Question

1. What two important physical properties contribute to the viscosity of DNA?

2. How is DNA made non-viscous by mechanical shearing? Use a labeled diagram to show what happens to the molecular structure of the DNA.

3. How is DNA made non-viscous by heating in a boiling water bath? Use a labeled diagram to show what happens to the molecular structure of the DNA.

4. Why is DNA in cells not viscous?

Answer 1

A,

Two important physical properties contribute to the viscosity of DNA.

1. DNA has vast length combined with its double stranded character .DNA is bonded by noncovalent chemical bonds, dominated by the hydrogen bonding.Also dsDNA is stable unless melted or unzipped by an external force.

2. DNA is rigid. Two main factors account for the molecule’s rigidity. Mechanically the base pair building blocks of the polymer are stacked together with sufficient force to impart stiffness to the structure. Allied to this is the fact that DNA has negative charges studded down its length to the molecule’s phosphate groups. These repel each other electrostatically, so that any bending of the molecule will bring the charges closer together - a situation that will be resisted.

B,Double stranded DNA can be broken by the shearing forces present in the solution.Very small fragment can be obtained (approx 3000 baepair in length) by subjecting the solution to sonication with ultra sound. The DNA molecule shared randomly along its length producing fragments with short single stranded ends.

C

When DNA is heated the double strands unwind and separate into single strands through the breaking of the hydrogen bonding between the bases. The term used to refer to this process is denaturation. Denaturation can be accomplished by other methods but in molecular diagnostic testing heat is the method of choice.

• The Temperature of Melting (Tm) is defined as the temperature at which 50% of double stranded DNA is changed to single-standard DNA. The higher the melting temperature the greater the guanine-cytosine (GC) content of the DNA.

The melting temperature depends on both the length of the molecule, and the specific nucleotide sequence composition of that molecule. The guanine-cytosine pair is bound by three hydrogen bonds, while adenine-thymine pairs are bound by two hydrogen bonds. DNA with high GC content is more stable than DNA with low GC content. In PCR experiments GC content of primers are used to predict their annealing temperature to the template DNA. A higher GC content level indicates a higher melting temperature.

D

DNA is made up of Deoxyribonucleic acids, which is a polymer with repeating nucleotide units of adenine, thymine, cytosine and guanine amino acids. The DNA is made up of a double helix, which is why these bonds contribute to the stability of the double helix. The double helix has two complementary single strands that are held together by non-covalent hydrogen bonds between the bases. DNA's viscosity is as a result of its long double bonded helix. When intact cells are lysed and denatured using detergents, the viscosity of the DNA increases. The higher the viscosity of a solution, the slower it will flow through an opening. A rigid molecule will not pass through a small opening easily compared to a small molecule. When a DNAmolecule is packed tightly, the cell suspension does not exhibit the viscosity