Questions tagged [dna-rna]
For questions regarding nucleic acids, their properties, structures, functions etc.
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Why do we call bonding between nucleotides 3'-5' phosphodiester linkage?
According to Wikipedia
Phosphodiester bonds make up the backbones of DNA and RNA. The phosphate is attached to the 5' carbon. The 3' carbon of one sugar is bonded to the 5' phosphate of the adjacent ...
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How do I make a 6-mercapto-1-hexanol (MCH) aqueous working dilution?
I am using 6-mercapto-1-hexanol (MCH) as part of the immobilization procedure for forming a self-assembled DNA monolayer on a gold surface (see the first figure of this paper for a good visual ...
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Methods for immobilization of DNA on gold surfaces?
I've been looking for methods for immobilizing 5'-Thiol modified dsDNA on gold slides. Most of what I've come across suggests using DTT followed by a desalting step or using TCEP. However, I haven't ...
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What do consecutive letters A and B in the 4th column of PDB file signify?
What do the consecutive A and B in the 4th column identify in a PDB file downloaded from rcsb.org?
The molecule name is 3CZ3 (...
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What is the origin of the name JOE - the dye used to mark DNA sequences?
I came across an article where JOE - a dye used to mark DNA sequences was mentioned. It was also stated that no one knows the origin of the name for the dye. Does anyone here have any clue?
Thanks!
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Calculating the net charge of DNA oligo
How can I calculate the net charge of a DNA oligo? I have a bunch of different sized oligos (vary from 9 to 50nt long) which I am using for microscopy (DNA-PAINT) and I need to know their charges ...
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DNA staining agent with good absorbance at 532 nm
I need to stain some double-stranded DNA with an intercalating fluorescent dye. For imaging, I am using a microscope setup equiped with a 532 nm green laser.
What is the staining agent of choice to ...
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Are the solid supports used in oligonucleotide synthesis reusable?
So in solid-support oligonucleotide synthesis, the protected nucleotides are attached at either the 3' or 5' end to a linker, which is then itself attached to a a solid support. After synthesis, the ...
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Does it matter, and if so, how should "dAMP" (meaning "deoxyadenosine monophosphate") be pronounced?
When an expert says "dAMP" (meaning "deoxyadenosine monophosphate") is it pronounced "dee ay em pee", "lowercase dee ay em pee", "damp", "dee amp&...
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Why is deoxyadenosine monophosphate called "dAMP" and not "DAMP"?
Why is deoxyadenosine monophosphate called "dAMP" and not "DAMP"?
After all, deoxyribonucleic acid is called "DNA", and not "dNA" (nor "dRNA", thanks ...
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DNA antiparallel strains and nitrogeous bases orientation
I have a question related to the orientation of DNA antiparallel strains. DNA strains are called antiparallel because one strain is orientated from 5' to 3' and the other one from 3' to 5'. Regarding ...
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How to dissolve and homogenize DNA
I have about 20-30 grams of purified mammalian DNA preserved in EDTA. It is clumped up and solid. I need to dissolve and homogenize it, so it can be aliquoted, without damaging or lysing or ...
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What do natural hybrids of peptides and nucleic acids look like?
Until recently I thought that there was a clean distinction between polypeptides and oligonucleotides, but apparently there are recent studies of therapeutic compounds that could be described as "...
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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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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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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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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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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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How does DeepHF (a CRISPR sgRNA design tool) compute binding free energy?
I am looking at the code of DeepHF[1] that computes $\Delta G_\text{binding}$, and I see that it breaks a sequence into overlapping dimers and compute a weighted sum according to a dictionary with 16 ...
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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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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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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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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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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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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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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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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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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 shows) I ...
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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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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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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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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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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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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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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., ...
user25327
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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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