Modeling the Dynamics of Gel Electrophorresis in the High School Classroom

Abstract

G el electrophoresis, used by geneticists and forensic experts alike, is an immensely popular technique that utilizes an electric field to separate molecules and proteins by size and charge. At the microscopic level, a dye or complex protein like DNA is passed through agarose, a gelatinous three-dimensional matrix of pores and nano-sized tunnels. When forced through a maze of holes, the molecule unravels, forming a long chain, slithering through the field of pores in a process colloquially coined "reputation." ' As a result, the smaller molecules travel farther through the gel when compared to molecules of larger molecular weight. This highly effective "molecular sieve" provides consistent data and allows scientists to compare similar sequences of DNA base pairs in a routine fashion.^ When performed at the high school level, gel electrophoresis provides students the opportunity to learn about a contemporary lab technique of great scientific relevance. Doing real science certainly excites students and motivates them to learn more.In many cases, students learn how to use a micropipette, create an agarose gel, and (if all goes to plan) have the opportunity to actually see dyes move across the gel. Instructors typically provide a qualitative explanation (the electric field/ current moves the molecules; the smaller the molecule, the faster and farther it moves across the gel, for example) or an explanation that is beyond the scope ofthe class.A common misconception held by students (and instructors alike) is that the electric field provides a force that continuously accelerates a charged molecule across the gel; this explanation is correct to some extent, but fails to explain the role ofthe molecules drag force and subsequent terminal velocity.^ In gel electrophoresis, the drag force plays a dominant role in the early stages ofthe dynamics, and, as a consequence, the molecule has no net acceleration through the duration of the experiment. Such details are trivial when introducing this lab to students at a conceptual level. Excited as the students are, many are left with little to no opportunity to explore on their own, and ultimately follow a rigid sequence of procedures that does little more than verify that the process actually works.This paper proposes an inquiry-based method to investigate the robust dynamics of gel electrophoresis at the high school level. The goal is to motivate students to develop a working kinematic model and to test the model experimentally. Such an exercise works best in an AP Physics classroom, at a point in the course when concepts in electrostatics, specifically dealing with charges and electric forces and fields, are fresh in students' minds. Student misconceptionsPrior to performing the experiment, it is important to address three common misconceptions (dealing with electric fields and forces) held by students and how this exercise may address these problems. As outlined by Randall Knight:'* The three-dimensionality of electric fieldsStudents are introduced to the concept ofthe electric...

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

“…Gel electrophoresis was used in this study as an example for visualizing the interactions of the various tested salts and molecules with DNA. It is a commonly used, simple, economic biochemical technique, available in most biological, biochemical, and/or biophysical laboratories [95][96][97]. Advantages of using gel electrophoresis to read out the signals of DNA interactions with other molecules amplified by the bent DNA bows include the accessibility, simplicity, economy and broad range [96,97], which are expected to make the bent DNA bows broadly useful.…”

“…It is a commonly used, simple, economic biochemical technique, available in most biological, biochemical, and/or biophysical laboratories [95][96][97]. Advantages of using gel electrophoresis to read out the signals of DNA interactions with other molecules amplified by the bent DNA bows include the accessibility, simplicity, economy and broad range [96,97], which are expected to make the bent DNA bows broadly useful. On the other hand, we should emphasize that the key role of our bent DNA bows is to amplify the interactions and thus improve the sensitivity of the original detection methods and techniques in general; therefore, many existing techniques are expected to work well with the bent DNA molecules for measuring and visualizing the signals of DNA interactions with other molecules.…”