A Method for Building Simple Physical Models Representing the Structures of Nucleic Acids Giorgio Benedetti and Stefano Morosetti University of Rome I, P.le A. Moro 5, 00185 Rome, Italy
In recent years there has been an increase in the understanding of the structure of tertiary nucleic acids relative to the roles they play (1-8).Thus, the connection between function and structure is now accepted for nucleic acids, as it has been for proteins.
(9), this method is more general in its applications, and it uses materials that are more common. In fact. with this
The Need for an Improved Model The physical ball-and-stick or space-filling molecular models commercially available are expensive, and building the models requires a long time. Moreover, they ofien emphasize details rather than the overall shape of the molecule, which gives information about the topological consequences derived from the helical nature of nucleic acids. The two-dimensional representations poorly express three-dimensional information, except for expensive com~ u t e era~hics. r his-Paper presents a low-resolution model made from inex~ensiveand common materials. Nevertheless this kindAofmodel retains the essential features of a three-dimensional high-resolution structure. I t also retains the general topology, which is one of the most important determinants in the biological behavior of these molecules. The main features retained by this low-resolution construct include the following.
the helical axis position the ribose-phosphate backbone pathway distinguishabilitybetween minor and major grooves t h e angles that the base pairs form with the helical axis The models constructed with this method are better visual aids for exploring DNA topology than previous models. Compared to the method described by N. C. Seeman
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Fiaure 1. Secondarv structure of veast ~ R N A ' ~The ~ . numbers of the ~,~ bases from ;eaular to irreaular rwions- are indi~~~~- invoked ~- in crossino --cated. The nomenclature we use to represent helical fragmentsthat are colinearly stacked (T@-M and AC-D) is shown alongside the standard nomenclature for the stems (T@, M , AC, and D). ~
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Figure 2. The individual components used in building the modei.
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FtgLre 3. Lefrscnemat coiagram ofthe materia s show ng the letters JSed n the text to dent f y the components. Center: en argement of tne 'cha n connector 'c. R ght: en argement of elenrical conneclorse ana f Tne hole maae by a ar in f 1s .no cated n o ack
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and f i n Fig. 3). In our model these segments are 8.8 cm long, which represents the average radius (8.8 A) of the ribose-phosphate backbone for A RNA(l2). To avoid confusion we will use the terms 'side rod" and "helical rod" to distinguish the rods according to their function. The side rod is inserted into one seat of the electrical connector (f in Fig. 3) and locked with the screw. The other seat is pierced by a drill so that the helical rod can be inserted into the hole. Another electric conneetor (e in Fig. 3) is pierced parallel to the two screw seats and between them. The end of the side rod is inserted in the hole. Showing the Grooves
At least one support must be used for each crossing from a regular to a nonregular region of the chain. Thus, two supports at the end of a double-helical region will form a 18V angle on a plane perpendicular to the helical axis. Here the supports are brought one over the other, as much as the connectors allow, to show chains with symmetric grwves. This is how RNA actually appears when the ribose-phosphate backbone is considered in its wholeness. The thickness of the connectors causes one sunnort to be higher than the other. This is useful in two wais. It accuratelv reflects that the base pairs in RNAare not oemendicuiar to the helical axis, and it distinguishes det\;een shallow and deep grooves. In fact, when the right support is higher than the left one, we are looking at the deep moove of the RNA helix. For each helical region of the tRNAPhcwe used six supports. Thev corresuond to the followinn - nucleotide residues. 1,72,53,61,7,49in the TyrC-AAregion
Figure 4. The final model of yeast ~ R N A ~ " . method it is possible to build RNA models that contain both regular and irregular motifs (e.g., tRNA). Materials and Methods
In the following description of our method, we will use the order we followed when building our model of the tRNAPhemolecule,in which 1cm represents 1A. Low-resolution drawings for this molecule can be easily found in the literature (10,II); the number of stems and nucleotide residues can also be retrieved, as shown in the scheme of Figure 1. The materials used in this section are shown in Figure 2. The materials are shown schematicallyand identified by letters in Figure 3. The final yeast ~ R N A model '~~ is shown in Figure 4. The Helical Axes
First, dl the helical regions are assembled. Arod represents the helical axis (a in Fie. 3). Aluminum or iron metal are chosen to facilitate any iistortion of the axis. The rod diameter is 3-4 mm to prevent unwanted bending under the weight of the model. These rods are inserted into wooden bases (bin Fig. 3). It is preferable to use separate bases instead of a single board so that each helical region can move in relation to the others. For the tRNAPhewe prepared two axes: one for the acceptor stem and the !byC stem (TyC-AA), and one for the anticodon stem and the D stem (AC-D) (see Fig. 1). The Side Rods
Afterwards we built an appropriate number of side supports (c in Fig. 3) to connect the ribose-phosphate backbone to the helical axis. Each side support is constructed by inserting a rod (din Fig. 3) into electrical connectors (e 570
Journal of Chemical Education
13,22,31,39,*5,10 in the AC-D region
We use 2.8 cm for the repeat and 33' for the twist, values that were derived from fiber X-ray data diffraction. When more accurate data can be obtained from the literature, it can be used. We did this (13) for a more realistic model of ~RNA~~". The Backbone
A flexible rubber tube represents the ribose-phosphate backbone (e in Fie. 3,. The lennh of the tube is calculated by the nGber oflnucleotides 2 connects and by the sugar puckering (14). We used 6 cm for every base-base conneetion of the ARNA. This tube can represent regular as well as irregular fragments of the chain when an electric wire (h in Fig. 3) is inserted to support the desired shape. The ends of the electric wire (i in Fig. 3) are loeked into the electric connectors (e in Fig. 3) of the side supports. Constructing the Stems
We show, as an example, the building process for the TyC-AA fragment only. The AA and TyC stems are stacked to form a s i d e reeular double helix (W AA) that comprises twelvelbase pairs. l b o side connectors are located on the helical rod at a vertical distance of 11 x 2.8 cm and at an angle of 11 x 32.7' = 36W. They hold the "chain tube", which is 11x 6 cm long, corresponding to the tract of bases 61-72. The opposite strand is broken in two regular parts: an AAstem with bases 1-7, and a TI@stem with bases 4%53. They are made as above. The ends of the TyC& stem are a dangling end that comprises bases 72-76 and a hairpin loop that comprises bases 53-61. The corresponding tube fragments are adjusted in the position obsewed in the X-ray diffraction structure.
In the final step, the TI@-AA stem and the AC-D stem are put in the characteristic "La shape. The two stems are connected hv two irremlar fraements that com~risebases 7-10 and bases 4 4 4 c Here alio the fragments' are folded into the form that was found ex~erimentallv. Conclusions We think this approach to building models can be useful in teachine the bioloeical ~ r o o e r t i e sof ~olvnucleotide chains, reldted to three:dimkibnal foldin;. ~ e s i d e being s inexpensive and easy.to-build, the models made by method show great flexibil~tyin applirat~on.They can represents the following. RNA molecules DNA molecules
.regular or irregular structures, such as RNA loops and pseudohots (15) 'bent DNA, such as that found in nudeosome structures (161, obtained bv simdv bendinz the "helicalrod" differentaspects df the st&eture I t may be useful to point out this last characteristic. It is possible to represent the phosphate charges or the average backbone position, simply by adjusting the length of the
side supports. It is also possible to show a n average steric hindrance by using a tube of suitable diameter for the ribose-ohos~hatebackbone.
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Acknowledgment This work was supported by Minister0 Pubhlica Istruzione Grant 89 20902 337. Literature Cited I hugA .I. ~ p mn , urceh~ R ..vurun I W . : I Z ~ . ~ ~ X 2 E w m n . L . P . E . t h - m . . l P . K p m n . 1 C Norun I W , 3 2 4 , 2 W ' h 2 3 L m d r k R:YmofAy.C .I HuJ Chrm 19R1.259. 115;O 1156; slnden R R J clan, E ~ U SISM ~ 2 9 k ? n 1
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