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APPENDIX 1: Structures of Base Pairs Involving at Least Two Hydrogen Bonds

Mark E. Burkard, Douglas H. Turner, Ignacio Tinoco, Jr.


The structures of 29 possible base pairs that involve at least two hydrogen bonds are given in Figures 1–5 (for further descriptions, see Saenger, in Principles of nucleic acid structure, p. 120. Springer-Verlag [1984]). A base pair that is not a Watson-Crick pair or a G·U wobble pair is called a base-base mismatch, or an internal loop of two nucleotides. All the base pairs can be divided into two classes: normal and flipped. The normal class is defined by the arrangement of the Watson-Crick base pairs. The hydrogen bonding occurs for nucleotides with antiparallel strands and anti orientation of the bases relative to the ribose rings. The 11 base pairs that can be made with this same arrangement of nucleotides are called normal; they are shown in Figures 1 and 2. The remaining 18 base pairs require that one of the bases be flipped (inverted) by either reversing the direction of the strand or by switching the base from anti to syn. (Figs. 3–5). Normal base-base mismatches are found more often than flipped mismatches.

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