Journal of Microbiology & Biology Education, Vol 12, No 1 (2011)

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

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

Sergei Kuchin
Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211.

INTRODUCTION

Explaining base pairing is an important element in teaching undergraduate genetics. However, the existing teaching approaches rely on complex diagrams and often fail to elevate the students’ perception of the material above its passive acceptance. Many students enter the course already knowing that “A pairs with T, and G pairs with C,” and finish the course with only marginal conceptual improvement. Even the most diligent students who memorize the base structures by heart often remain unsure how to apply this knowledge on their own.

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.

PROCEDURE

Bases expressed as shorthands

Figure 1 shows the idea behind the shorthands. Each represents the one-letter base name followed by the atoms involved in hydrogen bonding, in order of their appearance at the carbon-nitrogen- carbon (CNC) pairing face. In the case of guanine, for example, the key atoms are O, H, and H (at C6, N1, and C2, respectively), yielding the shorthand GOHH. The same logic yields AHN for A, IOH for I, CHNO for C, TOHO for T, and UOHO for U. The correct name of the base in inosine (which is a nucleoside) is hypoxanthine; however, for consistency with the nucleic acid nomenclature, the shorthand IOH is more appropriate (and less confusing) than HOH. The shorthands are easy to memorize, and pronunciation is a matter of personal preference.

 


 

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.

If the course covers mutagenic events such as base tautomerization and deamination, it may be advantageous to practice using the memorized shorthands for reverse-engineering the chemical structures of the CNC pairing faces. This could be done on the drawing board. When doing so, note that unlike in the pyrimidines, the bottom carbon of the CNC face in the purines (C2) has a double bond (Fig. 1), linking it to N3 (N3 is not shown).

Watson-Crick pairs

The shorthands offer a compact visual tool to better grasp the essence of the pairing rules. Figure 2(a) shows how the shorthands align to produce the Watson-Crick (WC) pairs, with hydrogen bonds running horizontally if the shorthands are spelled out as columns. In the AT and AU pairs, the last O of TOHO and UOHO remains unpaired, but this oxygen is important for the wobble-pairing properties of T and U (see below).

 


 

FIGURE 2 Regular Watson-Crick and wobble pairs: Watson- Crick pairs (a); Wobble pairs (b). Dotted lines represent hydrogen bonds. PU = purine; PY = pyrimidine.

Figure 2(a) also includes the IC pair. Although IC is clearly a WC pair, it is often perceived as a “wobble” as part of the trio IC, IU, and IA. However, only IU and IA in this trio are true wobbles from the structural point of view.

Textbook wobble pairs

Crick’s wobble hypothesis (1) is central to understanding the genetic code, yet textbooks typically present the wobble rules in a tabular form, without a detailed explanation. This is understandable, since using the same type of diagrams as for the WC pairs could only add to the students’ frustration without adding much to active understanding. In contrast, the shorthands work well for demonstrating the key translational wobbles — GU, IU, and IA (Fig. 2(b)). GU and IU are purine-pyrimidine pairs, but the hydrogen bonds are slanted rather than horizontal, twisting the bases out of the nose-to-nose alignment (the mutagenic GT wobble in DNA looks similar to GU and is not shown). In the AI pair, the hydrogen bonds run horizontally, but it is a purine-purine (wide) pair.

Non-textbook wobble pairs

Armed with the shorthands, students could discover additional wobble pairs in a matter of minutes with or without the instructor’s prompt. Figure 3(a) shows the GA, CU and UU pairs that can form via the standard faces. (Discussion of pairing configurations that involve unconventional pairing faces or fewer than two hydrogen bonds is outside the scope of this paper.) Together, the wobbles in Figs. 2(b) and 3(a) account for all wobble pairs considered by Crick in his seminal 1966 article (1). The non-textbook wobbles deviate from the WC pairs in more than one respect. GA is a purine-purine (wide) pair with an additional complication posed by the unpaired amino group at C2 of G (1). CU is a “close” (1) pyrimidine-pyrimidine pair with juxtaposed C2 carbonyl oxygens. The UU pair is both close and twisted. These pairs do, however, make a significant contribution to secondary structure formation in important RNA molecules such as ribosomal RNAs (2).

 


 

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.

The UU pair may be interesting for advanced in-class discussion, since there are two pairing configurations. If a UU pair is considered in isolation, the two configurations are identical and simply represent two views of the same object — from above and from below. However, if each U is considered in its own sequence context, these configurations are distinct. In this regard, the U2 small nuclear RNA (U2 snRNA) that is part of the yeast spliceosome offers a good example to analyze (Fig. 3(b)). Stem 1 of U2 snRNA contains two consecutive UU pairs whose structures have been resolved (3). The pair between U12 and U23 involves the C4 carbonyl oxygen of U12 and C2 carbonyl oxygen of U23, corresponding to the first UU configuration in Fig. 3(a). The adjacent pair formed by U11 and U24 corresponds to the second UU configuration. Since the hydrogen-bonding configurations of two adjacent UU pairs do not automatically alternate in this manner (4), the above pattern is one of as many as four configurations theoretically possible for a tandem of two UU pairs. The instructor may wish to discuss how the presence of one or more UU pairs could, in principle, contribute to the conformational diversity of a single RNA species.

CONCLUSION

In addition to canonical and wobble pairing, the shorthand approach can be further developed to explain mutagenic pairing. For example, the Supplemental Materials present an analysis of the mutagenic effects of base tautomerization and deamination. In summary, I hope that the proposed approach will ensure that more students gain a better understanding of base pairing — an active understanding that will help during the course and persist long after the textbook is closed.

SUPPLEMENTARY MATERIALS

Appendix: Analysis of Mutagenic Effects of Base Tautomerization and Deamination.

ACKNOWLEDGMENTS

I acknowledge support from NSF grant MCB-0818837. I thank my students LaKisha Barrett, Abigail Navarro, Vera Patskevich, and Marcin Maziarz, and my colleagues Graham Moran, Mark McBride, Daad Saffarini, and Marianna Orlova for encouragement and helpful comments. No potential conflict exists.

REFERENCES

1 Crick, F. H. 1966. Codon–anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19:548–555.
cross-ref  pubmed  

2 Lee, J. C., and R. R. Gutell. 2004. Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs. J. Mol. Biol. 344:1225–1249.
cross-ref  pubmed  

3 Sashital, D. G., V. Venditti, C. G. Angers, G. Cornilescu, and S. E. Butcher. 2007. Structure and thermodynamics of a conserved U2 snRNA domain from yeast and human. RNA 13:328–338.
cross-ref  pubmed  pmc  

4 Theimer, C. A., L. D. Finger, L. Trantirek, and J. Feigon. 2003. Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA. Proc. Natl. Acad. Sci. 100:449–454.
cross-ref  pubmed  pmc  


* 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: skuchin@uwm.edu.

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Supplemental material available at http://jmbe.asm.org ( Return to Text )


DOI: 10.1128/jmbe.v12i1.267
Journal of Microbiology & Biology Education, May 2011
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