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Double stranded RNA Single stranded DNA

Double stranded RNA Single stranded DNA



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I have seen in textbooks referring to ds RNA and ssDNA. How a RNA can be double stranded and likewise how a DNA can single stranded and if they do exist why are there names not interchanged?


The main differences between RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) is that DNA contains a hydrogen atom where RNA has a hyroxyl (-OH) group and RNA's uracil is substituted for DNA's thymine. The below image shows several deoxyribose molecules bound together, and off to the side, a ribose molecule. It is the OH group on the bottom right of the ribose molecule that is exchanged for a hydrogen in deoxyribose. The structures of RNA and DNA are almost identical, so there is no reason why you can't have double stranded RNA. Similarly DNA can be single stranded. In fact, for DNA replication and transcription, the DNA strands must be separated. dsRNA and ssDNA are most commonly found in viruses. Check out these lecture slides for more about them: http://www.columbia.edu/itc/hs/medical/pathophys/id/2009/viruses2Color.pdf


Complementary base-pairing is possible for RNA

As the poster is no doubt aware, the double-stranded structure of DNA is stabilized by A-T and G-C base pairs. He will also be aware that in transcription of DNA to RNA (in which A is replaced by U) A-U base pairing occurs. Hence, there is no physico-chemical reason why dsRNA cannot occur between suitable complementary strands.

Viruses provide examples of single- and double-stranded DNAs and RNAs

As is mentioned in another answer, the genomes of bacterial and eukaryotic viruses provide examples of dsDNA, ssDNA, dsRNA and ssRNA.

It takes two to tangle

Whether or not a particular DNA or RNA is double-stranded or single-stranded in Nature depends on whether both complementary strands are present. That depends on biology, not chemistry. Thus, a virus that is single stranded has evolved a replicative strategy whereby many copies of one strand are copied from a few copies of the complementary template. In double-stranded viruses (and organisms) the replication method starts with a double-stranded genome and makes a copy of each at the same time, resulting in equal numbers. (They are also synthesised in a way that allows them immediately to hydbridize.)

Nature is full of black swans

The fact that most DNA encountered is double-stranded and most RNA encountered is single-stranded, just reflects the nature of the genome and translation apparatus of cellular organisms. But transfer-RNA and ribosomal-RNA (and mRNAs) have double-stranded helical portions, and there are a variety of less abundant species of RNAs with individual functions that may involve helix formation. And, of course there are also DNA/RNA hybrids, for example the Okazaki fragments that occur during DNA replication.


I'll try a third pedagogical approach, the above answers are sufficient.

The typical college-entry level textbooks on biology will state that DNA is double-stranded and RNA is single-stranded. This is misleading later on, especially when you encounter an instance of single-stranded DNA and double-stranded RNA.

The posters above have already answered your question well - dsRNA and ssDNA exist all over the tree of life. However, I'd like to emphasize that they also exist transiently all the time in every single cell…

3 critical examples:

  1. DNA must unwind and become single-stranded for DNA replication.
  2. The same is true for transcription.
  3. RNA has a tertiary structure too. Ribozymes rely on this. However, the most abundant RNA species in all cells is ribosomal RNA. It forms these structures:

These are 'single-stranded', but are capable of dimerizing with another RNA species if there is sufficient complementarity between local regions. Below you see many RNA hairpins and loops and locally these are double-stranded, even though it's a single molecule.

In situ hybridization is also another common technique in biology, it takes advantage of pretty much all 'exceptions to the rule' you mention. Nowadays, RNA is increasingly probed. Here is a simple diagram of how it works:

If they do exist why are there names not interchanged?

The names for RNA and DNA are not interchanged because they are different chemically! They just share features, most notably the ability to complement and hybridize to themselves and other nucleic acids, given enough complementarity.


Differential distribution of single-stranded DNA, double-stranded DNA, and RNA in adenovirus-induced intranuclear regions of HeLa cells

We investigated in great detail the fine spatial distribution of nucleic acids within adenovirus-infected HeLa cells by various immunogold labeling procedures. To detect DNA, we used the in situ terminal deoxynucleotidyl transferase-immunogold technique. In addition to the expected evident label over the condensed host chromatin and the structures containing viral double- and single-stranded DNA, label was consistently revealed over round fibrillar spots. By contrast, other virus-induced substructures, such as compact rings, crystalloids, clear amorphous inclusions, and electron-dense amorphous inclusions, displayed no significant label. Except for the viral single-stranded DNA accumulation sites, identical labeling pattern was obtained with the in situ nick-translation-immunogold method. We further labeled the sections with anti-RNA antibodies. Label was present not only over the cytoplasm and the intranuclear fibrillogranular network but also quite obviously over the compact rings and interchromatin granule clusters. None was seen over the other nuclear structures of infected cells, notably over the fibrillar spots. We suggest that these fibrillar spots might be involved in the formation of the viral, non-encapsidated, double-stranded DNA storage site.


What Is Double Stranded RNA? (with pictures)

Double stranded ribonucleic acid (RNA) is a unique form of RNA that appears with two complementary strands, instead of a single strand in isolation, as is more common for this genetic material. RNA contains the code for a number of biological activities and plays an important role in living organisms. Double stranded RNA, also known as dsRNA, usually shows up in viruses and is somewhat unusual. In viruses, it is a unique characteristic, and only a small number of viral families exhibit this trait.

RNA is formed of chains of nucleic acids that attach to each other to form a connected strand. Single stranded forms can have a very complex structure because they fold on each other and create elaborate three dimensional forms. Double stranded RNA can become even more complex, as the two chains of genetic material will also fold and twist to accomplish different functions. Imaging RNA is challenging because of the extremely small size. Very sensitive and powerful imaging systems are necessary to see RNA in a lab setting.

Researchers with an interest in double stranded RNA can isolate it in the lab by introducing cutting enzymes to an RNA sample. The enzymes will target any single strings of RNA to separate them out, leaving the double strands behind. These enzymes are available from scientific suppliers, or labs can make their own for specific research. Usually a controlled environment is necessary for cleaving RNA with enzymes, as contaminants can interrupt the process.

One function of double stranded RNA is interference or silencing. The strands can change the way a gene expresses or turn it off altogether. For dsRNA viruses, this confers a distinct advantage. The virus can enter a cell and turn genes off to protect itself, and hijack the cell to produce more copies of the virus. Viruses in this group can be difficult to treat, as they may become a moving target in the body and can fight the medications a doctor might prescribe to treat them.

Like its more well known counterpart, DNA, RNA can be sequenced with equipment that will identify the chemical chain in each strand. The nucleic acids in RNA will form complementary pairs, and this can make it easier to extrapolate a pattern. Sequencing the genetics of double stranded RNA can be important for understanding how it works in living organisms, which will allow researchers to develop antiviral drugs to target viruses that carry this unique genetic payload.

Ever since she began contributing to the site several years ago, Mary has embraced the exciting challenge of being a InfoBloom researcher and writer. Mary has a liberal arts degree from Goddard College and spends her free time reading, cooking, and exploring the great outdoors.

Ever since she began contributing to the site several years ago, Mary has embraced the exciting challenge of being a InfoBloom researcher and writer. Mary has a liberal arts degree from Goddard College and spends her free time reading, cooking, and exploring the great outdoors.


What is dsRNA?

dsRNA stands for double-stranded RNA. In dsRNA, there are two complementary strands of RNA. These strands are paired with each other by forming bonds between complementary bases. Unlike ssRNA, dsRNA is not long – it is a short molecule. dsRNA is formed when complementary DNA strands are transcribed into RNA by symmetrical transcription from opposing promoters. Moreover, ssRNA can form intra-strand double helixes which are dsRNA by complementary base pairing. dsRNA can also be formed by base pairing of complementary ssRNAs resulting from transposons and repetitive genes.

Figure 02: dsRNA Virus

Some viruses have dsRNA genomes. These viruses have a wide host range. Rotaviruses and picobirnaviruses are dsRNA viruses. The dsRNA genome of these viruses is transcribed into mRNA by RNA dependant RNA polymerase. Then, mRNA molecules translate into viral proteins. Furthermore, the positive sense RNA strand again can be used to produce dsRNA genomes for new viral particles. In the Baltimore classification, dsRNA belongs to Group III. dsRNA viruses infect all organisms including mammalians, bacteria, plants and fungi.

Small interfering RNA or siRNA is a type of dsRNA which can trigger RNA interference in eukaryotes, as well as interferon response in vertebrates.


Viruses

David P. Clark , Nanette J. Pazdernik , in Molecular Biology (Second Edition) , 2013

2.3 DNA Viruses of Higher Organisms

Most DNA viruses of animals contain double-stranded DNA. For example, Simian virus 40 (SV40) is a smallish, spherical virus that causes cancer in monkeys by inserting its DNA into the host chromosome. Another double-stranded DNA virus , herpesvirus, is spherical with an extra outer envelope of material stolen from the nuclear membrane of the host cell ( Fig. 21.14 ). The internal nucleic acid with its protein shell is referred to as the nucleocapsid. This family includes viruses that cause cold sores and genital herpes as well as chickenpox and infectious mononucleosis. The herpesviruses are difficult to cure completely as they are capable of remaining in a latent state where they cause no damage but merely replicate in step with the host cell. Latent herpesviruses are found in the nucleus where they replicate as circular extrachromosomal plasmids. Active infections may then break out again after a long period of quiescence, due to stress or other factors.

Figure 21.14 . Herpesviruses and Poxviruses

Many animal viruses use double-stranded DNA for their genomes. Herpesvirus is a simple virus that has a protein coat and outer envelope surrounding the double-stranded DNA genome. Poxvirus has two envelope layers. A protein layer, known as the palisade, is embedded within the core envelope. In addition, pre-made viral enzymes are also packaged with the genome to allow replication immediately upon infection. These viruses infect animals and in both cases the outermost viral membrane is derived from the membrane of the previous host cell.

Herpesviruses can remain latent for long periods of time.

Poxviruses are the most complex animal viruses and are so large they may just be seen with a light microscope ( Fig. 21.14 ). They are approximately 0.4 by 0.2 microns, compared to 1.0 by 0.5 microns for bacteria like E. coli. Unlike other animal DNA viruses which all replicate inside the cell nucleus, poxviruses replicate their double-stranded DNA in the cytoplasm of the host cell. Virus particles are manufactured inside subcellular factories known as inclusion bodies. Poxviruses have 150–200 genes, about the same number as the T4 family of complex bacterial viruses.

Poxviruses are the largest animal viruses.

Plant viruses containing DNA are relatively rare. One example is cauliflower mosaic virus (CMV), which has circular DNA inside a small spherical shell and kills cauliflower and its relatives such as cabbages and Brussels sprouts. This virus is of note because the promoters from some of its genes are extremely strong and have been used in plant genetic engineering to express insect-killing toxins or other transgenes. Most plant viruses have RNA genomes, as will be discussed below.

Strong promoters from cauliflower mosaic virus are used to express genes in the genetic engineering of plants.


Why is DNA double-stranded, but RNA single-stranded?

Actually, a better question is to ask why DNA is double stranded in the first place. Many people assume that being double-stranded allows for it to be copied, but that explanation doesn't hold water. It could just as well be single-stranded - both RNA and DNA are only copied from a single strand of DNA anyway. In fact, it would save on the whole 'unzipping' process that DNA has to undergo just to present a single strand to RNA or DNA polymerase*.

42 comments:

Yes, it is a good reason for DNA to be double and RNA as single strand, i want to add a point, this DNA contains thymine instead of uracil(RNA), this might give the enzymes of replicatory and translation pathway to recognise its parent strand..

please let me knoe the details of it,.

its really autheintic proof
i wanna ask 1 thng tht why there s 2 H-bond b/w adinine n thymine while 3 H-bonds b/w guanine n cytocine
THANKS, MAIRA

One is a purine and one is a pyrimidine.

To DNA, the number of hydrogen bonds don't matter rather, it is the ability of the bases to form ANY hydrogen bonds that is at issue. T can only form hydrogen bonds with A, and C can only form hydrogen bonds with G. Any other form doesn't work, and pairing can't take place.

As to exactly why there are three H-bonds in the G-C interaction but 2 H-bonds in the A-T interaction, the reason is quite complicated, and has to do with the three dimensional shapes of the various bases, as determined by their molecular makeup. In the A-T interaction, there simply isn't an opportunity for a third H-bond to form. Have a look at this picture to see why.

Can you please clarify - DNA sense anti-sense strand both are involved in DNA replication as per my understanding.

Yeah. Perhaps a clarification has to be made. both the strands can be used as template for DNA replication, but only the 3'-5' (anti-sense) is used during transcription. the reason being RNA polymerase only reads from the 3'-5' DNA strand and synthesize RNA in the 5'-3' direction.

do correct me if i am wrong. =)

why dna isnt in the form of ladder or not straight??

why does dna form a double helix what forces are responsible for the structure of dna. plzz hurry ans..tomorrow is my presentation.

thank you so much! this helped me tremendously with my AP Biology homework.

why is DNA a double stranded (double helix) instead of single stranded?

cool helped me with some of my biology homework

Thank You. was really helpful. I have a question in this regard. Does RNA exist as dsRNA in a cell normally? Is keeping the genome intact,the sole purpose of DNA being double stranded? Kindly explain

thanks for the post.. its help me a lot

Awesome post. Eukaryotic biochemistry is complex. It is no wonder natural selection took billions of years to reach this stage of life.

very helpful and good at describing the reason WHY!

yeah, understand now why dNA is doubled stranded. There is an explanation for everything.

still this doesnt give an explanation why RNA is single stranded?
and why uridine is found in RNA and not in DNA??

Sudheesh, I think it does answer the first question. Read the final paragraph again.

Re: the second question, have a look here.

for the reason number one,'safeguard'can also be acted if it is present as triple or more.
if anyone has answer.

Thank you for being clear.

can anyone tell me why DNA is designated as acid(deoxyribonucleic acid)

sir, I'm still confusd bout wat's da reason of single strandedness of RNA . HOW dis structure stable ? nd is dis a GENITIC MATERIAL or not ?

This comment has been removed by the author.

RNA do not exist as single stranded because:

RNA in a cell is produced only by transcription and no other means. Remember that only one strand of DNA gets transcribed. So obviously only one RNA strand gets synthesized.

one more possible explanation would be:
The complementary strand of DNA is synthesized by DNA dependent DNA polymerase (during replication). And no such RNA dependent RNA polymerase exist in the nucleus to synthesize a complementary RNA strand.

Also dsRNA is of no biological significance as,
# It cannot pass the nuclear pore. (I hope)
# It cannot be translated by the ribosomes (basic principle of antisense RNA therapy)


Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

Experimental introduction of RNA into cells can be used in certain biological systems to interfere with the function of an endogenous gene 1 , 2 . Such effects have been proposed to result from a simple antisense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA transcripts. RNA interference has been used in the nematode Caenorhabditis elegans to manipulate gene expression 3 , 4 . Here we investigate the requirements for structure and delivery of the interfering RNA. To our surprise, we found that double-stranded RNA was substantially more effective at producing interference than was either strand individually. After injection into adult animals, purified single strands had at most a modest effect, whereas double-stranded mixtures caused potent and specific interference. The effects of this interference were evident in both the injected animals and their progeny. Only a few molecules of injected double-stranded RNA were required per affected cell, arguing against stochiometric interference with endogenous mRNA and suggesting that there could be a catalytic or amplification component in the interference process.


Conversion of mRNA into Double-Stranded cDNA

Enzymatic conversion of mRNA into double-stranded insert DNA can be accomplished by a number of different procedures. All of them involve the action of reverse transcriptase and oligonucleotide-primed synthesis of cDNA. After that, the procedures in common use diverge considerably. There are a number of methods for synthesizing the second strand and several procedures for producing suitable ends for making clonable DNA. The major goals of these procedures are to construct insert DNA that is as long as possible, with a high yield of conversion of mRNA into DNA that can ligate to vector DNA. The following protocols require only commercially available reagents and are usually successful in producing good cDNA libraries. The basic protocol describes a method for making blunt-ended cDNA that can then be ligated to linkers for subsequent cloning into a unique restriction site such as EcoRI. The

takes advantage of a linker-primer consisting of (in order from 3' to 5') an oligo(dT) primer, a restriction site for the XhoI endonuclease, and a (GA)20 repeat to protect the restriction site during generation of the blunt-ended cDNA. The internal XhoI sites on the individual cDNA molecules are protected by incorporation of 5-methyl-dCTP in the first-strand nucleotide mix. The resulting cDNAs having unique ends can be cloned into EcoRI /XhoI -digested vectors after ligation of EcoRI adaptors to the 5' end and digestion by XhoI to release the 3' XhoI sites that were incorporated into the cDNA by the linker-primer. These changes result in a considerably streamlined procedure that is substantially faster and easier than the basic protocol.


Cellular proteins specifically bind single- and double-stranded DNA and RNA from the initiation site of a transcript that crosses the origin of DNA replication of herpes simplex virus 1

The small-component origins of herpes simplex virus 1 DNA synthesis are transcribed late in infection by an RNA with heterogeneous initiation sites approximately 290-360 base pairs from the origins. We report that cellular proteins react with a labeled RNA probe representing the 5' terminus of a subset of this RNA but not with the complementary strand of this RNA. The proteins form two complexes. Complex 2 was formed by all nuclear extracts tested, whereas complex 1 was invariably formed by proteins present only in nuclear extracts of mock-infected cells. Complex 1 protects a contiguous stretch of 40 nucleotides of the labeled RNA probe from nuclease degradation. Formation of complex 1 was competitively inhibited in a sequence-specific fashion by single-stranded RNA and DNA and by double-stranded RNA and DNA. The protein(s) forming complex 1 is, thus, quite distinct from known nucleic acid-binding proteins in that they recognize a specific nucleotide sequence, irrespective of the nature (single- and double-stranded RNA and DNA) of the nucleic acid. We conclude the following: (i) the proteins forming complex 1 and 2 are probably different, (ii) complex 1 is neither required throughout infection for viral replication nor able to hinder viral replication in cells in culture, and (iii) cells susceptible to infection encode one or more proteins that recognize specific sequences in single-stranded nucleic acids either these proteins impart a compatible conformation on single-stranded nucleic acids with the conformation of the same strand in the double-stranded nucleic acid, or these proteins confer a specific, distinct conformation to both single-stranded and double-stranded nucleic acids.


Double stranded RNA Single stranded DNA - Biology

While DNA and RNA are similar, they have very distinct differences. Table 1 summarizes features of DNA and RNA.

Table 1. Features of DNA and RNA
DNA RNA
Function Carries genetic information Involved in protein synthesis
Location Remains in the nucleus Leaves the nucleus
Structure DNA is double-stranded “ladder”: sugar-phosphate backbone, with base rungs. Usually single-stranded
Sugar Deoxyribose Ribose
Pyrimidines Cytosine, thymine Cytosine, uracil
Purines Adenine, guanine Adenine, guanine

One other difference bears mention. There is only one type of DNA. DNA is the heritable information that is passed along to each generation of cells its strands can be “unzipped” with small amount of energy when DNA needs to replicate, and DNA is transcribed into RNA. There are mutliple types of RNA: Messenger RNA is a temporary molecule that transports the information necessary to make a protein from the nucleus (where the DNA remains) to the cytoplasm, where the ribosomes are. Other kinds of RNA include ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), and microRNA.

Even though the RNA is single stranded, most RNA types show extensive intramolecular base pairing between complementary sequences, creating a predictable three-dimensional structure essential for their function.

As you will learn later, information flow in an organism takes place from DNA to RNA to protein. DNA dictates the structure of mRNA in a process known as transcription, and RNA dictates the structure of protein in a process known as translation. This is known as the Central Dogma of Life, which holds true for all organisms however, exceptions to the rule occur in connection with viral infections.

In Summary: DNA and RNA

Nucleic acids are molecules made up of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA. DNA carries the genetic blueprint of the cell and is passed on from parents to offspring (in the form of chromosomes). It has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other. RNA is single-stranded and is made of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) is copied from the DNA, is exported from the nucleus to the cytoplasm, and contains information for the construction of proteins. Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis, whereas transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. microRNA regulates the use of mRNA for protein synthesis.


Molecular Biology

The helical structure of a molecule of DNA engaged in replication is illustrated in Figure 1.13. The nonreplicated region consists of the parental duplex, opening into the replicated region where the two daughter duplexes have formed. The double helical structure is disrupted at the junction between the two regions, which is called the replication fork . Replication involves movement of the replication fork along the parental DNA, so there is a continuous unwinding of the parental strands and rewinding into daughter duplexes.

  • Endonucleases cut individual bonds within RNA or DNA molecules, generating discrete fragments. Some DNAases cleave both strands of a duplex DNA at the target site, while others cleave only one of the two strands. Endonucleases are involved in cutting reactions, as shown in Figure 1.14.