SIMPLE DOUBLE HELICAL MODELS
On the chemical level, each bead represents a nucleotide. A nucleotide contains a sugar, phosphate group, and nitrogenous base. Many nucleotides connect together like beads on a string to create a polynucleotide chain. Each chain is twisted in a spiral or corkscrew shape. The two chains twist around one another to form a double helix.
The simple helix with 2 bead colors model shows double stranded DNA. Each chain is a different color because each of the single strands of DNA is different. The use of a sinlge color of beads allows easier visualization of the individual spiral chains.
top photo caption: Two left-handed chains (1 yellow and 1 blue), each with 35 beads, form a double stranded helix. Optionally, one can make a similar right-handed double helical model.
Using four colors of beads, this simple helix model shows each polynucleotide chain consists of four different nucleotides. The order of the colored beads on the two chains is not identical. One uses Watson-Crick base-pairing rules to form complimentary base pairs.
second photo caption: Two right-handed chains, each with a specifically arranged color sequence of 30 beads, illustrate the 3D structure of double stranded B-DNA for the oxytocin gene.
Optionally, any random nucleotide sequence can be illustrated on one strand with the correct matching bases incorporated on the second strand.
DNA DOUBLE HELICAL MODELS
These models show more chemical detail than the simple helical models described above. Here, the beads represent the sugars held together by the string which represents the phosphate groups. Perpendicular to these two sugar-phosphate backbones, are parallel "steps" consisting of N-base pairs. The number of steps per spiral turn and the turning direction of the spirals is used to classify different forms of DNA.
Different colors of beads (in the third photo, red and green) are used to show the two different sugar-phosphate backbones. The 30 steps are decorated with colored rectangles and/or Braille letters to represent the complimentary N-base pair sequence found in a double stranded DNA molecule for oxytocin.
A-DNA models: Two right-handed helices, with 11-12 steps per turn, create a double helical form of A-DNA (third photo). Alpha or A-DNA exists in nature. It forms during the dehydration process to prepare DNA for crystallographic studies.
B-DNA models:Two right-handed helices, with 10 steps per turn, create a double helical form of B-DNA. Beta or B-DNA is also known as Watson-Crick DNA. The polynucleotide sequence codes for a physiological useful product. A DNA sequence that usually codes for a protein is referred to as a gene.
The B-DNA model, in the fourth photo, uses different colored pipe cleaners to show the correct number of hydrogen bonds between the N-base pairs. Stars at the end of the sugar-phosphate backbones point in opposite directions to indicate the 3' to 5' direction of each polynucleotide chain.
Z-DNA models: Two left-handed helices, with 12 steps per turn, create a double helical form of Z-DNA (top photo). Z-DNA forms when the DNA sequence has many GC base pairs. The GC base pairs are shorter than AT base pairs. Thus the true 3D structure of double stranded Z-DNA would form a zig zag around the central axis. Presently a better 3D visual model is being designed to illustrate this Z shape. The exact role and function od Z-DNA is still being explored.
The visually impaired or blind can feel the shape of the helixes, the N-base holding steps, and read the DNA sequence by taping Braille code on the N-base pair steps.
The bottom photo shows a tactile B-DNA model without any Braille code. Here the butterfly bead (representing A, the bicyclic N-base) pairs with a ridged bead (T, a N-base with only one chemical ring). Likewise, the heart shaped bead (representing the N-base G) pairs with the smooth bead (representing the N-base C). The direction of the beads is antiparallel to indicate the polarity of the two polynucleotide chains.
These sturdy, inexpensive models with 30 base pairs measure 2.5 inches x 10.5 inches. They can be made in about 3 hours. The models can be varied to show more or less chemical detail to match the grade level of the students. The variablity of this model to show different levels of structural and chemical detail is discussed in the January 2005 issue, p. 79-84 of the Journal of Chemical Education.
More information about these copyrighted models and requests to order reprints, instruction and supply kits, completed models, and classroom workshops. Inquire via DNA3Dmodels at hotmail dot com.
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"All material presented is copyrighted by S. Cady 2004."