You were going to sequence a rice DNA fragment whose sequence was only know at one end, as shown below.5’ AAACGATCGAGTCGCATCCAAAATCGATACCC—unknown region3’ TTTGCTAGCTCTGCGTAGGTTTTAGCTATGGG—unknown regionAfter several tries, you obtained a beautiful sequencing image as shown here:The worked out well partially because you had designed a primer for sequencing the unknown region according to the following guideline: Tm is 55 – 60°C.Ensures primer had a appropriate melting temperature for PCR ans sequencing. The GC content of the primer is the same as the genome/template (rice = 60%, human/Drosophila = 45-50%). A same nucleotide cannot be more than 2 in a row, e.g. CCC, GGGGG, AAA. The secondary structure of the primer must be none or weak. No primer dimers (The primer anneals to itself). 3’ end is the most important: it should not end in A, preferably ends in GG, GC, CG or CCThis website can help you design the primer: http://www.oligoevaluator.com/OligoCalcServlet Question 1A. What is the primer sequence you designed? Please include the 5’ and 3’ ends. Question 1B. Why did you select the sequence as your primer? The image shows a gel electrophoresis pattern typically used in DNA sequencing. At the top of each lane, the abbreviations ddA, ddC, ddG, and ddT are indicated, representing the four dideoxynucleotides used in Sanger sequencing: dideoxyadenosine, dideoxycytidine, dideoxyguanosine, and dideoxythymidine.### Gel Electrophoresis Explanation1. **Lanes:** - There are four distinct lanes in the gel, each corresponding to a reaction mixture that includes DNA polymerase, primers, normal deoxynucleotides (dNTPs), and one type of dideoxynucleotide triphosphate (ddNTP). The presence of these ddNTPs causes chain termination at specific nucleotides.2. **Bands:** - The bands within each lane represent DNA fragments of varying lengths. Each band corresponds to a DNA fragment terminated at a specific point, where a ddNTP was incorporated into the growing DNA chain.3. **Reading the Sequence:** - To determine the sequence of the DNA, read the bands from the bottom to the top of the gel. The sequence order is determined by the position of each band in relation to the ddNTP lane from which it originated.This gel electrophoresis pattern is integral to determining the nucleotide sequence of a DNA strand using the chain termination method pioneered by Frederick Sanger.

Answered: You were going to sequence a rice DNA…

Human Anatomy & Physiology (11th Edition)

11th Edition

ISBN:9780134580999

Author:Elaine N. Marieb, Katja N. Hoehn

Publisher:Elaine N. Marieb, Katja N. Hoehn

Chapter1: The Human Body: An Orientation

Section: Chapter Questions

Problem 1RQ: The correct sequence of levels forming the structural hierarchy is A. (a) organ, organ system,...

See similar textbooks

Related questions

Concept explainers

Question

100%

You were going to sequence a rice DNA fragment whose sequence was only know at one end, as shown below.

5’ AAACGATCGAGTCGCATCCAAAATCGATACCC—unknown region

3’ TTTGCTAGCTCTGCGTAGGTTTTAGCTATGGG—unknown region

After several tries, you obtained a beautiful sequencing image as shown here:

The worked out well partially because you had designed a primer for sequencing the unknown region according to the following guideline:

Tm is 55 – 60°C.

Ensures primer had a appropriate melting temperature for PCR ans sequencing.

The GC content of the primer is the same as the genome/template (rice = 60%, human/Drosophila = 45-50%).
A same nucleotide cannot be more than 2 in a row, e.g. CCC, GGGGG, AAA.
The secondary structure of the primer must be none or weak.
No primer dimers (The primer anneals to itself).
3’ end is the most important: it should not end in A, preferably ends in GG, GC, CG or CC

This website can help you design the primer: http://www.oligoevaluator.com/OligoCalcServlet

Question 1A. What is the primer sequence you designed? Please include the 5’ and 3’ ends.

Question 1B. Why did you select the sequence as your primer?

The image shows a gel electrophoresis pattern typically used in DNA sequencing. At the top of each lane, the abbreviations ddA, ddC, ddG, and ddT are indicated, representing the four dideoxynucleotides used in Sanger sequencing: dideoxyadenosine, dideoxycytidine, dideoxyguanosine, and dideoxythymidine.

### Gel Electrophoresis Explanation

1. **Lanes:**
- There are four distinct lanes in the gel, each corresponding to a reaction mixture that includes DNA polymerase, primers, normal deoxynucleotides (dNTPs), and one type of dideoxynucleotide triphosphate (ddNTP). The presence of these ddNTPs causes chain termination at specific nucleotides.

2. **Bands:**
- The bands within each lane represent DNA fragments of varying lengths. Each band corresponds to a DNA fragment terminated at a specific point, where a ddNTP was incorporated into the growing DNA chain.

3. **Reading the Sequence:**
- To determine the sequence of the DNA, read the bands from the bottom to the top of the gel. The sequence order is determined by the position of each band in relation to the ddNTP lane from which it originated.

This gel electrophoresis pattern is integral to determining the nucleotide sequence of a DNA strand using the chain termination method pioneered by Frederick Sanger.

Expert Solution

Step 1: Definition of primer sequence

A primer is a brief sequence of single-stranded DNA that is utilized in the PCR method of polymerase chain reaction. It normally has a length of $space 18 space t o space 25 space$ nucleotides and serves as the foundation for DNA synthesis. A distinct region of the genome can be identified with the aid of the primer sequence, which is made to be complementary to the template DNA.

Trending now

This is a popular solution!

Step by step

Solved in 4 steps with 15 images

SEE SOLUTION Check out a sample Q&A here

Knowledge Booster

Learn more about

Need a deep-dive on the concept behind this application? Look no further. Learn more about this topic, biology and related others by exploring similar questions and additional content below.

Similar questions