Question

Dr. M. B. Goshe PROBLEM SET 5 BCH 351 (c) (0.1 pts) There was a design decision to add (N-aminohexyl)carbamoyl group to the C5 rather than the C6. Why might addition to C6 probably result in an unusable nucleotide analog? 4 0.6 pts) The research group described in Question #2 went to the trouble of solving the structures of several of the modified double strand DNAs to determine the position of the (N aminohexyl)carbamoyl group. One of their structures is shown below. carbamoyl (#2) carbamoyl (#1) (a) (0.3 pts) To get orientated with the structure you need to know the polarity of the two strands. Is the terminus at "l" a 5' or 3' end of the strand? How can you tell? (b) (0.3 pts) Two (N-aminohexyl)carbamoyl groups are pointed out in the structure. Are the first and second (N-aminohexyl)carbamoyl groups in major or minor grooves? How can you tell? 4

Answer 1

a) the terminus at "1" is 3'OH end of the DNA strand. if you look at the structure and IUPAC nomenclature and numbering of nucleotide you'll find that base is attached to the 1st carbon of the sugar, 5th carbon contains PO4 group and 3rd carbon contains OH group. now look at the structure below and compare with the structure.

NH2 O-P-O-CH2 OH OH AMP

2) deeper area in double helix is the major groove and the shallow area is the minor groove. both the aminohexyl carbamoyl group are presen at major groove site.