Questions tagged [dna-rna]

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

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Do you need concentrated sulfuric acid to make Dische diphenylamine reagent and test for DNA?

I'd like to do a DNA quantification experiment for a college project. I don't want to use 16 M sulfuric acid. Is it possible to use more dilute acid and get a reasonably good result?
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How do point mutations affect complementary base-pairing and widths of the nucleotide pairs?

Point mutations are divided into two categories: transitions and transversions. Since point mutations only occur during DNA replication (an integral process of both mitosis and meiosis), the mutated ...
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How to model CRISPR/Cas9 binding and cleavage using a generalized Kittel's zipper model?

I am thinking about how to model the binding of a CRISPR/Cas9+guide-RNA complex to a double-stranded DNA that cause its cleavage. This post describes four steps at which a CRISPR/Cas9 system binds and ...
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What is the composition, function, and classification of “6-Thio-2-Deoxyguanosine” and “13-mer thio-phosphoramidate”? How do I learn more about them?

I am assigned the task of explaining a biomedical research paper, it is about telomere and telomerase , and it talks a lot about the molecule Thio-2-Deoxyguanosine , 13-mer thio-phosphoramidate and &...
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1answer
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Is the ratio between base pairs by chargaff accurate? [closed]

I am reading Lehninger's biochemistry textbook. It mentions that DNA may rarely contain uracil. Then it mentions that Chargaff found that the ratio of adenosine bases to thymine bases in DNA is 1. ...
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1answer
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How many possible nucleotide types can be created? [closed]

In the RNA world hypothesis, it has been argued that RNA is made of 4 nucleotides and it can act as a template to create another copy of itself. And it's been claimed that we only have 5 nucleotides, ...
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1answer
57 views

Can molecule have just h-bonds between its parts

I'm just starting to study chemistry so sorry for the probably obvious question to you, guys. According to the definition of molecule in Wikipedia: A molecule is an electrically neutral group of two ...
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1answer
104 views

What's special about the purine scaffold?

Purine is a remarkable substance, given Nature has chosen it as the scaffold for two nucleobases from DNA/RNA: adenine (A) and guanine (G). Its structure also appears in several other substances of ...
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1answer
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How does DeepHF (CRISPR sgRNA design tool) compute $\Delta G_{\text{binding}}$?

I am looking at the code of DeepHF that computes $\Delta G_{\text{binding}}$, and I see that it breaks a sequence into overlapping 2-mers and compute a weighted sum according to a dictionary with 16 ...
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25 views

3' terminal phosphate (p at the end of RNA sequence)

I am reading the paper: Petersheim, M. and Turner, D.H. (1983) Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ...
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'Ab initio' couplings for DNA used in charge transport

I came across a publication by Senthilkumar et al. [1] in order to compute charge transfer through the DNA. Table 3, for instance, gives the coupling between bases along the leading (or retarded) ...
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120 views

What Chemical Could This Represent [closed]

Update I found someone else who has been trying to solve the same problem and they said that my drawing was not correct. We had a discussion and I conceded that his monochrome picture is more square ...
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1answer
120 views

Cis and trans electrodes

I have come across use of the terms cis and trans electrodes in the context of nanopores and driving charged biomolecules through a pore using an electric field [1]: FIG. 1. Drawing of the cis ...
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Dispersity of synthetic DNA [closed]

Recently I was reading an article about DNA nanostructures and I was wondering-- I know that DNA in living systems is monodisperse, but when we make DNA synthetically, is it truly monodisperse or ...
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45 views

Meaning of hydrogen bonds for life [closed]

Why are hydrogen bonds so important for life? Or more generally asked: Why is water so important for life / biological systems? Or maybe again in other words: Why does especially water provide this ...
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2answers
84 views

How do we explain mutations, in the deterministic world of chemical reactions?

I'm not a chemist, neither a molecular biologist. But I'm fascinated with science. The way I understood, DNA is a macro-molecule which is made of atoms. And in reproduction, either mitosis or meiosis ...
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2answers
55 views

What is meant by position 5' or 3' [closed]

I'm a self-learner that likes to keep up with current research. However, I can't find what is meant by expressions such as 5' or 3' positions on chemical structures. But , in particular, what is meant ...
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1answer
690 views

Theory behind Experiment: Extraction and Identification of DNA

A few days ago, in my chemistry lab class, I performed an experiment aimed at extracting and identifying DNA. The class is mostly practical oriented, so I thought of asking my theoretical doubts on ...
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Is presence of air necessary for silica gel to absorb moisture?

I am a biologist currently doing field work where I need to quickly dry leaf samples using silica gel crystals. I use the orange indicating kind that are 2-4mm in size. The setup is like this. I stuff ...
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1answer
278 views

DFT vs. MP2 for stacked dimer

Recently, I looked at these two papers analyzing the excited-state properties of modified DNA bases (2-aminopurine and 8-vinyl-A) and how they are influenced by stacking with natural nucleobases: ...
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1answer
96 views

What do GGN, AAP, TCN, CAP, CCN, TGQ, etc. mean in DNA analysis?

What do the letters Y, Q, P and N mean in three-letter combinations involving DNA and/or RNA? I know, of course, about the bases A, C, G, T and U but..... Especially in articles (and forensic tv ...
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356 views

DNA-Sequencing (detection of the change of pH-value) after emulsion PCR

I have troubles with understanding the exact order of the steps for DNA-sequencing after the Emulsion PCR (EmPCR). The EmPCR fills each bead with the same DNA strand (copies it $n$ times, till the ...
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1answer
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Why do we have only one DNA? [closed]

I've been crossed a very interesting thought.. Why is it that our body has only single form of DNA, and what would happen if we had multiple forms of DNA?
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Why would decreasing ionic strength of buffer disrupt hydrogen bonds

I'm reading about cDNA synthesis in my textbook and it mentions that: The captured mRNAs are subsequently released and collected, for example, by decreasing the ionic strength of the buffer so that ...
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1answer
178 views

Complementary base pairing

In the molecular structure of a DNA it is seen that purines (adenine and guanine) bind with pyrimidines (cytosine, uracil and thymine) through hydrogen bonds, and this is always between a purine and a ...
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87 views

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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133 views

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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1answer
29 views

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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1answer
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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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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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760 views

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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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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644 views

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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3answers
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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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1answer
292 views

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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1answer
1k views

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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1answer
46 views

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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1answer
120 views

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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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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2k views

net charge nucleobases at alkaline conditions

While doing anion exchange chromatography of a 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 ...
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149 views

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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2answers
206 views

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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1answer
128 views

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 is DNA 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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1answer
813 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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469 views

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. ...