Hello Jery,
DNA is a negatively charged polymer that is made up of nucleotide building blocks. Before we discuss where its negative charge comes from, let’s take a close-up view of the nucleotide monomers that make up DNA.

Four different nucleotides are covalently linked to build DNA molecules: adenine (A), guanine (G), cytosine (C), and thymine (T). Each nucleotide consists of a phosphate group, a deoxyribose sugar group, and a nitrogenous base. Nucleotides are covalently linked to one another via the formation of phosphodiester bonds between the sugar group of one nucleotide and the phosphate group of a second nucleotide.

As you likely know, most DNA is found in a double-stranded form with complementary base pairing between the two DNA strands: A pairs with T, and C pairs with G. The formation of phosphodiester bonds between adjacent nucleotides forms alternating sugar and phosphate groups, called the “sugar-phosphate backbone” of a DNA molecule. Furthermore, DNA forms a double helix. In a nutshell, the structure of DNA can be thought of as a twisted ladder with its complementary base pairs making up the rungs of the ladder and the sugar-phosphate backbone of each strand making up each side of the ladder.

So, where does DNA’s negative charge come from? The phosphate groups that make up the sugar-phosphate backbone are responsible. You might be interested to read that molecular biologists capitalize on this property of DNA to isolate DNA fragments of differing sizes. Because DNA is negatively charged, molecular biologists often use agarose gel electrophoresis to separate different sized DNA fragments when DNA samples are subjected to an electric field — due to their negative charge, all of the DNA fragments will migrate toward the positively charged electrode, but smaller DNA fragments will migrate at a faster pace than larger DNA fragments. This simple, yet powerful, technique allows researchers to isolate DNA fragments of different sizes.

Supercoiling is a term used to describe what happens when the two strands of a double-stranded, double helical DNA molecule are separated from each other, which occurs during DNA replication and transcription. One way to visualize supercoiling is to think about what happens when you twist a rubber band and then hold onto one end of it while trying to open it in the middle — the original coils will twist on top of each other to form a condensed, twisted ball. This is what supercoiling is like.

Prokaryotic and eukaryotic chromosomal DNA is organized in different ways. Due to the circular nature of most prokaryotic chromosomes, they are often highly supercoiled under normal growth conditions. In contrast, eukaryotic chromosomes are linear and packaged using histone proteins, which are not present in most prokaryotic cells. As a result, eukaryotic chromosomes are not nearly as supercoiled as prokaryotic chromosomes. Intriguingly, genomes can be negatively supercoiled, (i.e., the DNA is twisted in the opposite direction of the double helix) or positively supercoiled (i.e., the DNA is twisted in the same direction as the double helix). We encourage you to follow the links we’ve provided below to learn more about this fascinating process.

For more information about DNA and its nucleotide building blocks, check out these links:

http://www.nature.com/scitable/topicpage/dna-is-a-structure-that-encodes-biological-6493050

http://www.nature.com/scitable/topicpage/discovery-of-the-function-of-dna-resulted-6494318

http://www.nature.com/scitable/topicpage/Discovery-of-DNA-Structure-and-Function-Watson-397

http://nobelprize.org/educational_games/medicine/dna_double_helix/readmore.html

To learn more about DNA supercoiling and DNA packaging, follow these links:

http://www.nature.com/scitable/topicpage/genome-packaging-in-prokaryotes-the-circular-chromosome-9113

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=mboc4&part=A975&rendertype=figure&id=A1006

http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=mcb&part=A802#A818

http://www.nature.com/scitable/topicpage/dna-packaging-nucleosomes-and-chromatin-310

To learn more about agarose gel electrophoresis, check out these links:

http://www.nature.com/scitable/content/gel-electrophoresis-can-be-used-to-separate-44970

http://learn.genetics.utah.edu/content/labs/gel/

Hi Mithun,
DNA is a negatively charged polymer that is made up of nucleotide building blocks. Before we discuss where its negative charge comes from, let’s take a close-up view of the nucleotide monomers that make up DNA.

Four different nucleotides are covalently linked to build DNA molecules: adenine (A), guanine (G), cytosine (C), and thymine (T). Each nucleotide consists of a phosphate group, a deoxyribose sugar group, and a nitrogenous base. Nucleotides are covalently linked to one another via the formation of phosphodiester bonds between the sugar group of one nucleotide and the phosphate group of a second nucleotide.

As you likely know, most DNA is found in a double-stranded form with complementary base pairing between the two DNA strands: A pairs with T, and C pairs with G. The formation of phosphodiester bonds between adjacent nucleotides forms alternating sugar and phosphate groups, called the “sugar-phosphate backbone” of a DNA molecule. Furthermore, DNA forms a double helix. In a nutshell, the structure of DNA can be thought of as a twisted ladder with its complementary base pairs making up the rungs of the ladder and the sugar-phosphate backbone of each strand making up each side of the ladder.

So, where does DNA’s negative charge come from? The phosphate groups that make up the sugar-phosphate backbone are responsible. You might be interested to read that molecular biologists capitalize on this property of DNA to isolate DNA fragments of differing sizes. Because DNA is negatively charged, molecular biologists often use agarose gel electrophoresis to separate different sized DNA fragments when DNA samples are subjected to an electric field — due to their negative charge, all the DNA fragments will migrate toward the positively charged electrode, but smaller DNA fragments will migrate at a faster pace than larger DNA fragments. This simple, yet powerful, technique allows researchers to isolate DNA fragments of different sizes. We hope you’ll check out the links below to learn more about DNA structure and the phosphate groups that make up its backbone.

For more information about DNA and its nucleotide building blocks, check out these links:

http://www.nature.com/scitable/topicpage/dna-is-a-structure-that-encodes-biological-6493050

http://www.nature.com/scitable/topicpage/discovery-of-the-function-of-dna-resulted-6494318

http://www.nature.com/scitable/topicpage/Discovery-of-DNA-Structure-and-Function-Watson-397

http://nobelprize.org/educational_games/medicine/dna_double_helix/readmore.html

To learn more about agarose gel electrophoresis, check out these links:

http://www.nature.com/scitable/content/gel-electrophoresis-can-be-used-to-separate-44970

http://learn.genetics.utah.edu/content/labs/gel/

Welcome back Sanjeevsingh,
You seem interested in broadening your interests beyond peppers to learn about eggplant genetics and breeding. In particular, you’d like to learn more about genes and breeding strategies linked to eggplant color, shape, and disease-resistance. Let’s start by providing you with some background information about eggplants, then we’ll help you search for answers to your specific questions.

Eggplants belong to the genus Solanum. Although eggplants are native to India, they are grown throughout the world. In line with our previous answers to your questions about pepper plants, the Solanum genus includes many different varieties of eggplants that come in different sizes, shapes, and colors (e.g., purple, green, white). As you noted, eggplants are also susceptible to many types of pathogens and insects — with bacteria and fungal wilts being the most detrimental.

As we mentioned in our previous answer about peppers, spontaneous mutations are often responsible for the variety of traits within populations. By selecting desirable traits and breeding Solanum plants, people have been able to develop all the different varieties of eggplants.

To help you track down some answers to your specific questions about eggplant genes and breeding strategies associated with diverse traits (e.g., color, shape, disease-resistance), we encourage you to carry out some searches using the PubMed website or Google Scholar to identify research articles:

http://www.ncbi.nlm.nih.gov/pubmed/

http://www.scholar.google.com

You might want to try using the following some general queries to begin: “Solanum” and “genes”; or “eggplant” and “genes.” Then, you might want to carry out some more specific searches using additional search terms, such as: “eggplant/Solanum” and “genes” and “color”; or “eggplant/ Solanum” and “genes” and “disease-resistance”; or “eggplant/ Solanum” and “shape” and “genes.” You might also want to include the search term “breeding” in your searches. If you’d like to obtain review articles related to these topics, you might also want to include the search term “review.”

We’ve also identified some articles in our own searches that may help you get started. Best of luck to you with your searches!

Please follow these links to learn more about eggplant breeding and genetics:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712397/?tool=pubmed

http://www.genetics.org/cgi/content/full/161/4/1713

http://www.ncbi.nlm.nih.gov/pubmed/20714999

Hello again Sanjeevsingh,
Now, you’d like to know about genes that determine the color of Capsicum fruits and how they are selected in open field conditions. This is a great question! As we discussed previously, Capsicum is a genus that includes many different types of peppers. These peppers range in intensity from mild bell peppers to hot chili peppers. They also come in a wide variety of colors, sizes, and shapes. Although they were first domesticated in the Americas, many different Capsicum varieties have been bred since then.

As we mentioned in our previous answer, spontaneous mutations are often responsible for the variety of traits within populations. By selecting desirable traits and breeding Capsicum plants, people have been able to develop different varieties of peppers, including different colored peppers.

In order to answer your specific question about genes determining Capsicum color in open fields, we encourage you to try some searches using the PubMed website or Google Scholar to identify primary research articles:

http://www.ncbi.nlm.nih.gov/pubmed/

http://www.scholar.google.com

You might want to try using the following query to begin: “capsicum” and “color” and “genes.” If you’d like to obtain review articles related to these topics, you might also want to include the search term “review.”

We’ve also identified some articles in our own searches that may help you get started. Happy reading — and best of luck to you!

Please follow these links to two articles that discuss genes linked to Capsicum color:

http://jhered.oxfordjournals.org/content/99/2/105.long

http://jxb.oxfordjournals.org/cgi/content/full/58/14/3841?view=long&pmid=18037678