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Questions tagged [dna-rna]

For questions regarding nucleic acids, their properties, structures, functions etc.

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Charge of nucleosides at 7.3 p

I am looking for electric charge values of adenine ($\ce{C5H5N5}$), cytosine ($\ce{C4H5N3O}$), thymine ($\ce{C5H6N2O2}$), guanine ($\ce{C5H5N5O}$) and uracil ($\ce{C4H4N2O2}$) at $\mathrm{pH} = 7.3$ ...
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How are elements used in the human body (for example) encoded for in the genome? [closed]

Given that bones require calcium and iron is used in red blood cells, how are these materials gathered by the developing organism? Is it possible that very small quantities used as "references" are ...
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Two-part fluorescence behaviour of DNA oligo tagged with Cy5 fluorophore. Explanations?

We have designed a 56nt single-stranded DNA oligo. Its sequence has no predicted secondary structure, and no predicted reaction with other similar oligos. A Cy5 fluorophore is attached at the 5 prime ...
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Are we capable of deliberatly creating DNA from inorganic compounds?

Good day The Miller–Urey experiment showed that organic compound can naturally form from inorganic substances. What i wish to know is this: Could we as humans deliberately create a DNA molecule ...
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Find volume of sample such that it contains 100ng of DNA

Im struggling with the maths of concentrationsand volumes and things..Ill give the question, then my thoughts on it: A DNA trimer strand, ab, has moleuclar weight of $9309ng/\mu mol$. I#m designing a ...
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How are Quantum effects involved in DNA, Genome and RNA conformation and operation?

What is the current hypothesis that explain how QM affects the structure and functions of RNA and DNA strands or the Genome? I didn't find any work besides Quantum entanglement between the electron ...
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862 views

Most basic nitrogen in Adenine

I need to find the most basic site of Adenine: The $\ce{NH2}$ group and $\ce{NH}$ cant be strong base as electrons are delocalised. This leaves us with $1,7,3$. I thought that electron density on $1,...
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Deoxyribose nucleotide structure anomeric carbon

Is the anomeric carbon always going to be beta in DNA or RNA (so the hydroxyl group is always pointing up) ? It seems to be the way I see it all the time but I have not read this as a rule.
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Why does the keto tautomer of guanine have lower energy?

Looking at the keto and enol forms of guanine, it would seem as if the enol form is more stable, due to the fact that aromaticity is established with the enol form. However, according to a question on ...
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Wouldn't radiolabelled phosphorus in DNA break it apart as it disintegrates?

The Hershey-Chase experiment was designed to prove that DNA is the genetic material in organisms. In this experiment, two batches of viruses were grown in two separate media A and B, with A having an ...
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Is DNA a base inside the cell?

DNA is deoxyribonucleic acid because it has phosphate groups in every one of it's nucleotides. However, in aqueous solutions protons will ionize, leaving phosphates alone as negative groups, i.e., ...
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Thought experiment about nucleic acids oligomerization

A thought experiment: suppose you have managed to contain a pair of nucleic acids in a container in close proximity. How could you encourage oligomerization to occur using only non-enzymatic, physical ...
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Thermodynamics of DNA double helix formation?

The entropy of a system decreases when 2 single stranded DNA molecules come together and form a double stranded molecule. For this to occur the total entropy of the universe must increase. Thus, heat ...
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Which is more stable chemically: DNA or peptide

Assuming enzyme-free environment, and the DNA and peptide are lyophillized, and then stored in vials under the same conditions (temperature and humidity). On average, which would be more chemically ...
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Pi electron stacking, how does it work?

I've come across the term base-pair stacking (with reference to B-DNA) in my school text book, and I had posted a question in that regard on Bio.SE. I've also seen a similar (albeit brief) version ...
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Logic behind this statement (On Transcription)

There's this little paragraph in my textbook, parts of which I find redundant. My teacher is absolutely fine with this ("Aaron, you've got to write down what's in the textbook if you want to score in ...
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Which base pair is more stable, U:G or I:C?

As a result of damage (usually deamination), DNA will sometimes contain uracil and inosine bases. I am trying to determine which unnatural base pairing combo would be more stable: uracil paired with ...
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Gel electrophoresis separates proteins on the basis of what property?

In SDS-PAGE for separation of proteins, SDS is an ionic detergent that coats the unfolded protein to mask its native charge and give at a uniform charge to length ratio. Since the length of the ...
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Chemical Biology - synthesizing/designing siRNA [closed]

I was reading an article on siRNA, and from what I read it sounded like we can edit genes using siRNA. First, did I even interpret this correctly? Second, I read that siRNA was being used to create ...
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Why does a larger DNA gel box require a higher voltage to move DNA at the same speed?

If I run a small agarose DNA gel and use a voltage of 90V, the DNA migrates the length of the gel in about an hour. If I use a medium size gel I have to use a voltage of 140V to move the same DNA the ...
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In dsDNA which force is stronger, base stacking or hydrogen bonds?

I've seen many articles that state that hydrogen bond (2 to 3kTs) is stronger than base stacking, but lately I got into Sponer's article 'Nature and magnitude of aromatic base stacking in DNA and RNA' ...
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How to tell when DNA will be positively or negatively supercoiled?

Is there any indication of when DNA will be + or - supercoiled based on the number of base pairs or number of pairs per turn or any other metric?
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What do DNA crystals look like?

I had about 5 ug DNA suspended in water, which I dried thoroughly in a vacufuge. I obtained a whitish crystal (very similar to table salt, although the structure seems uneven and it's hard to tell) ...
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net charge nucleobases at alkaline conditions

While doing anion exchange chromatography of short oligonucleotide, I have noticed that at $\rm pH=12$, the oligo- retains longer on the column than the same oligo- at $\rm pH=8$. I thought the reason ...
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DNA's physical properties

If we took a bunch of DNA molecules and put them together what properties would it have? I learned that long molecules tend to make a solid substance because they get tangled. A single DNA molecule ...
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How do biochemists seperate nucleotides from DNA to add to the PCR

How do chemists separate single nucleotides from DNA strands? How do they add those nucleotides to e.g. a PCR reaction in order to replicate DNA? I ask this because in my microbiology class, my ...
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Nucleic Acids Bonds

In a paper I am reading regarding instability and decay of DNA, the author says: "The chemical price paid for the greatly increased resistance of the nucleic acid phosphodiester bond (gained by ...
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What is palindromic DNA?

What is palindromic DNA and why isn't every complementary strand palindromic? I know AGCT is palindromic, but what is an example of a strand that isn't?
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Why DNA is negatively charged and what makes it so?

What part in the strand contributes to the overall non neutral charge? DNA is not isolated in the body, so what keeps it stable while being charged? Why is it important for DNA to be charged?
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What is the reason behind the numbering of nitrogen bases?

I am studying nitrogen bases and their structures and roles in nucleotide, polynucleotides and nucleic acids formation. In the structures of the nitrogen bases like Adenine, Guanine, Cytosine and ...
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606 views

Denaturing of Proteins and Nucleic Acids - Effect of Temperature (Heating VS Cooling)

Heating a protein/nucleic acid will disrupt inter-molecular and intra-molecular forces in the tertiary structure. It will also interfere with the shape of the active site if the protein. Does this ...
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Influence of Temperature on Biochemical Reactions [closed]

Short question How (quantitatively speaking) does temperature influences rate of decay of proteins? I am looking for some general number/function, the influence of temperature on an average protein. ...
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Predicting 260/280 of DNA or RNA from sequence?

I asked this in biology, but I think they don't want to deal with the chemistry behind UV-Vis. My question has to do with the Poly A tails on mRNA. I've been doing in vitro transcription and tailing ...