1.-For a double stranded DNA molecule in which 15% of the bases are A, what can
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Question
1.-For a double stranded DNA molecule in which 15% of the bases are A, what can you conclude about the base C? Would you expect the Tm of this DNA? (Refer the figure below)
2.-You measure the concentration of DNA in a preparation of nucleic acid using a diphenylamine assay. You also measure the absorbance of the preparation at 260 nm. Another assay indicates that there is no RNA contaminating the preparation. Two days later, you continue your study by measuring absorbance of the preparation again. The absorbance has increased significantly. A quick check reveals that the DNA concentration has not changed. There is no microbial contamination in the preparation that may account for this seeming oddity. What has happened?
3.You isolate some DNA and monitor its dimensions. This particular DNA has a greater number of base pairs per turn of the helix than is normally the case. What is a possible explanation?
100 M. phlei 80 Serratia E. coli Pneumococcus Calf thymus 40 Yeast Salmon sperm a 20 Bacteriophage T4 0 60 70 80 90 100 Tm(C)Explanation / Answer
A DNA molecule is composed of two strands of deoxyribonucleotide polymers, in a very special geometric relationship in which one is entwined about the other such that an overall helical shape results. This is the familiar "double helix", described by Watson and Crick, in which the two helices share a common axis, and both are wound in a right-handed manner. A "right-hand" rule is a mnemonic that will allow you to always visualize this directionality correctly. Make a fist with your right hand, with the thumb pointing upward. As the helix rises in the direction of the thumb, the fingers curl in the direction of the turn.
Each nucleotide base of one strand is paired with a nucleotide base on the other strand to create a stable structure of the two polymers. Early on, Erwin Chargaff recognized that, in DNA molecules, the number of A molecules equaled the number of T molecules, and that the number of G molecules equaled that of C molecules. A similar relationship did not hold for RNA, however. This was before the discovery of the double-helical structure of DNA, and it is explained by the further demonstration that the pairing of bases is not random, but rather follows the rule that an A pairs with a T and a G pairs with a C. These relationships are known as "complementarity rules". The nature of the forces between the complementary bases is hydrogen bonding and vanderWaals forces and the hydrophobic force. We will say more about these later.
It turns out that it takes a stretch of 10.5 paired nucleotide bases to make a complete turn of the helix. When we look at DNA topology below, we will approximate this as 10 bases per turn to make the mathematics simpler. Looking at the dimer drawn above, then, we can pair it to its complementary dimer, d(CTp) ,where we have written from the direction 5' -3', but we cannot appreciate the double-helical nature of DNA until we have 10-11 bases on one strand paired with their complements on the other. (Note that this discussion has centered on DNA. RNA is not a double-stranded helical molecule. It is usually single-stranded, although small stretches of it may be doubly wound if the right relationship between contiguous bases in the "linear" strand exist. RNA does not, therefore, display "Chargaff"s Rules".) It should be readily apparent that the direction of the strand complementary to the 5'-3'- strand is 3'-5'.
The double helical structure of DNA can be described as analogous to a helical staircase, with the two chains of sugar-phosphate bonds representing the rails. Since the bases are attached to the sugars, and each base is paired to its complementary base, the edges of the bases are exposed to solvent within two grooves along the helix, the "major groove" and the "minor groove". It is within these grooves that DNA interacts with solvent molecules, ions, protein and other molecules. Structural variation of these grooves is one mechanism by which reactivity of DNA is modulated. There are three major structural variations that we will come across, "A", "B" and "Z" DNA, and they differ in the relationship between the bases and the helical axis:
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