Hien Pham
Chem 263, Spring 2011
Summary of Project
06/01/2011
Chemistry of Nucleic Acids
Nucleic acids are macromolecules linked by many nucleotides at phosphate groups. Each
nucleotide is composed of a ring sugar (known as backbone) which binds to a phosphate group and a
nitrogenous base. There are two types of nucleic acid: deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA). DNA is a blue print for organism’s life. It stores the genetic material which will be transmitted
from parent to offspring. RNA is generated from DNA by transcription. The information in RNA is used to
synthesis protein and amino acid which are essential for the function of cellular and organism [1].
Nucleic acid was named because DNA was first found in the nuclei of white blood cells (an acidic
environment) in 1869. Until 1951, Rosalind Franklin, who graduated from Cambridge University in
London, worked in a lab at King’s College, and studied X-ray crystallography, figured out the structure of
DNA through X-ray; Unfortunately, Franklin died in 1958
[2]
. In 1953, James Watson and Francis Crick
had visited Franklin’s lab and they had seen
the X-ray of DNA that Franklin took. James
Watson and Francis Crick had identified the
three dimensional model of DNA, and they
won the Nobel Prize in 1962.
DNA is composed of two strands
which are anti- parallel to each other. Each
stand is a polynucleotide. Two strands
connect to each other by hydrogen bonds
between H with O, or N which are in bases [3].
This makes DNA look like a ladder. There are
Figure 1: Difference in structure of DNA and RNA
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Hien Pham
Chem 263, Spring 2011
Summary of Project
06/01/2011
four types of base, which bind to sugar backbone, in nucleic acid: Adenine (A), Guanine (G), Cytosine
(C), and Thymine (T). Adenine bind to Thymine and Cytosine binds to Guanine by hydrogen bonds. If one
strand has Adenine, Thymine and Cytosine, so the other strand must have Thymine, Adenine and
Guanine [3]. The difference of those bases and its arrangement makes different organism and species
(due to genetic variation).
Having Thymine as a base of structure of DNA also helps to prevent mutation for the following
reasons: Cytosine can undergo deamination (a reaction of removing amino group) to become Uracil.
When Uracil presents in DNA structure, it will be recognized by an enzyme as a mistake. The enzyme
repairs this by cutting out the Uracil and
replacing with Cytosine before DNA
undergoes
Following
transcription
is
the
process.
mechanism
when
Cytosine undergoes deamination [1].
Figure 2: Cytosine deamination [6]
RNA is a single strand which is
transcribed from DNA [1]. Basically, the
RNA strand has same structure of the
DNA template except Thymine (T) base
in DNA is replaced by Uracil base in RNA
and RNA contain a hydroxyl (OH) in the
sugar backbone. Having a hydroxyl in
each sugar makes the RNA easier to be
Figure 3: Mechanism for degraded RNA
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Hien Pham
Chem 263, Spring 2011
Summary of Project
06/01/2011
degraded after it has done its job. The mechanism is shown on the right.
In general, understanding the DNA structure helps scientists to figure out the method to treat
cancer. According to Benno Neto and Alexandre Lapis [7], a quercetin zinc (II) can be synthesized by
quercetin-a compound is found in food and vegetable- and zinc (II). The quercetin zinc (II) would interact
with DNA in tumor cells, and inhibit growth and proliferation of tumer cells. This complex makes tumor
cells undergo apoptosis (program cell dead). The scheme 9 and scheme 10 in the journal shows how a
quercetin zinc (II) is synthesized and interacts with DNA molecule.[7]
Figure 4: Quercetin Zinc (II) complex formation
Source: Molecules, May2009, Vol. 14 Issue 5, p1725-1746.
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Hien Pham
Chem 263, Spring 2011
Summary of Project
06/01/2011
Figure 5: Proposed intermediate of DNA binding with Quercetin zinc (II) and DNA cleavage mechanism
Source: J. Tan et al./Bioorg. Med. Chem. 17 (2009) 614-620
Literature Cited:
1. Bruice, P. Y. (2011). Organic Chemistry, Sixth Edition. Prentice Hall
2. MSU Gallery of Chemists' Photo-Portraits and Mini-Biographies
http://www.chemistry.msu.edu/Portraits/PortraitsHH_Detail.asp
Women's Interchange at SLAC
http://www-project.slac.stanford.edu/wis/pages/past_seminars/nextseminar56.htm
3. Watson, J. D., Crick, F.H.C. (1953). A structure of Deoxyribose Nucleic Acid. Nature 1953,
171:737-738
4. Allen, F. W. (1954). Nucleic Acids, 23, 99-124. doi: 10.1146/annurev.bi.23.070154.000531
5. Roth, C. M., Yarmush, M. L. (1999) Nucleic Acid Biotechnology, 1, 265-297 doi:
10.1146/annurev.bioeng.1.1.265
6. Volker, J., Klump, H. H., Manning, G. S. (2001). Counterion Association with Native and
Denatured Nucleic Acids: An Experimental Approach. doi:10.1006/jmbi.2001.4841
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Hien Pham
Chem 263, Spring 2011
Summary of Project
06/01/2011
7. Neto, B., Lapis A. (2009). Recent Developments in the Chemistry of Deoxyribonucleic Acid
(DNA) Intercalators: Principles, Design, Synthesis, Applications and Trends. 14, 1725-1746 doi:
10.3390/molecules14051725
8. J. Tan et al./Bioorg. Med. Chem. 17 (2009) 614-620
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