# Tag Info

Accepted

### Why is DNA negatively charged and what makes it so?

As cibrail said, DNA is a polymer of nucleotides. They join themselves through phosphodiester bonds (a specific kind of covalent bond) that can grow to as much as millions of nucleotides. What part ...
• 336
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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 ...
• 30k
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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 ...
• 27.1k

### 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
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### What is the reason behind the numbering of nitrogen bases?

ACDLabs maintains a nice summary of the IUPAC nomenclature rules with examples: Heterocyclics (pyrimidine): http://www.acdlabs.com/iupac/nomenclature/79/r79_702.htm Fused heterocycles (purine): http:...
• 41.6k
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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, ...
• 1,819
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### What is palindromic DNA?

A palindromic stretch of DNA is a strand whose reverse complement is itself. So 5'-AAAT-3' is not palindromic. It's reverse complement is ...
• 20.3k
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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 ...
• 42.4k
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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 ...
• 39k

### 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 ...
• 28.5k

### 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 ...
• 10.4k

### 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 ...
• 1,552

### Why does a larger DNA gel box require a higher voltage to move DNA at the same speed?

It's actually a physics question. The speed of the particle in the gel is proportional to the force that acts on it. The force that acts on the charged particle is proportional to the strength of the ...
• 6,789
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### net charge nucleobases at alkaline conditions

The conjugate acids of the adenine and guanine have pKa's between 9-10. Guanine also has a nitrogen with a pKa of 12.3, which would be mostly protonated at pH 12. The pKa for the phosphoric acid ...
• 3,225
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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 ...
• 35.4k

### 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 ...
• 66.2k

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

Complimentary nucleic acids are held together mainly by hydrogen bonding, so I'm not sure if they are able to be cold denatured, but cold denaturation is a well known phenomenon for proteins. Here is ...
• 12.6k
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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 ...
• 2,665
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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 ...
• 33.1k
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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 ...
• 30.8k

### Nucleic Acids Bonds

I am trying to understand the link between the two chemical bonds. Are they dependent on each other (e.g. one causes the other?) One does not "cause" the other. Instead, the author is only trying to ...
• 20.3k

### 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 ...
• 64.4k

### 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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### 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 ...
• 1,354
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### Gel electrophoresis separates proteins on the basis of what property?

It is probably a good thing to compare protein electrophoresis with DNA electrophoresis here. For DNA, you know that it has a phosphosugar backbone that comes with a negative charge at ambient \$\...
• 64.4k

### 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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### Predicting 260/280 of DNA or RNA from sequence?

The problem with doing this, especially with RNA, is that secondary structure can have a large impact on the absorption properties of the molecule. Interactions between bases will change the molar ...
• 12.6k

### Why is DNA negatively charged and what makes it so?

DNA is basically a polymer of nucleotides. These are held together by covalent bonds formed between the phosphate groups, each of which forms and ester with a hydroxyl group of the pentose of the NEXT ...
• 39