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In addition to the canonical pairing, some conditions can also favour base-pairing with alternative base orientation, and number and geometry of hydrogen bonds. These pairings are accompanied by alterations to the local backbone shape.
The most common of these is the [[wobble base pair]]ing that occurs between [[tRNA]]s and [[mRNA]]s at the third base position of many [[codon]]s during [[Transcription (biology)|transcription]]<ref>{{Cite journal|last=Murphy|first=Frank V|last2=Ramakrishnan|first2=V|date=2004-11-21|title=Structure of a purine-purine wobble base pair in the decoding center of the ribosome|url=http://dx.doi.org/10.1038/nsmb866|journal=Nature Structural & Molecular Biology|volume=11|issue=12|pages=1251–1252|doi=10.1038/nsmb866|issn=1545-9993}}</ref> and during the charging of tRNAs by some [[Aminoacyl tRNA synthetase|tRNA synthetases]].<ref>{{Cite journal|last=Vargas-Rodriguez|first=Oscar|last2=Musier-Forsyth|first2=Karin|date=June 2014|title=Wobble puts RNA on target|url=https://www.nature.com/articles/nature13502|journal=Nature|language=en|volume=510|issue=7506|pages=480–481|doi=10.1038/nature13502|issn=1476-4687}}</ref> They have also been observed in the secondary structures of some RNA sequences.<ref>{{Cite journal|last=Garg|first=Ankur|last2=Heinemann|first2=Udo|date=2017-11-09|title=A novel form of RNA double helix based on G·U and C·A+wobble base pairing|url=http://dx.doi.org/10.1261/rna.064048.117|journal=RNA|volume=24|issue=2|pages=209–218|doi=10.1261/rna.064048.117|issn=1355-8382|pmc=5769748}}</ref>
Additionally, [[Hoogsteen base pair]]ing (typically written as A•U/T and G•C) can exist in some DNA sequences (e.g. CA and TA dinucleotides) in dynamic equilibrium with standard Watson–Crick pairing.<ref name="Nikolova2">{{cite journal|author1=Evgenia N. Nikolova|author2=Eunae Kim|author3=Abigail A. Wise|author4=Patrick J. O'Brien|author5=Ioan Andricioaei|author6=Hashim M. Al-Hashimi|year=2011|title=Transient Hoogsteen base pairs in canonical duplex DNA|journal=Nature|volume=470|issue=7335|pages=498–502|bibcode=2011Natur.470..498N|doi=10.1038/nature09775|pmc=3074620|pmid=21270796}}</ref> They have also been observed in some protein–DNA complexes.<ref name="Aishima">{{cite journal|author=Jun Aishima, Rossitza K. Gitti, Joyce E. Noah, Hin Hark Gan, [[Tamar Schlick]], Cynthia Wolberger|year=2002|title=A Hoogsteen base pair embedded in undistorted B‐DNA|journal=Nucleic Acids Res|volume=30|issue=23|pages=5244–5252|doi=10.1093/nar/gkf661|pmc=137974|pmid=12466549}}</ref>
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