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Covering All the Bases in Genetics: Simple Shorthands and Diagrams for Teaching Base Pairing to Biology Undergraduates

    Author: Sergei Kuchin1
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    Affiliations: 1: Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 19 May 2011
    • †Supplemental material available at http://jmbe.asm.org
    • *Corresponding author. Mailing address: Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave., Milwaukee, WI 53211. Phone: (414) 229-3135. Fax: (414) 229-3926. E-mail: [email protected].
    • Copyright © 2011, American Society for Microbiology
    Source: J. Microbiol. Biol. Educ. May 2011 vol. 12 no. 1 64-66. doi:10.1128/jmbe.v12i1.267
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    Abstract:

    Explaining base pairing is an important element in teaching undergraduate genetics. I propose a teaching approach that aims to close the gap between the mantra “A pairs with T, and G pairs with C” and the “intimidating” chemical diagrams. The approach offers a set of simple “shorthands” for the key bases that can be used to quickly deduce all canonical and wobble pairs that the students need to know. The approach can be further developed to analyze mutagenic mismatch pairing.

References & Citations

1. Crick FH 1966 Codon–anticodon pairing: the wobble hypothesis J Mol Biol 19 548 555 10.1016/S0022-2836(66)80022-0 5969078 http://dx.doi.org/10.1016/S0022-2836(66)80022-0
2. Lee JC, Gutell RR 2004 Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs J Mol Biol 344 1225 1249 10.1016/j.jmb.2004.09.072 15561141 http://dx.doi.org/10.1016/j.jmb.2004.09.072
3. Sashital DG, Venditti V, CG Angers, Cornilescu G, Butcher SE 2007 Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human RNA 13 328 338 10.1261/rna.418407 17242306 1800520 http://dx.doi.org/10.1261/rna.418407
4. Theimer CA, Finger LD, Trantirek L, Feigon J 2003 Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA Proc Natl Acad Sci 100 449 454 10.1073/pnas.242720799 12525685 141015 http://dx.doi.org/10.1073/pnas.242720799

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/content/journal/jmbe/10.1128/jmbe.v12i1.267
2011-05-19
2020-10-25

Abstract:

Explaining base pairing is an important element in teaching undergraduate genetics. I propose a teaching approach that aims to close the gap between the mantra “A pairs with T, and G pairs with C” and the “intimidating” chemical diagrams. The approach offers a set of simple “shorthands” for the key bases that can be used to quickly deduce all canonical and wobble pairs that the students need to know. The approach can be further developed to analyze mutagenic mismatch pairing.

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Author and Article Information

  • Published 19 May 2011
  • †Supplemental material available at http://jmbe.asm.org
  • *Corresponding author. Mailing address: Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave., Milwaukee, WI 53211. Phone: (414) 229-3135. Fax: (414) 229-3926. E-mail: [email protected].
  • Copyright © 2011, American Society for Microbiology

Figures

Covering All the Bases in Genetics: Simple Shorthands and Diagrams for Teaching Base Pairing to Biology Undergraduates
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Citation: Kuchin S. 2011. Covering all the bases in genetics: simple shorthands and diagrams for teaching base pairing to biology undergraduates . J. Microbiol. Biol. Educ. 12(1):64-66 doi:10.1128/jmbe.v12i1.267
/content/jmbe/10.1128/jmbe.v12i1.267.f1-jmbe-12-1-64
FIGURE 1

Derivation of the shorthands. Each shorthand represents the one-letter base name followed by the list of atoms participating in hydrogen bonding. Only the standard pairing faces of the bases are shown.

jmbe/12/1/jmbe-12-1-64f1_thmb.gif
jmbe/12/1/jmbe-12-1-64f1.gif
Image of FIGURE 1

Click to view

FIGURE 1

Derivation of the shorthands. Each shorthand represents the one-letter base name followed by the list of atoms participating in hydrogen bonding. Only the standard pairing faces of the bases are shown.

Source: J. Microbiol. Biol. Educ. May 2011 vol. 12 no. 1 64-66. doi:10.1128/jmbe.v12i1.267
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FIGURE 2

Regular Watson-Crick and wobble pairs: Watson-Crick pairs (a); Wobble pairs (b). Dotted lines represent hydrogen bonds. PU = purine; PY = pyrimidine.

jmbe/12/1/jmbe-12-1-64f2_thmb.gif
jmbe/12/1/jmbe-12-1-64f2.gif
Image of FIGURE 2

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FIGURE 2

Regular Watson-Crick and wobble pairs: Watson-Crick pairs (a); Wobble pairs (b). Dotted lines represent hydrogen bonds. PU = purine; PY = pyrimidine.

Source: J. Microbiol. Biol. Educ. May 2011 vol. 12 no. 1 64-66. doi:10.1128/jmbe.v12i1.267
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v12i1.267.f3-jmbe-12-1-64
FIGURE 3

Additional wobble pairs: Pairing diagrams (a); Pairing configurations for two consecutive UU pairs in stem 1 of yeast U2 snRNA (b). Dotted lines represent hydrogen bonds. PU = purine; PY = pyrimidine.

jmbe/12/1/jmbe-12-1-64f3_thmb.gif
jmbe/12/1/jmbe-12-1-64f3.gif
Image of FIGURE 3

Click to view

FIGURE 3

Additional wobble pairs: Pairing diagrams (a); Pairing configurations for two consecutive UU pairs in stem 1 of yeast U2 snRNA (b). Dotted lines represent hydrogen bonds. PU = purine; PY = pyrimidine.

Source: J. Microbiol. Biol. Educ. May 2011 vol. 12 no. 1 64-66. doi:10.1128/jmbe.v12i1.267
Download as Powerpoint

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