Sequencing 

1. DNA sequencing information is important for planning the procedure and method of gene
manipulation. 

2. DNA sequencing is used for construction of restriction endonuclease map.

3. It is used to find tandem repeats or inverted repeat for the possibility of hairpin formations.

4. The sequences can be used to find whether any open reading frame (ORF) coding for a
polypeptide exists.

5. DNA sequences can be used to find a polypeptide sequence from the data bank or to compare
with DNA sequences from other animals for phylogenetic analysis.

6. They are used to construct the molecular evolution map.

7. They are useful in identifying exons and introns.

Calvin College Developmental Cell Biologist Steve Mathesonpoints to an
interesting series of papers highlighting the importance of new rapid-fire DNA
sequencing technologies for the study of evolution.

The “$1,000 Genome” has been in the news a great deal from a health care
perspective: the advances in sequencing technology have brought the cost of
sequencing whole genomes down to just a fraction of what they were when
Francis Collins began the laborious sequencing of the Human Genome back in
the early 1990s. See, for example, the new book by Kevin Davies of Bio-IT
World.

In a matter of a few years (if not months), you and I will be able to get our
complete genome sequenced for the cost of a night out at a decent restaurant.
Biotechnology and pharmaceutical companies have high hopes for the kind of
therapies that can be developed in response to what we learn cumulatively
from thousands of people’s genomes about the genes that predispose an
individual to diseases such as Cystic Fibrosis, Parkinson’s, Alzheimer’s, and
Diabetes.

But the same technology, as Matheson’s essay helps to illustrate, is also

shedding new light on questions of evolution and fitness that have intrigued
scientists ever since Darwin. In that sense, the more we move forward, the
more we learn from the past.
DNA Sequencing

The Problem

Interest in DNA and how it functions is on the rise. Examples are even found in popular literature such as
Michael Crichton's fictional Jurassic Park, where recovered dinosaur DNA was used to create new dinosaurs.
The Human Genome Program has made great strides in sequencing human DNA to achieve a better
understanding of our own DNA. Deoxyribonucleic acid, DNA, consists of four nitrogenous bases, adenine (A),
cytosine (C), guanine (G), and thymine (T). The sequence of these four bases constitutes the code which
enables the DNA to control the characteristics of a cell or organism.

Chromosome Mapping

The human genome consists of seven billion bases in 24 types of chromosomes made up of DNA. These
chromosomes are organized as 23 pairs of chromosomes, with 22 somatic chromosome pairs and a pair of
either two X chromosomes (in females) or one X and one Y chromosome (in males). Within individual
chromosomes are areas where genetic activity takes place along with areas of inactivity. One task of the
Human Genome Project is to locate and map areas of activity and inactivity. The active areas contain genes
and a coding region, which typically specify which protein will be fabricated. The coding region regulates
when and how certain proteins are produced.

Discontinous Coding Regions

A DNA sequence contains many levels of structure and information. Adding to the complexity, the coding
regions are sometimes interrupted and continued further downstream like portions of an article may be
continued on different pages of a newspaper. However, unlike a newspaper, there are no instructions or
markers for where the remainingportion of the coding region may be
found in the DNA. Instead the cellular machinery manufacturing the
protein uses subtle signals from the DNA to determine where the
protein coding region will resume.

Beta-hemoglobin Gene Study

One of the genes being studied is the beta-hemoglobin complex. This

complex is actually a collection of seven genes lying next to each
other that are expressed at different times or stages of development.
There are different versions of the complex expressed in the embryo,
the fetus, and the adult, as well as other variations. The beta-
hemoglobin protein associates with the alpha-hemoglobin protein, to
form hemoglobin. Hemoglobin is a protein contained in red blood cells
that produces the cell's coloration, and is responsible for carrying oxygen throughout the body.

Organization Detection

Structurally DNA must curl around itself forming the famous double helix (additional curling of this double
helix is called supercoiling). This results in the human genetic blueprint, consisting of billions of bases,
hundreds of millimeters long, being packed into the tiny nucleus of every single cell. Detection of the levels
of organization is possible because of the long range correlations between bases. Some correlations are due
to protein coding, while others are due to the helical structure, superhelical structure and chromosome
organization.