# Tag Info

## Hot answers tagged dna-rna

19

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 in the strand contributes to the overall non neutral charge? The reason why DNA is negatively charged is the phosphate group that makes up every nucleotide (...

13

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 be DNA , since the decayed atom would no longer be $\rm P$. Also, the product would no longer be radioactive, so we wouldn't be able to detect it anyway. The ...

11

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 interaction to be attractive the two molecules have to be displaced slightly, this prevents direct electron repulsion between $\pi$ electrons on one molecule with ...

10

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 location at any given instant of time, resulting in a 'partial' negative charge being formed there. The other regions of the electron cloud probably acquire a '...

10

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://www.acdlabs.com/iupac/nomenclature/79/r79_960.htm Briefly, apply the following rules: Number your rings so that the nitrogens end up with the lowest number ...

9

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, effective way for this scaffold to be prepared in the pre-biotic earth. After all, the first organisms to contain purine scaffolds did not have "access&...

7

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 5'-ATTT-3'. Those two pieces of DNA are not identical. However, 5'-GGATCC-3' is palindromic, because the reverse complement is identical.

7

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 thankfully have more developed methods available, and one should check whether the results found back then are still consistent. An (admittedly also a bit ...

6

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 reactions are not deterministic. Generally, on molecular level, there is less than 100% probability the desired and expected reaction happens, and more than 0% ...

5

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 under question. From the original paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2147348/) it appears that 1-2 days would be maximum for needed for a set ...

5

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 electric field $E$. The strength of the electric field is proportional to the voltage $U$ and inverse proportional to the length of the gel $d$. E = \frac{U}{...

4

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 proton of a nucleotide is significantly lower than 7. Therefore, in a pH 8 buffer, the basic nitrogens of each adenine and guanine are protonated, while the ...

4

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 reading. An example of a very noisy four-color chromatogram from a sequencer (sanger): As you would notice, there are several ambiguous spots and the computer ...

4

According to Ionization constants and thermal stabilities of uracil and adenine under hydrothermal conditions as measured by in situ UV–visible spectroscopy Geochimica et Cosmochimica Acta Volume 93, 15 September 2012, Pages 182-204 Adenine undergoes two ionization reactions. Density function calculations in the gas phase carried out by Russo et al. (1998)...

4

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 and cell gets broken) and nuclear membranes that protect the DNA. This will help the cell membranes to separate and expose the chromosomes that contain the DNA....

4

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 oblivion. No, cis and trans can never mean cathode or anode. It refers to the chambers in which the electrode is place. I looked up the Oxford's Latin Dictionary: ...

3

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 say that removing the 2' hydroxyl group from nucleotides does two things: (a) vastly increases stability of 3' bond to phosphate, and (b) decreases the ...

3

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 strands to form a double-strand is energetically favourable — for entropic reasons. This should be a combination of the hydrophobic effect the liberation of a few ...

3

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 inorganic substances. Commercial labs routinely build long strands of DNA from individual nucleotides. You can tell them what sequence you need and they will make it ...

3

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 is an evolutionary one. In polypeptides, particular sequences of amino acids fold in ways that provide function. Tiny variations in this sequence can render the ...

3

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 $\mathrm{pH}$ per phosphate group. This means, that the charge-to-mass ratio, as the quote implies, is similar, no matter how long the DNA fragment is. (Not identical, ...

3

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://doi.org/10.1016/S0022-2836(61)80003-X The abstract says the following (mμ is the same as nm): The spectra of deoxyadenylic, deoxyguanylic, deoxycytidylic and ...

3

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 absorptivities in ways that may not be easily predictable. The "ideal" ratios are only guidelines and I wouldn't worry too much that a long string of a single base ...

3

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 nucleotide. This uses two of the three acidic 'OH' groups of the acid, leaving the last free to ionize. This ionization leaves a negative charge on each ...

3

It has nothing to do with the complementarity (of the other strand). Try this to figure out whether some sequences are palindromic: #!/usr/bin/env python3 def is_palindromic(seq): translation_table = str.maketrans('ACGT', 'TGCA') translation = seq.translate(translation_table) #print(seq, translation[::-1]) return seq == translation[::-1] ...

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, Tymoczko, Stryer] Backbones of DNA and RNA. The backbones of these nucleic acids are formed by 3′-to-5′ phosphodiester linkages. A sugar unit is highlighted in red ...

2

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 joins with 3' -OH of previous nucleotide to form $\ce{H2O}$ during DNA replication. 1 OH joins with H of next nucleotide to form $\ce{H2O}$ during DNA replication....

2

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 a decent review of the processes involved. In short, most proteins' tertiary structure is dominated by hydrophobic interactions and the energy barrier to ...

2

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 abundance of negative - repulsive - charges. Increasing the ionic strength of the solution, such as high concentration of sodium acetate should neutralize the ...

2

You just buy the nucleoside triphosphates from your favorite supplier, they're commercially available. As far as I know the NTPs you can buy are still produced biologically and not synthesized (see this example from Sigma Aldrich, which states a microbial source). So you grow a large amount of bacteria, lyse the cells to get at the contents and then digest ...

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