Question

1. The restriction enzyme SauIIIA recognizes the 4 bp sequence GATC, and the "6-cutter" enzyme BamHI recognizes the sequence GGATCC. Digestion of a particular bacteriophage genome produced a total of 160 SauIIIA fragments. Approximately how many BamHI fragments would you expect if:
A) the phage genome has a “G+C” content of 50%?
B) the phage genome is 80% G+C?

2. At least some of the RNA sequences below include significant regions that are self-complementary, and therefore might form secondary structures such as hairpins or stem-loops. For purposes of this problem, you should identify which sequences have any secondary structures that fit the following criteria:

a minimum length of 5 base pairs

only “Watson/Crick” pairings (i.e., A-U or G-C), with NO mismatches or unpaired bases within the helical/paired region

connecting "hairpin" turns or loops that consist of at least 3 unpaired bases.

(Note that these conditions do not always apply to the secondary structures formed by naturally occurring RNA molecules.)

Answer 1

1. (A) SaulllA has a recognition sequence that is present within the recognition sequence of BamHl which is G(GATC)C. The sequence under the brackets represents the recognition sequence for SaulllA. In this condition we are given that the digestion of bacterial genome reoprted 160 SaulllA sites. So for BamHl, we can predict if the recognition sequence of SaulllA is sandwitched between G and C. We can estimate to have 160 _GATC_ sites, and for BamHl we need to fill the first _ with G and Second_ with C. The condition given is 50% GC content in phage genome. So for the first _ the probability of G stands 1/4, and the probability of C stands 1/4. When we combine the chances the probability of having G in first place of blank and C in the second place of blank is 1/4 x 1/4 = 1/16. Taking into the case that wwe have 50% more chances of occourence of GC then our resulting probability for the above case comes as 1/16 x 2= 1/8. So number of BamH1 can pe predicated as 1/8 x 160= 20 sites.

when the G+C contect is 80 % , we can predicat to have more occourence of Gand C in their respective sites. So a rough assumption considering the existance of 160 SaulllA sites and the blanks have 80% cahnces to be occupies as G or C respective to site of BamHl, there can be 80% to the no. of SaulllA sites which is 160 x 80/100= 128.

2. Satisfying the all the 3 conditions as given in the question, which are minimum length of 5bp,Watson-Crick pairing with no mismatch, and a span of atleast 3bp if they connect the turns of loops. The structures or sequences identified are-

(a) tRNA- the D-loop and D-arm, The anticodon loop and its arm, T(psi)C loop and arm repesents self complementarity with all satisfying conditions.

(b) Primer-dimer- sometimes if the primer has some complementary region it binds to itself forming a primer-dimer resulting a failing of working of primers. So this structure also satisfies all the given condition.