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DEOXYRIBONUCLEIC ACID (DNA)

OBJECTIVE: to examine the basic structure and properties of DNA

CONTENT1. Definition of DNA2. Primary structure of DNA3. Double helix structure of DNA4. Super helix structure of DNA5. Hybridization

The Discovery of the Molecular Structure of DNA – The Double Helix

A Scientific Breakthrough

The sentence "This structure has novel features which are of considerable biological

interest" may be one of science's most famous understatements. It appeared in April

1953 in the scientific paper where James Watson and Francis Crick presented the

structure of the DNA-helix, the molecule that carries genetic information from one

generation to the other. Nine years later, in 1962, they shared the Nobel Prize in

Physiology or Medicine with Maurice Wilkins, for solving one of the most important of 

all biological riddles. Half a century later, important new implications of this

contribution to science are still coming to light.

I. DEFINITION OF DNA

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in

the development and functioning of all known living organisms. The main role of DNA

molecules is the long-term storage of information and instructions needed to construct other 

components of cells, such as proteins and RNA molecules. The DNA segments that carry

this genetic information are called genes, but other DNA sequences have structural

 purposes, or are involved in regulating the use of this genetic information.

II. STRUCTURE OF DNA

 A. DNA is a polymer of deoxyribonucleoside monophosphates;  1. Each nucleotide is made up of a sugar, one or more phosphate groups

and a base.2. the bases are adenine, guanine, cytosine, and thymine;3. the bases are on the inside and sugar-phosphate backbone on outside;4. base pairs are formed through hydrogen bonding;

5. the nucleotides are linked through phosphodiester bonds(sugar-acid)6. the DNA molecule is a right handed helix;6. bases are perpendicular to the helical axis stacked on top of each

other(superposé ou paral) and interacting through hydrophobic interactionsand van der Waals interactions;

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8. approximately 10 base pairs per(double) helical turn;9. every DNA molecule has a specific sequence of nucleotides called its primary

structure where genetic information is stored. B. Most DNA in a cell exists as the Watson-Crick double helix which

is known as B form DNA.

 Figure 1: Francis Crick and David Watson (1953) Figure 2: Bruce Wilkins

In 1951, the then 23-year old biologist James Watson travelled from the United States to work with Francis Crick, an English physicist at the

University of Cambridge. Crick was already using the process of X-ray crystallography to study the structure of protein molecules. Together,Watson and Crick used X-ray crystallography data, produced by Rosalind Franklin and Maurice Wilkins at King's College in London, to

decipher DNA's structure.

Figure 3: The original DNA model by Watson and Crick

Major features of DNA

The two strands of the double helix are anti-parallel, which means that they run in

opposite directions.

The sugar-phosphate backbone is on t he outside of the helix, and the bases are on

the inside (Figure 4 )

Two base pairs can be formed - either an adenine-thymine pair that form a two-

hydrogen bond together, or a cytosine-guanine pair that form a three-hydrogen bond.

The base pairing is thus restricted. This restriction is essential when the DNA is being

copied: the DNA-helix is first denatured in two long stretches of sugar-phosphate

backbone with a line of free bases sticking up from it. Each half will then be thetemplate for a new, complementary s trand.

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The coding regions in the DNA strand, the genes, make up only a fraction of the

total amount of DNA. The stretches that flank the coding regions are called introns,

and consist of non-coding DNA. Today, biologists and geneticists believe that this

non-coding DNA may be essential in order to expose the coding regions and to

regulate how the genes are expressed.

 

Figure 5: The sugar-phosphate backbone is on the outside and the four different

bases are on the inside of the DNA molecule.

  C. DNA supercoiling1. a supercoil is when the double-helix twists around itself;

2. supercoils can be positive or negative but natural DNAs exist inthe negative supercoiled form;3. DNA can be supercoiled if it is circular or if it is linear and has

fixed ends;4. supercoiled DNA is more compact than relaxed DNA;5. negatively supercoiled DNA molecules are easier to unwind than

relaxed molecules;6. DNA unwinding is required for replication and transcription.

D. Topoisomerases are enzymes that catalyze changes in DNA supercoiling1. Type I topoisomerases function by breaking a phosphodiester bond

of one strand, passing the other strand through the break and resealingthe break--they can only remove supercoils;

2. Type II topoisomerases function by breaking both strands andpassing a double strand region through the break before resealing thebreak. This process requires ATP;

3. topoisomerases are targets of numerous chemotherapeutic drugs:adriamycin, VP16 (tenoposide), VM26 (etoposide), camptothecin.

E. Nucleases--enzymes that catalyze hydrolysis of phosphodiester bonds in nucleic acids

1. exonucleases cleave terminal nucleotides from either the 5' or 3'

end of a polynucleotide;2. endonucleases cleave in the interior of nucleic acid molecule.

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3. restriction enzymes are endonucleases that cleave at specificsequences of DNA.

F. DENATURATION AND RENATURATION OF DNA 

1. Denaturation is the conversion of the double stranded form of DNAinto single stranded form

a. DNA can be denatured by heat or alkaline treatment;b. The temperature at which half the DNA is unwound is defined as

the melting temperature (Tm);--Tm is dependent on the GC content of the DNA, on the solvent, and on theionic strength. 

2. Renaturation--under proper conditions, complementarysingle-stranded nucleic acids can renature into a double-stranded form.

3. Denaturation and Renaturation is the basis of hybridizationexperiments--this type of analysis is central to recombinant DNAtechnology and gene manipulation.

4. Hybridization

Hybridization is the process, discovered by Alexander Rich, of combining complementary,

single-stranded nucleic acids into a single molecule. Nucleotides will bind to their 

complement under normal conditions, so two perfectly complementary strands will bind to

each other readily. This is called annealing. However, due to the different molecular 

geometries of the nucleotides, a single inconsistency between the two strands will make

 binding between them more energetically unfavorable. Measuring the effects of base

incompatibility by quantifying the rate at which two strands anneal can provide information as

to the similarity in base sequence between the two strands being annealed. Annealing may be

reversed by heating the double stranded molecule of DNA (or RNA or DNA:RNA) to break 

the hydrogen bonds between bases and separate the two strands. This is called melting or 

denaturation.