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Biochem Molecular Bio Educ - 2017 - Zhang - A Comprehensive Experiment For Molecular Biology Determination of Single
Biochem Molecular Bio Educ - 2017 - Zhang - A Comprehensive Experiment For Molecular Biology Determination of Single
Xu Zhang†,‡*
A Comprehensive Experiment for Molecular Meng Shao‡
Biology: Determination of Single Nucleotide Lu Gao§
Yuanyuan Zhao§
Polymorphism in Human REV3 Gene Using Zixuan Sun†
Liping Zhou†
PCR–RFLP Yongmin Yan†,‡
Qixiang Shao‡
Wenrong Xu‡
Hui Qian†,‡*
Abstract
Laboratory exercise is helpful for medical students to under- extraction, gene amplification by PCR, and genotyping by
stand the basic principles of molecular biology and to learn RFLP. By combining these activities, the students are not
about the practical applications of molecular biology. We only able to learn a series of biotechniques in molecular biol-
have designed a lab course on molecular biology about the ogy, but also acquire the ability to link the learned knowl-
determination of single nucleotide polymorphism (SNP) in edge with practical applications. This comprehensive
human REV3 gene, the product of which is a subunit of DNA experiment will help the medical students improve the con-
polymerase f and SNPs in this gene are associated with ceptual understanding of SNP and the technical understand-
altered susceptibility to cancer. This newly designed experi- ing of SNP detection. V C 2017 by The International Union of
ment is composed of three parts, including genomic DNA Biochemistry and Molecular Biology, 45(4):299–304, 2017.
rose gel electrophoresis. The PCR products were visualized extracted genomic DNA. The genomic DNA prepared by
under a UV transilluminator and photographed. groups 1 and 10 had an OD260/230 value less than 2.0, indicat-
ing the contamination of organic compounds such as remain-
RFLP Analyses of PCR Products ing ethanol. To examine the integrity of the prepared genomic
The verified PCR products were used for restriction enzyme DNA, agarose gel electrophoresis was performed. As shown
digestion. The PCR products that contain an AGATCT in Fig. 2, the genomic DNA extracted by most groups could be
sequence from nucleotides 66–70 will be cut by restriction visualized on the gel under the UV illuminator. The prepared
endonuclease BglII while the PCR products containing a genomic DNA had a size around 15 kb, indicating the high
GGATCT sequence will not. The components of the restric- integrity of DNA samples. The signal intensities of different
tion enzyme digestion reaction were as follows: 10 lL PCR DNA samples are positively correlated to their concentrations
product, 2 lL 103 restriction enzyme digestion buffer, 0.5 lL as provided by NanoDrop 1000.
Concentration
Group ID (ng/lL) OD260/280 OD260/230
Agarose gel electrophoresis of genomic DNA Agarose gel electrophoresis of restriction enzyme
FIG 2 extracted from human peripheral blood samples. FIG 4 digested products. PCR products were digested
Genomic DNA was isolated from 200 lL of human with Bgl II overnight. As indicated, only one band
peripheral blood and dissolved in a final volume of (312 bp) was detected for GG alleles, two bands
50 lL of elution buffer. Five microliters of genomic (242 and 70 bps) for AA alleles, and three bands
DNA solution were loaded into the agarose gel for (312 bp, 242 bp, and 70 bps) for AG alleles. The
electrophoresis. M: DL15000 DNA marker; 1–12: genotypes of sample 1, 2, 3, and 4 were AG, 5, 6,
individual genomic DNA sample. and 7 were AA, 8 and 9 were GG.
shown in Fig. 4, only one band (312 bp) was detected for and detected the SNP by RFLP. This experiment is designed
GG alleles, two bands (242 bp and 70 bps) for AA alleles, as an exploratory experiment. The students will be encour-
and three bands (312 bp, 242 bp, and 70 bps) for AG aged to identify the genotypes of different individuals. These
alleles. activities will facilitate the students’ learning enthusiasm.
Thus, the students’ study results will be improved through
Outcome Evaluation Results this process of education.
The comparison of the examination scores showed a signif-
We found that the students performed better on the
icant difference between the students who participated in
exam questions specifically related to SNPs after the intro-
this lab course (80.1 6 6.1 points) and those who did not
duction of this lab course. The initial assessments of the
participate in this lab course (74.1 6 7.6 points), p 5 0.014 course indicate that the students were more satisfied with
(Fig. 5A). Analysis of the scores in the exam questions spe- it after the introduction of this lab course. The students
cifically related to SNPs revealed significant differences, express an increased interest in learning molecular biology
p 5 0.017 (Fig. 5B); the students who participated in this and performing research. The students also express an
lab course (18.4 6 3.4 points) performed better than those increased understanding of how SNPs are detected in the
who did not participate in this lab course (14.5 6 3.6 laboratory. They would be better able to describe the
points). results of SNP analyses. This study will be conducted in a
large group of students to verify group differences. A ques-
tionnaire will be designed to collect the feedback from the
Discussion students about this lab course [16]. Moreover, the influence
In this comprehensive experiment, we combined three activi- of this lab course on the long-term performance of the stu-
ties together to help medical students improve their under- dents will be assessed.
standing about SNP. We designed this comprehensive experi- This lab course provides a chance for the students to
ment based on the procedure of SNP detection. In general, better understand the clinical application of basic science.
10 teaching hours were used to complete this comprehensive After they completed these experiments, the students ana-
experiment. The students were divided into several groups lyzed the data and interpreted the results based on what
with two students in each subgroup. They used three teach- they had learned in the theory course. The students were
ing hours for genomic DNA isolation and characterization, stimulated to think, to discuss, and to solve problems. For
three teaching hours for PCR amplification, and four teach- instance, the students were asked to compare the tradition-
ing hours for RFLP analysis. By performing this experiment, al approaches for SNP detection with the advanced ones.
the students can better understand the principles of DNA Thus, the students had an improved understanding about
isolation, amplification, and detection. The students also SNP by both acquiring theoretical knowledge in the class-
receive trainings in multiple bio-techniques [2, 13–15]. room and obtaining practical knowledge in the laboratory
For medical students, it’s better to let them “see” the [4, 12]. The two types of knowledge are complementary,
SNP in the lab rather than “teach” the SNP in the classroom. and facilitate a more comprehensive understanding of the
In this lab course, the students isolated genomic DNA from topic. The additional active learning provided by the lab
human peripheral blood, amplified the target gene by PCR, experience (a completely different learning style from
passive learning in classroom lectures or while reading) is [2] Zhang, B. Wang, Y. Xu, X. Guan, X., and Bai, Y. (2013) Using PCR–RFLP
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During this experiment, the students were given feedback
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PCR products were discussed in this course. The instructor
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The determination of genotype by RFLP is based on the [10] Varadi, V., Bevier, M., Grzybowska, E., Johansson, R., Enquist, K.,
Henriksson, R., Butkiewicz, D., Pamula-Pilat, J., Tecza, K., Hemminki, K.,
pattern of digested DNA in the electrophoresis. There are
Lenner, P., Fo € rsti, A. (2011) Genetic variation in genes encoding for
several factors that may influence the final readout of the polymerase f subunits associates with breast cancer risk, tumour char-
results. The proper separation of the digested DNA by elec- acteristics and survival. Breast Cancer Res. Treat. 129, 235–245.
trophoresis is required. The instructor introduced the prin- [11] Zhang, S., Chen, H., Zhao, X., Cao, J., Tong, J., Lu, J., Wu, W., Shen,
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of DNA in the gel were also discussed. grating teaching and research in undergraduate biology laboratory edu-
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[13] DiBartolomeis, S. M. (2011) A semester-long project for teaching basic
composed of several experiments is set up in this study.
techniques in molecular biology such as restriction fragment length
This lab course not only facilitates the learning interest of polymorphism analysis to undergraduate and graduate students. CBE
the students but also improves their study results. Life Sci. Educ. 10, 95–110.
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lactase persistence: An exercise for teaching molecular biology techni-
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