Editing Denaturation (biochemistry) (section)

=== Biologically-induced denaturation ===
[[Image:DNA Denaturation.png|thumb|DNA denaturation occurs when hydrogen bonds between base pairs are disturbed.]]
The [[non-covalent interactions]] between [[Antiparallel (biochemistry)|antiparallel strands]] in DNA can be broken in order to "open" the [[Nucleic acid double helix|double helix]] when biologically important mechanisms such as DNA replication, transcription, [[DNA repair]] or protein binding are set to occur.<ref name="1st">{{cite journal|last2=Destainville|first2=Nicolas|last3=Manghi|first3=Manoel|date=21 January 2015|title=DNA denaturation bubbles: Free-energy landscape and nucleation/closure rates|journal=The Journal of Chemical Physics|volume=142|issue=3|pages=034903|doi=10.1063/1.4905668|pmid=25612729|last1=Sicard|first1=François|arxiv=1405.3867|bibcode=2015JChPh.142c4903S|s2cid=13967558}}</ref> The area of partially separated DNA is known as the denaturation bubble, which can be more specifically defined as the opening of a DNA double helix through the coordinated separation of base pairs.<ref name="1st" />

The first model that attempted to describe the [[Nucleic acid thermodynamics|thermodynamics]] of the denaturation bubble was introduced in 1966 and called the Poland-Scheraga Model. This model describes the denaturation of DNA strands as a function of [[temperature]]. As the temperature increases, the hydrogen bonds between the base pairs are increasingly disturbed and "denatured loops" begin to form.<ref>Lieu, Simon. "The Poland-Scheraga Model." (2015): 0-5. Massachusetts Institute of Technology, 14 May 2015. Web. 25 Oct. 2016.</ref> However, the Poland-Scheraga Model is now considered elementary because it fails to account for the confounding implications of [[Nucleic acid sequence|DNA sequence]], chemical composition, [[stiffness]] and [[torsion (mechanics)|torsion]].<ref>Richard, C., and A. J. Guttmann. "Poland–Scheraga Models and the DNA Denaturation Transition." ''Journal of Statistical Physics'' 115.3/4 (2004): 925-47. Web.</ref>

Recent thermodynamic studies have inferred that the lifetime of a singular denaturation bubble ranges from 1 microsecond to 1 millisecond.<ref name="2nd">{{cite journal|last2=Libchaber|first2=Albert|last3=Krichevsky|first3=Oleg|date=1 April 2003|title=Bubble Dynamics in Double-Stranded DNA|journal=Physical Review Letters|volume=90|issue=13|pages=138101|doi=10.1103/physrevlett.90.138101|pmid=12689326|last1=Altan-Bonnet|first1=Grégoire|s2cid=1427570|bibcode=2003PhRvL..90m8101A}}</ref> This information is based on established timescales of DNA replication and transcription.<ref name="2nd" /> Currently,{{when|date=December 2017}} biophysical and biochemical research studies are being performed to more fully elucidate the thermodynamic details of the denaturation bubble.<ref name="2nd" />