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Article

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†,‡*

From the †Department of Molecular Biology and Diagnostics, School


of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China,
‡Jiangsu Key Laboratory of Medical Science and Laboratory Medicine,
Zhenjiang, Jiangsu, China, §Experimental Teaching Center, School of
Medicine, Jiangsu University, Zhenjiang, Jiangsu, China

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.

Keywords: Laboratory exercise; molecular biology; SNP; PCR–


RFLP

Introduction diseases, revealing the mechanisms of disease and enabling


healthcare at an individual level. Molecular diagnostics can
Molecular diagnostics detect and measure the presence of
facilitate the practice of personalized medicine and precision
nucleic acids or proteins that are associated with health or
medicine. For undergraduate students in medical school, the
molecular biology course generally includes two parts: intro-
ducing the basic principles of molecular biology and the
Volume 45, Number 4, July/August 2017, Pages 299–304
applications of molecular biology in medical practice. Com-
*To whom correspondence should be addressed. E-mail: xuzhang@ujs.
edu.cn or 15951285038@163.com. pared to the other courses, molecular biology course de-
**This work was supported by Jiangsu Province’s Qing Lan project, mands lab activities to help students understand the molecu-
the Research on the Reform of Higher Education Grant of Ministry of lar mechanisms of disease and the diagnosis at molecular
Education (2015Y0603, JX2016-203, JX2016-Y002), the Starting
level [1]. Lab activities will enable students to learn the basic
Foundation for Senior Talents of Jiangsu University (Grant No.
13JDG086), the Construction Fund for the Brand Major of Jiangsu molecular biology techniques, get familiar with the general
Province (Grant No. Yj201612), the Research on the Reform of procedure of molecular diagnostics, and gain systemic train-
Education Grant of Jiangsu University (Grants No. 2013JGZD001 and ing in scientific research [2, 3]. Moreover, lab course may
2015JGZZ008), the Research on the Reform of Higher Education Grant include different but related activities, which will improve
of Jiangsu Province (Grants No. 2013JSJG030 and 2013JSJG280).
Disclosure—The authors have no conflict of interest to be declared.
the learning ability of the students [2, 4].
Received 1 April 2016; Revised 31 October 2016; Accepted 29 Genetic variation at the nucleotide level is the most
November 2016 fundamental difference between two individuals, which is
DOI 10.1002/bmb.21037 commonly referred to as single nucleotide polymorphism.
Published online 1 February 2017 in Wiley Online Library Single nucleotide polymorphisms (SNPs) are abundant in
(wileyonlinelibrary.com) human genome and can occur approximately once every

Biochemistry and Molecular Biology Education 299


Biochemistry and
Molecular Biology Education

several hundred base pairs. SNPs localize in both coding


and noncoding regions of the genome. SNP is emerging as
the third generation of genetic markers. SNP detection has
been used in epidemiological studies, medical examina-
tions, and drug development. SNP is one of the most impor-
tant topics for molecular biology course [2]. Although a
number of new technologies for SNP detection such as DNA
microarray and next-generation sequencing (NGS) have
been developed in the past few years, the undergraduate
students in medical school have few chance to perform
these techniques. Therefore, a lab course that allows the
students to detect SNP using traditional and affordable
techniques is required.
Laboratory techniques to analyze SNP involve the use
of DNA restriction enzymes to generate DNA molecules of
varying length depending on the presence or absence of The principle of genotyping by PCR–RFLP in this
restriction sites. The length variations in DNA molecules FIG 1 experiment. [Color figure can be viewed at
wileyonlinelibrary.com]
caused by restriction enzyme cutting are called restriction
fragment length polymorphism (RFLP). As a molecular
marker, RFLP is frequently used in genome mapping and concept of SNP, the association of SNP with disease, and
in variation analysis such as genotyping, forensics, paterni- the commonly used methods for SNP detection. Three
ty tests, and hereditary disease diagnostics. Polymerase major parts are included in this lab course, which are
chain reaction (PCR) is a sensitive and efficient method for genomic DNA extraction, gene amplification by PCR, and
amplifying the DNA fragment within a specific region of the genotyping by RFLP. This lab course has several advan-
target gene. When the two techniques are combined, the tages. First, this course includes a variety of experiments
method is referred to as PCR–RFLP. To resolve and mea- that are combined in a logical and systematic manner. Sec-
sure the length of the digested products after the restriction ond, this experiment is performed in an exploratory way,
enzyme reaction, a separation step by electrophoresis is which will stimulate the learning enthusiasm of the stu-
needed. Altogether, these procedures offer a rapid and reli- dents. Third, this experiment mimics the process of scien-
able method for detecting SNP in the lab [2]. tific research, which will be helpful for the students to per-
REV3 gene locates on chromosome 6q21 and contains form gene-disease association study in the future [12].
34 exons and 33 introns. REV3 gene encodes the catalytic Taken together, this laboratory exercise will stimulate the
subunit of DNA polymerase f, which plays an important medical students to understand the relationship between
role in DNA damage repair [5–7]. REV3 is reported to play SNP and disease and to learn the regular procedure for
as a tumor suppressor in cancer [8]. Loss of REV3 causes SNP detection.
chromosomal instability in mammalian cells and enhances
spontaneous tumorigenesis [9]. Genetic variations in REV3
are associated with breast cancer risk [10]. In addition, Course Information
SNP in 30 -UTR of REV3 contributes to altered lung cancer Experimental Design
susceptibility through the disruption of miRNA-mediated This comprehensive experiment contains three parts,
regulation [11]. The tagSNP rs12211763 (A/G) of REV3 including genomic DNA extraction from human peripheral
gene is included in a restriction enzyme cutting site (Fig. blood samples, PCR amplification of specific region in REV3
1). The SNP site and its flanking sequence is A/GGATCT. gene, and identification of the genotype by RFLP analyses.
There is a restriction site of Bgl II in the allele A but not in
the allele G. Therefore, The PCR product spanning this SNP Materials
site can be distinguished by Bgl II digestion. The restriction Peripheral blood samples were collected from healthy
enzyme digestion will generate two products in individuals donors who received medical examination in the Staff Hos-
with A allele, while those with G allele have one product pital of Jiangsu University. The use of human samples was
and the heterozygous individuals have three products. approved by the Ethics Committee of Jiangsu University.
Thus, the genotype of each individual can be easily de- The samples were obtained in a blinded way and no identi-
tected by PCR–RFLP. fication information was included with the samples. Geno-
Herein, we reported the design of a molecular biology mic DNA isolation kit was purchased form Qiagen (Germa-
lab course, which includes several experiments modified ny). PCR reagents were provided by Takara (Japan).
from one of our research projects. This lab course is Restriction endonuclease Bgl II was bought from NEB (Chi-
designed for medical students to better understand the na). Agarose was provided by Biowest (Spain)

300 A Comprehensive Experiment for Molecular Biology


Methods BglII restriction endonuclease. Double distilled water was
Isolation of Genomic DNA from Human Peripheral added to a final volume of 20 lL. The restriction enzyme
Blood Samples digestion reaction mixture was incubated at 378C waterbath
To save time and ensure lab safety, we used commercial overnight. All the restriction enzyme digested products were
kit to isolate genomic DNA from human peripheral blood verified by 1.5% agarose gel electrophoresis and visualized
samples. Briefly, 200 mL human peripheral blood sample under a UV transilluminator and photographed.
were taken into a tube that contained 20 mL protease. The Outcome Evaluation
blood sample was mixed with 200 mL lysis buffer by vortex- The written examination was used to evaluate the study.
ing for 1 min. The mixture was incubated at 568C water- The performance of the students on the exam questions
bath for 10 min. Two hundred microliters of ethanol were specifically related to SNPs was compared. The examina-
added and mixed by vortexing. All the solution was trans- tion was designed as follows: explanation of terms, short-
ferred to a spin column which was attached to a collection answer questions, and discussion essays: 10 explanation of
tube and centrifuged at 10,000 rpm for 1 min. The filtrate terms (three point per question, that is, a maximum of 30
was then discarded. After being washed with 75% ethanol points in total could be obtained), 5 short-answer questions
twice, the spin column was attached to a new collection (8 points per question were possible, i.e., the maximum
tube and 50 mL elution buffer was added into the center of score was 40 points) and 2 discussion essays (15 point per
the spin column. The spin column was recentrifuged at question, i.e., the maximum score was 30 points). The
10,000 rpm for 1 min to collect the eluted DNA. Finally, the exam questions specifically related to SNPs included one
concentration of the extracted genomic DNA was measured explanation of terms, one short-answer question, and one
in a UV spectrophotometer and calculated by using the fol- discussion essay (the maximum score was 26 points). Stan-
lowing formula: DNA concentration (ng/lL) 5 50 3 OD260. dard answers for all questions were defined by the instruc-
The purity of the extracted genomic DNA was evaluated by tor before students’ answers in the examination were
OD260/280 and OD260/230 values. The integrity of the ext- scored.
racted genomic DNA was evaluated by 1% agarose gel
Statistical Analysis
electrophoresis.
Data are presented as means 6SD. Two-tailed t-test was
PCR Amplification of REV3 Gene used to assess the differences of the data by SPSS software
The specific primers for the amplification of REV3 gene (version 22.0).
were designed by using Primer Premier 5.0 software. The
sequences of the primers are listed below (Forward: GCAA
CAAAGCGAGATTCCGA, and Reverse: TCTTGTCTTGTTGCA Results
TAGCTGT). PCR amplification of REV3 gene by using this Genomic DNA Isolation and Measurement
pair of primers generates a 312 bp product. The extracted The genomic DNA could be rapidly prepared from human
genomic DNA was used as the template for PCR. The com- peripheral blood samples by the students in three teaching
ponents of the PCR reaction mixture were as follows: geno- hour. The quantity and quality of the extracted genomic DNA
mic DNA (200 ng), 2.5 lL 103 PCR buffer, 1 lL dNTP were determined by using NanoDrop 1000 spectrophotometer
(10 mM/L), 1 lL forward primer (5 lM/L), 1 lL reverse prim- and agarose gel electrophoresis. The concentration of the iso-
er (5 lM/L), 0.5 lL Taq DNA polymerase. Double distilled lated genomic DNA varied from 50 to 200 ng/lL among differ-
water was added to a final volume of 25 lL. The PCR reac- ent groups (Table I). The total DNA yields from all the groups
tion mixture was predenatured at 948C for 5 min, followed met the general expectation. The purity of the prepared geno-
by 35 cycles of PCR amplification including denaturation at mic DNA was evaluated by OD260/280 and OD260/230 values as
948C for 30 sec, annealing at 618C for 30 sec, extension at provided by NanoDrop 1000. The genomic DNA prepared by
728C for 30 sec. A final extension at 728C for 10 min was most groups had an OD260/280 value around 1.8 and an OD260/
performed. All the PCR products were verified by 1.5% aga- 230 value higher than 2.0, suggesting a good purity of the

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.

Zhang et al. 301


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Molecular Biology Education

The quantity and quality of genomic DNA


TABLE I isolated from human peripheral blood samples
(analyzed by NanoDrop 1000)

Concentration
Group ID (ng/lL) OD260/280 OD260/230

1 46.8 1.82 1.63


2 72.5 1.85 2.27 Agarose gel electrophoresis of PCR products.
FIG 3 The PCR-amplified REV3 gene spanning tagSNP
3 101.6 1.80 2.6
rs12211763 was resolved in 1% agarose gel; 5 lL
4 113.7 1.84 2.31 of PCR product were loaded into the agarose gel
for electrophoresis. M: DL2000 DNA marker; B:
5 151.5 1.84 2.6 blank; 1–12: individual PCR product.

6 200.2 1.78 1.97


reagents. The quality of the genomic DNA used as PCR
7 231.1 1.81 2.45 template has also been verified. Problems may come from
8 201.1 1.80 2.04 the missing of some PCR components in the reaction mix-
ture or the improper mixing of genomic DNA sample with
9 115.5 1.83 2.04 the other PCR components.
10 50.1 1.82 1.74 Genotyping by RELP
11 133.6 1.81 2.45 To avoid loss of PCR products, the purification step was
skipped in this experiment. To ensure complete digestion,
12 138.8 1.84 2.46 the PCR products were incubated with restriction endonu-
clease BglII overnight. The digested products were ana-
lyzed on 1.5% agarose gel. The SNP genotype of different
PCR Amplification of REV3 Gene individuals was determined according to the profiles of
The amplified DNA fragment span the SNP rs12211763 in digested DNA in electrophoresis. The restriction endonucle-
REV3 gene. The size of the PCR products was verified by ase BglII specifically recognizes the AGATCT sequence and
agarose gel electrophoresis. All groups except group 11 got cuts the PCR products between nucleotide A and G, thus
positive results and the length of the amplified DNA frag- generating two products with the sizes of 70 and 242 bp. If
ment was consistent with our expectation (Fig. 3). The stu- the nucleotide A changes to G, the PCR products will not be
dents’ main problem in this step is pipetting errors. The cut, thus generating a product with the size of 312 bp. As
failure to get PCR product by group 11 may be due to this
reason since the PCR parameters have been optimized and
the PCR components used were from the same batch of

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.

302 A Comprehensive Experiment for Molecular Biology


Comparison of the two groups’ examination scores. A, the total examination scores of students from two groups.
FIG 5 B, the SNP-related questions examination scores of the students from two groups. *p < 0.05.

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

Zhang et al. 303


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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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Although the students may have experience of technical the experimental study of protein–protein interactions. Biochem. Mol.
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304 A Comprehensive Experiment for Molecular Biology

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