Single-Strand DNA Binding Protein

The molecule of life is the DNA as it contains information on the heredity and genetic makeup of an organism. All characteristics, from height to skin color to intelligence, and the rest are encoded in this small but mighty molecule. 

However, due to compartmentalization, the DNA molecule is supercoiled. Hence, other molecules are present to help to uncoil and read its information and also in the application of DNA. They also help in the stability and excitement of mutagenic parts of DNA which can prove to be harmful later on in life. 

These types of molecules are called binding proteins and this article provides an overview of how they function and their overall contribution to the genetic system in the body.

What is DNA?

DNA, otherwise known as Deoxyribonucleic acid, is the foundation of molecular biology and its central dogma.

It is a supercoiled molecule with a shape of a double helix made up of 2 polynucleotide chains that enable a cell to reproduce; thus creating a copy of itself.

That is to say, DNA stores hereditary and genetic information that is needed for reproduction to occur.

DNA is also involved in the regulation, development and overall functioning, and growth of cells and organisms. 

However, the definition above is for double-stranded DNA, which is the norm for eukaryotes(organisms that possess a true nucleus). Single-stranded DNA also exists in prokaryotic organisms and viruses, and its shape is like that of a half ladder with bases that are broken.

What is a DNA Binding Protein?

DNA binding proteins are proteins or molecules that have DNA binding domains(these are specific regions on a protein that contains structural modifications that can identify single or double-stranded DNA).

These domains have various functions linked with

• DNA replication
• Storage,
• Repair,
• Modification of DNA molecule

Also, many proteins that are involved in the process of gene regulation possess these domains eg proteins that are involved in the transcription of DNA are called transcription factors.

There are different types of domains and they are listed as follows:

• Helix turn Helix 
• Zinc finger
• Leucine zipper
• Winged helix
• Winged helix turn helix
• Helix loop helix
• HMG box
• WOB-folding
• OB-fold domain

Examples of DNA Binding Proteins

Several examples of DNA binding proteins are well-known transcription factors that help to regulate the process of DNA transcription. Others are

• DNA polymerases
• Histones
• Nucleases

All of them use diverse types of domains like zinc finger, helix turn helix, etc.

Types of DNA

Based on the location of the DNA molecule(recall it is found in cells), DNA has 2 types:

1. Nuclear DNA

Nuclear DNA is typically located in the nucleus of the cells. It has several characteristics like: 

• Linear and open structure
• Diploid in nature, gotten from both parents 
• Has 46 chromosomes 

2. Mitochondrial DNA

Mitochondrial DNA is found in the mitochondria of the cell. Characteristics include the following:

• The closed and circular structure
• Haploid in nature, gotten from only the mother

Single-Stranded DNA

Under normal conditions, DNA is a double-stranded molecule(dsDNA). But during the replication process, when DNA polymerase zips the helix, we get two halves of the helix- now single-stranded DNA(ssDNA).

It also exists in certain organisms; bacteriophages such as microviridae and viruses eg Parvoviridae.

Single strand DNA can also be gotten from the denaturation of double-stranded DNA either from heat or chemical action.

The single-stranded DNA is not as stable as its double-stranded counterpart(in eukaryotes) thus it must be bound to another single-stranded DNA molecule to form a double-stranded DNA molecule or it will be destroyed.

Note: The single-stranded DNA in the organisms listed as examples above still possesses the ability to store and retain genetic information required for reproduction.

Single-strand DNA can be utilized for:

• DNA sequencing
• Microarray
• Hybridization techniques

Single strand DNA Binding Proteins

Only a distinct group of proteins can bind to the single-strand DNA molecule, unlike the double-strand DNA molecule.

One example is replication protein A. It is the most studied out of all of them and is used in reaccess where DNA is cleaved to form single, separate strands such as DNA replication, DNA recombination, and DNA repair.

The proteins help the single strands of DNA to be stable so as not to form loops, or be destroyed by nucleases(a class of enzymes that hydrolyzed the phosphodiester bonds of DNA and RNA)

Uses of Single-Strand DNA Binding Proteins

• Stability of Single-Strand DNA

Single strand DNA binding proteins help to maintain the structure of single-strand DNA. The proteins bind strongly to the DNA molecule but in no specific order.

This is done mostly through the formation of hydrogen bond linkages between the phosphate and ribose. 

• Mismatch Repair

Mismatch repair involves the correction of mismatched nucleotides in the complementary paired DNA strands that occur from errors in DNA replication and recombination.

•  DNA replication

DNA replication is a process where a double-stranded DNA molecule is duplicated to give two similar copies of single-strand DNA molecules. 

• DNA recombination

Conclusion

Single strand DNA binding proteins are ad important as even the DNA itself; since they help in the stability of the DNA molecule.

Their functions and applications are given in the article above, and it is seen that they are truly indispensable for the continuity of life itself.