate buffer]] is added.<ref name=":02" />

==== Denaturation due to air ====
Small, [[Electronegativity|electronegative]] molecules such as [[nitrogen]] and [[oxygen]], which are the primary gases in [[Atmosphere of Earth|air]], significantly impact the ability of surrounding molecules to participate in [[hydrogen bond]]ing.<ref name=":1">{{cite journal|last2=Schoeffler|first2=G.|last3=McGlynn|first3=S. P.|date=July 1985|title=The effects of selected gases upon ethanol: hydrogen bond breaking by O and N|journal=Canadian Journal of Chemistry|volume=63|issue=7|pages=1864–1869|doi=10.1139/v85-309|last1=Mathers|first1=T. L.|doi-access=free}}</ref> These molecules compete with surrounding hydrogen bond acceptors for hydrogen bond donors, therefore acting as "hydrogen bond breakers" and weakening interactions between surrounding molecules in the environment.<ref name=":1" /> [[Antiparallel (biochemistry)|Antiparellel strands]] in DNA double helices are non-covalently bound by hydrogen bonding between base pairs;<ref>{{cite book|title=Lehninger principles of biochemistry|date=2008|publisher=W.H. Freeman|isbn=9780716771081|edition=5th|location=New York|last1=Cox|first1=David L. Nelson, Michael M.|url-access=registration|url=https://archive.org/details/lehningerprincip00lehn_1}}</ref> nitrogen and oxygen therefore maintain the potential to weaken the integrity of DNA when exposed to air.<ref name="DNA Air">{{cite journal|last2=Schoeffler|first2=G.|last3=McGlynn|first3=S. P.|date=1982|title=Hydrogen-bond breaking by O/sub 2/ and N/sub 2/. II. Melting curves of DNA|doi=10.2172/5693881|last1=Mathers|first1=T. L.|osti=5693881|url=https://digital.library.unt.edu/ark:/67531/metadc1089485/m2/1/high_res_d/5693881.pdf |archive-url=https://web.archive.org/web/20180724122925/https://digital.library.unt.edu/ark:/67531/metadc1089485/m2/1/high_res_d/5693881.pdf |archive-date=2018-07-24 |url-status=live}}</ref> As a result, DNA strands exposed to air require less force to separate and exemplify lower [[Nucleic acid thermodynamics|melting temperatures]].<ref name="DNA Air" />