13
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Pi electron stacking, how does it work?
You going along the right track. The stacking attraction occurs when two molecules with $\pi$ orbitals come face to face with one another, typically their separation is 0.34 nm. However, for the ...
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13
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Wouldn't radiolabelled phosphorus in DNA break it apart as it disintegrates?
Of course it would break, just like you said; also, a high-energy $\beta$ particle would kill quite a lot of bystander molecules. Also, if not for other reason, the resulting molecule would no longer ...
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12
votes
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What's special about the purine scaffold?
It is important to remember that the purine scaffold is one of the most fundamental organic structures in all lifeforms. From an evolutionary standpoint, this means that there must have been a simple, ...
- 2,010
11
votes
Pi electron stacking, how does it work?
I thought about it for a bit, and I realized that if you consider the fact the the pi-electrons, despite being de-localized all over the plane of the aromatic ring, can only be found at one particular ...
- 111
7
votes
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Most basic nitrogen in Adenine
According to Ref.1:
Adenine undergoes two ionization reactions. Density function calculations in the gas phase carried out by Russo et al. (1998) indicate that protonation occurs preferentially on ...
- 41k
7
votes
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DFT vs. MP2 for stacked dimer
Both papers you refer to used methods which were basically state of the art at their time (Gaussian 98/03 compared to Gaussian 16 today). But that is almost twenty (or fifteen) years ago. Nowadays we ...
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6
votes
How do we explain mutations, in the deterministic world of chemical reactions?
The topic is much larger than a scope for a single answer. But staying at general, low level chemical principles, it can be pinned down to several mechanisms leading to possible mutations:
Chemical ...
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6
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Why is deoxyadenosine monophosphate called "dAMP" and not "DAMP"?
See this result from Biology: The Dynamic Science. Peter J. Russell, Paul E. Hertz, and Beverly McMillan, p.65-66 (2007):
The lowercase d in the abbreviation indicates that the nucleoside contains a ...
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6
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Why is deoxyadenosine monophosphate called "dAMP" and not "DAMP"?
While the current answers say what d stands for, they don't really explain why D wasn't chosen instead. We could, for example, equally say that "D shows that it has deoxyribose..."
I offer ...
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6
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What do consecutive letters A and B in the 4th column of PDB file signify?
Your counting of columns possibly is influenced by awk* counting whitespace. But the .pdb file format's count of columns takes columns as in characters on a punch ...
- 31.3k
6
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What do consecutive letters A and B in the 4th column of PDB file signify?
On visualizing it, A and B denote the two strands of a dsRNA molecule.
No, A and B denote two alternate conformations. For example, the dsRNA made of chain G and H almost has two-fold symmetry, and ...
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6
votes
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How many molecules in DNA?
When you take a single somatic cell that is not replicating, lyse it, remove the membrane lipids, remove all the protein, you would be left with just nucleic acids.
If each DNA strand were intact, and ...
- 42.3k
5
votes
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Theory behind Experiment: Extraction and Identification of DNA
1) Sodium dodecyl sulfate (SDS) is a solid anionic detergent. It can solubilize proteins and lipids that frame the cell membranes by degrading the cell (the proteins from the cell membrane get damaged ...
- 42.1k
5
votes
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What do GGN, AAP, TCN, CAP, CCN, TGQ, etc. mean in DNA analysis?
It is not always possible to obtain an absolutely precise result from automated DNA sequencers, mostly due to too much background noise or two very close peaks which the computer has difficulty ...
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5
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Wouldn't radiolabelled phosphorus in DNA break it apart as it disintegrates?
Why the disintegration of $\ce{^32_15P}$ does not affect the experiment. Following reasons:
As mentioned since the experiment is relatively short relative to the half-life of the radioactive element ...
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5
votes
How many molecules in DNA?
Is each chromosome a separate molecule or pair of molecules (hence 23 or 46) or is the whole of the DNA a single molecule or pair (hence 1 or 2).
None of the options.
Chromosomes are organelles, ...
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4
votes
Are we capable of deliberatly creating DNA from inorganic compounds?
Yes we could.
It wouldn't be worth the effort since all the building blocks are available from biological sources, but if you really wanted to you could have a chemist prepare nucleotides from ...
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4
votes
Predicting 260/280 of DNA or RNA from sequence?
You could try a different pH to get rid of secondary structure. It might change the absorbance spectra as well, though. Here is a paper where they measured spectra of DNA and its constituents: https://...
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4
votes
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Can molecule have just h-bonds between its parts
There are some grey areas in the normal usage of the word 'molecule'
The normal usage of the term molecule is accurately described by your quote from the Khan Academy. The majority of molecules ...
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4
votes
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Cis and trans electrodes
Sometimes authors use buzz words in their paper in order to make their work novel or fancier than it should be. However, such newly coined terms never get popular and vanish with the author into ...
- 42.6k
4
votes
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How does DeepHF (a CRISPR sgRNA design tool) compute binding free energy?
The simplest model for estimating binding energies (or melting temperatures) is to consider each base pair individually, without regard to sequence context. This is the rationale for the 4 deg vs. 2 ...
- 42.3k
3
votes
What is meant by position 5' or 3'
Here is a link to a more than half-decent biochemistry textbook chapter explaining the numbering: https://www.ncbi.nlm.nih.gov/books/NBK22490/
And the relevant figure from that chapter:
[Berg, ...
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3
votes
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.
Are you sure?
I would argue that association of two single-stranded DNA ...
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3
votes
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Logic behind this statement (On Transcription)
This textbook would never have made it into my classroom. The second "answer" is an arguably correct concept but is specious as a reason. The first "point" has a silly justification.
The real reason ...
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3
votes
DNA antiparallel strains and nitrogeous bases orientation
The bases are roughly perpendicular to the axis of the double helix. In two-dimensional figures, the structure is flattened to make it easier to see.
The two strands are in the same conformation, just ...
- 42.3k
3
votes
Are the solid supports used in oligonucleotide synthesis reusable?
No, you cannot reuse a solid support.
See, the solid support is usually a polymer, as for instance a silica based resin, chemically functionalized with something that will be attached to this resin, ...
- 131
3
votes
Methods for immobilization of DNA on gold surfaces?
The most of the procedures you have described are for binding single-stranded DNA (ss-DNA) to gold surfaces via thiolate bonds. To my knowledge, I'm not sure (note that I'm not an expert on this field)...
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2
votes
DNA's physical properties
Regarding first of two questions:
Assuming duplex DNA (dsDNA), the molecules should repel each other and thus stay in solution at low ionic strength, such as in Tris/EDTA buffer. This is due to the ...
- 1,379
2
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Why is DNA negatively charged and what makes it so?
DNA contain negative charge because the presence of phosphate group. Generally, hydrogen is not shown in DNA structure.
DNA
There are 3 hydrogens in phosphoric acid, each of them leaves as:
1 H ...
- 21
2
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How are elements used in the human body (for example) encoded for in the genome?
No. DNA is not a blueprint, it is an integral part of the machine. There aren't little people in your cells who can read an instruction set. DNA, together with a living cell, produces (actually is ...
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