Gene Sequencing: From Molecules to Data

A Process Explained

Why Learn about Gene Sequencing?

Gene sequencing is the process by which a specific gene is isolated and translated into a
readable sequence. Many biological scientists will use this or a similar process at some point in
their academic career. Basic biology courses tend to guide their students in the steps of carrying
out a laboratory procedure without explaining the details of how and why. These details are
crucial in understanding how such a small, yet important, piece of information can be
converted to a readable sequence. This document provides detailed explanations of each step
to guides future scientists towards understanding this process. Due to the increased necessity
for genetic analysis in the majority of current biological research, the information provided is
knowledge all students of the biological sciences should have in order to exemplify a strong
grasp on current research in their field.

Introduction
Most cells carry information controlling the life functions of the cell. In eukaryotes (animal cells,
plant cells, etc.), this information is contained in chromosomes as double-stranded chains of
base pairs. Groups of bases may be categorized into genes based on their molecular function.
Each gene is transcribed into RNA which is
then translated into a protein that a cell
may use to carry out cellular processes
(Figure 1). The base pairs in a gene
determine which protein is created and
when that gene is read. Scientists
sequencing a gene aim to determine the
sequence of base pairs that occur within its
DNA. In the same way that the cell is able
to read and use a genetic sequence through
transcription and translation, scientists may
read it through modern gene sequencing
techniques and use this information to
Figure 1: Genes on the DNA strand are translated to RNA within the
nucleus and this RNA is transcribed into protein in the cytoplasm. determine its function within a cell.
http://ghr.nlm.nih.gov/handbook/howgeneswork/makingprotein
The Process
Gene sequencing is characterized by a series of steps which allow a target gene to be read.
First, the two strands of DNA in a chromosome must be separated from one another to allow
replication machinery to bind to it. Then the target gene must be replicated at an exponential
rate, such that the remaining amount of excess genetic information is negligible and the target
alone is detectable. Next, specialized molecules divide the gene at each base pair and mark
them with readable dyes. These pieces are then separated and the dyes allow the reader to
know which base occurs at each location on the gene. This data is then computerized into a
sequence of bases that together make up the molecular sequence of the gene. These steps are
elaborated upon below.

Polymerase Chain Reaction

Polymerase Chain Reaction (PCR) is a process that involves the separation and replication of
DNA strands. This is traditionally divided into three steps.

1) Denaturation: This is the heating

of a sample such that the molecular
bonds between DNA bases weaken
and become unable to hold the two
strands together. Separating the
strands will later allow new bases to
bind to the strands to create two
new DNA molecules.

2) Annealing: In this step, a primer is

added to the sample and the
temperature is lowered, allowing the
primer to bind to the DNA strands. A
primer is a strand of DNA that
matches the sequence of the target
gene. Primers are synthetically
created to mark the ends of a
sequence to replicate.

3) Extension: In order to replicate

the sequence between the primers,
single, free-floating bases bind to the
Figure 2: Steps 1, 2, and 3 of PCR replicate the target gene at an exponential rate.
th
unmatched bases on the DNA Campbells Biology: 5 Edition, pp. 371
strand. A base is added to a strand next to a primer, causing another base to be added next to
it, continuing across the strand, and resulting in two double stranded DNA molecules.

The three steps of the PCR process are repeated a number of times, growing the number of
replicates of the gene exponentially. This process is visualized in Figure 2.

Splicing and Marking

After the initial amplification, the DNA must be replicated again but
with two stark differences: the addition of dye and the use of
modified bases. In PCR extension, the addition of bases automatically
signaled the addition of another; however, this next step involves
broken bases which prevent more bases from being added next to
them. Bases sequentially bind to the strand until a broken base is
added, whereby bases cease to bind. This causes DNA fragments of
varying lengths to be created. A different batch of samples must be
created for each of the four bases, containing a faulty version of one
base along with a specific color dye. In this way, all strands that stop
at one base will be marked with one dye while all strands that stop at
another base will be marked with another dye. The result is many
gene fragments of varying lengths visibly marked by the last base on

Figure 3: DNA is fragmented and the strand (see Figure 3). Theoretically, due to variation in the
each end base is marked with a
different color. replication process, there should be strands that have halted base
http://www.genomenewsnetwork
.org/resources/whats_a_genome/ addition at each and every point on the original strand.
Chp2_2.shtml

Electrophoresis

This last step involves sorting all the

fragments by their length. Because
there are strands with halted
replication points dyed at
(theoretically) every point on the
gene, grouping strands of similar
length together and placing all
fragments in order by length should
produce a sequence of colored dyes

that corresponds to the base Figure 4: Dyes are detected by the machine and translated into a sequence.
http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp2_2.shtml
sequence of the gene. This part of the process relies on the negative charge of DNA. Basic
physics tells us positive charges attract negative ones and electric current is the movement of
negatively-charged electrons towards an area of positive charge. Therefore, running a current
through a sample of DNA fragments will move the fragments through a liquid/gel medium.
Smaller fragments have a lower mass and will move at a greater velocity, travelling a greater
distance than their larger counterparts. As the strands move across the medium, the DNA
sequencing machine detects and records the location and order of each dye. The machine uses
the recorded information to determine the likelihood of the presence of each base at each
location on the gene (see Figure 4.)

Conclusion
Gene sequencing is a complex process, but a firm understanding of the process and its
components not only makes the researcher well-informed about the details of the process but
expands their knowledge of the properties of DNA and other molecular functions. Practices
such as these came about through the intelligence and creativity of scientists of the past.
Learning more about them can only further prepare the scientists of tomorrow for developing
future innovations.

Additional Information
Genome News Network Whats Genome Sequencing?
http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp2_1.shtml

Campbells Biology Textbook

University of Michigan (1)How do we sequence DNA? and (2)DNA Denaturation, Annealing
and Replication
(1) http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/sequencing.html
(2) http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/pg2.html