Page 41 - Genetics_From_Genes_to_Genomes_6th_FULL_Part3

Solved Problems 335

II. In the course of sequencing a genome, a computer is Vocabulary
trying to assemble the following six DNA sequences 1. Match each of the terms in the left column to the best-
into contigs (that is, stretches of contiguous sequences fitting phrase from the right column.
that can be obtained from overlapping clones):
a. oligonucleotide 1. gene in a vector that enables isolation
5' A G CA AA TT AC AG CA AT AT GA AGAG AT C 3' of transformants
5' A A AA TG CC CT AA AG GA AA TG AG AT TT T 3'
5' TG AT CTCT TC A TAT TG CT GT AA TTT GC 3' b. vector 2. a collection of the DNA fragments of
5' TC CT TT TA AAAA TCTC AT TT CC TTT AG 3' a given species, inserted into a vector
5' T ACA GC AA TA TG AA GA GA TC AT AC AG T 3' c. sticky ends 3. synthetic DNA element in a cloning
5' AAA TG CC CT AA AG GA A AT GAGA TTTTT 3' vector with unique restriction sites

a. How many contigs are represented by this set of DNA used for insertion of foreign DNA
sequences, and what is the sequence of each contig? d. recombinant DNA 4. stable binding of single-stranded DNA
molecules to each other
b. Some of these sequences are complementary to each e. ddNTPs 5. method for separating DNA molecules
other in the region of overlap, while other sequences by size
overlap but represent the same DNA strand. How is f. genomic library 6. oligonucleotide extended by DNA
this possible? polymerase during replication
c. If these sequences are all derived at random from the g. genomic equivalent 7. contains genetic material from two
human genome, why would you actually expect them different organisms
not to overlap with each other? h. gel electrophoresis 8. the number of DNA fragments
d. If you had enough sequence reads to cover all the sufficient in aggregate length to
base pairs in the human genome, how many contigs contain the entire genome of a
would there be? specified organism
i. selectable marker 9. short single-stranded sequences
Answer found at the ends of many restriction
a. Two contigs exist. fragments
j. hybridization 10. a short DNA fragment that can be
Sequences 1, 3, 5: synthesized by a machine
5' A G CA AA TT AC AG CA AT AT GA AGAG AT C ATA CAGT 3' k. primer 11. DNA chain-terminating subunits
3' T C GT TT AA TG TC GT TA TA CT TCTC TA G TAT GT CA 3' l. polylinker 12. a DNA molecule used for transporting,
Sequences 2, 4, 6: replicating, and purifying a DNA
fragment
5' T C CT TT TA AA AA TCTC AT TT CC TT TA GG GC AT TT T 3'
3' A G GA AA AT TT TT AGAG TA AA GG AA AT CC CG TA AA A5'
When solving the problems in this chapter, unless in-
The orientation in which these fragments are written structed otherwise, make the simplifying assumptions that
does not matter. base pair sequences are random and that the number of
b. You are sequencing different molecules of DNA in A–T and G–C base pairs are equivalent.
clones that are overlapping. The clones are ligated
into a vector in random orientations, and it’s the Section 9.1
orientation that determines which DNA strand is 2. For each of the restriction enzymes listed below:
used as a template. Therefore, some of the se- (i) Approximately how many restriction fragments
quences read the same strand but start in different would result from digestion of the human genome
places, and others read the complementary strand. (3 × 10 bases) with the enzyme? (ii) Estimate the
9
c. If you only had six short sequences from the entire average size of the pieces of the human genome
3 billion bp human genome, the chances would be van- produced by digestion with the enzyme. (iii) State
ishingly small that these few sequences all come at ran- whether the fragments of human DNA produced by
dom from the same small region of the genome. Thus, digestion with the given restriction enzyme would
six random sequences of the human genome should not have sticky ends with a 5′ overhang, sticky ends
overlap. Clearly, these sequences were not derived at with a 3′ overhang, or blunt ends. (iv) If the enzyme
random but were instead selected. (For example, these produces sticky ends, would all the overhangs on all
could be sequences all derived from a mini-library made the ends produced on all fragments of the human
from a particular human DNA insert in a BAC vector.) genome with that enzyme be identical, or not? (The
d. Each human chromosome is a contig. A human male recognition sequence on one strand for each enzyme
genome sequence would have 24 contigs, and a is given in parentheses, with the 5′ end written at
female genome 23 contigs. the left. N means any of the four nucleotides; R is