The following dideoxy DNA sequencing gel is produced in a laboratory.

What is the double-stranded DNA sequence of this molecule? Label the polarity of each strand.

Suppose you have a 1-kb segment of cloned DNA that is suspected to contain a eukaryotic promoter, including a TATA box, a CAAT box, and an upstream GC-rich sequence. The clone also contains a gene whose transcript is readily detectable. Your laboratory supervisor asks you to outline an experiment that will (1) determine if eukaryotic transcription factors (TF) bind to the fragment and, if so, (2) identify where on the fragment the transcription factors bind. All necessary reagents, equipment, and experimental know-how are available in the laboratory. Your assignment is to propose techniques to be used to address the two items your supervisor has listed and to describe the kind of results that would indicate binding of TF to the DNA and the location of the binding.

In a dideoxy DNA sequencing experiment, four separate reactions are carried out to provide the replicated material for DNA sequencing gels. Reaction products are usually run in gel lanes labeled A, T, C, and G.

How does PCR play a role in dideoxy DNA sequencing?

In a dideoxy DNA sequencing experiment, four separate reactions are carried out to provide the replicated material for DNA sequencing gels. Reaction products are usually run in gel lanes labeled A, T, C, and G.

Why is incorporation of a dideoxynucleotide during DNA sequencing identified as a 'replication-terminating' event?

In a dideoxy DNA sequencing experiment, four separate reactions are carried out to provide the replicated material for DNA sequencing gels. Reaction products are usually run in gel lanes labeled A, T, C, and G.

Identify the nucleotides used in the dideoxy DNA sequencing reaction that produces molecules for the A lane of the sequencing gel.

Using an illustration style and labeling, draw the electrophoresis gel containing dideoxy sequencing fragments for the DNA template strand 3'-AGACGATAGCAT-5'.

A PCR reaction begins with one double-stranded segment of DNA. How many double-stranded copies of DNA are present after the completion of 10 amplification cycles? After 20 cycles? After 30 cycles?

Alkaptonuria is a human autosomal recessive disorder caused by mutation of the HAO gene that encodes the enzyme homogentisic acid oxidase. A map of the HAO gene region reveals four BamHI restriction sites (B1 to B4) in the wild-type allele and three BamHI restriction sites in the mutant allele. BamHI utilizes the restriction sequence 5′-GGATCC-3′. The BamHI restriction sequence identified as B3 is altered to 5′-GGAACC-3′ in the mutant allele. The mutation results in a Ser-to-Thr missense mutation. Restriction maps of the two alleles are shown below, and the binding sites of two molecular probes (probe A and probe B) are identified.

DNA samples taken from a mother (M), father (F), and two children (C1 and C2) are analyzed by Southern blotting of BamHI-digested DNA. The gel electrophoresis results are illustrated.

In a separate figure, draw the gel electrophoresis band patterns for all the genotypes that could be found in children of this couple.

The electrophoresis gel shown in part (a) is from a DNase I footprint analysis of an operon transcription control region. DNA sequence analysis of a 35-bp region is shown in part (b). The control region, labeled with ³²P at one end, is shown in a map in part (c). Separate samples of control-region DNA are exposed to DNase I, and the resulting DNase I–digested DNA is run in separate lanes of the electrophoresis gel. Unprotected DNA is in lane 1, DNA protected by repressor protein is in lane 2, and RNA polymerase–protected DNA is in lane 3. The numbers along the electrophoresis gel correspond to the 35-bp sequence labeled on the map in part (c). Use the information provided to solve the following problems.

Determine the DNA sequence of the 35-bp region examined.