I know that parallel DNA helices exist and are governed by Hoogsten base pairing, but why can’t they be possible with Watson-Crick pairing? In the diagram below, if we were to flip one of the strands while keeping the other the same, it appears as though hydrogen bonding is still possible.  The only specific suggestions that I could find was because of the DNA replication process and the negative polarity of hydoxyl group on the phosphates. Moreover, after flipping one strand, the DNA nucleotides form enantiomers. Are these possible reasons, or are there others?
100862
My biology textbook mentions that DNA is antiparallel and it got me wondering... Can DNA be parallel? What would happen if it was parallel? could DNA still replicate right?
30223
The E. coli has a genome with approximately 5×106 bp. The main DNA polymerase involved in its chromosome duplication (DNA pol III , the one with highest processivity) can polymerize ~103 nucleotides per second. By a simple calculation, we would conclude that the whole chromosome duplication would take ~ 5000 seconds ( about 80 minutes, so more than an hour). The whole cell duplication would probably take much more than that, considering not only DNA Pol III is involved. However, in optimal conditions, E. coli can actually duplicate in ~30 minutes. How could that be possible?  OBS.: all the numbers used here are aproximate, but sufficient to account for the correct orders of magnitude.
3185
As far as I know, DNA is the construction protocol of all organisms on Earth.  Does it change when influenced by time and environment (physical laws)?  As parents with schizophrenia are more likely to have children with schizophrenia and an individual with no genetic predisposition for schizophrenia can suffer from such a condition because of drug abuse or environmental influence, does this prove that human DNA is changing during our lifespan?
109929
We know that the protons in a nucleus are positively charged, whereas the neutrons do not possess a charge; we also know that unlike charges attract. So why does the nucleus stay intact, even though there isn't supposed to be any electrostatic force of attraction within it? Instead, why isn't there any repulsion between the protons which are like-charged?
89379
I understand that they arise due to the pairing of bases of two opposite stands and are sites through which important proteins needed for replication and transcription of DNA interact. But I don't get how the arrangement of bases really generate the grooves.
50501
In the textbook that I'm using, it explains that bacteria does not digest its own chromosomal DNA because the sites that would be cut by its own endonuclease are methylated. Is there a similar mechanism involved for protecting its own plasmids? If so, how are plasmids cut while serving as vectors?
61026
Motivating question:    I'm aware that one can construct a hierarchy of number systems via the Cayley–Dickson process:  $$\mathbb{R} \subset \mathbb{C} \subset \mathbb{H} \subset \mathbb{O} \subset \mathbb{S} \subset \ldots $$  "Reals" $\subset$ "Complex" $\subset$ "Quaternions" $\subset$ "Octonions" $\subset$ "Sedenions" $\subset$ $\ldots$  and that at each step you're given a multiplication table that tell how the elements interact. As you move up the ladder, certain "nice" properties are lost: ordering,  commutativity, associativity, multiplicative normedness, etc... Given the multiplication table, you can show that these properties don't hold.   Eric Naslund noted that "the first 4 are very special as they are the unique 4 normed division algebras over ℝ", no surprise then that these $2^n$-ions have found quite a bit of use. I'm interested in the sequence itself however, irrespective of how useful a $2^{256}$-ion might be (ducenti-quinquaginta-sex-ion?).   I feel like something deeper is going on here though that I don't understand. Why are these particular properties lost at each step? Is it possible to quantify the process such that, at the $2^n$-ion you can say something about the symmetry of the multiplication table*?  * I'm making an ansatz that there is a connection between the symmetry of the multiplication table and these "nice" properties.
94254
During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?
105820
So, 2 days ago I learned that quantum entanglement is just about our perception. There is not an active link between particles and they are not communicating with each other. But then, while surfing on the internet this page came up   It says: ""If I jiggle one electron, the other electron 'senses' this vibration instantly, faster than the speed of light. Einstein thought that this therefore disproved the quantum theory, since nothing can go faster than light," Kaku wrote."  and then I read about EPR paradox and really confused. If there is not an active link between quantum particles what Kaku is talking about ? Can someone explain?
2720
If you've ever been annoyingly poked by a geek, you might be familiar with the semi-nerdy obnoxious response of      "I'm not actually touching you! The electrons in the atoms of my   skin are just getting really close to yours!"   Expanding on this a little bit, it seems the obnoxious geek is right. After all, consider Zeno's paradox. Every time you try to touch two objects together, you have to get them halfway there, then quarter-way, etc. In other words, there's always a infinitesimal distance in between the two objects.   Atoms don't "touch" each other; even the protons and neutrons in the nucleus of an atom aren't "touching" each other.  So what does it mean for two objects to touch each other?   Are atoms that join to form a molecule "touching"? I suppose the atoms are touching, because their is some overlap, but the subatomic particles are just whizzing around avoiding each other. If this is the case, should "touching" just be defined relative to some context? I.e, if I touch your hand, our hands are touching, but unless you pick up some of my DNA, the molecules in our hands aren't touching? And since the molecules aren't changing, the atoms aren't touching either?  Is there really no such thing as "touching"?
97016
It seems like there is no trivial isomorphism between them and both are abelian and non-cyclic, so, it makes it even harder to conclude anything. I need some hints.  If I had to make a guess, I'd probably say there is no isomorphism between them.
84466
So I know that the major/minor groove arise from the offset pairing of the two strands in the helix.  All my textbook tells me is that "pitch causes the off-set pairing of DNA and this gives rise to the major and minor grooves."  I'm not too sure what this is saying.  What exactly is pitch and how does it give rise to the grooves?
79698
A DNA molecule can be represented as a string of symbols $A$, $C$, $G$ and $T$, such as  $$GGATAATTCTAG. . .GACCGTACCC$$ For the purposes of this question, we will assume that all DNA molecules contain the same (large!) number $N$ of symbols. Thus, a DNA molecule is an $N$-tuple $x = (x_1, . . . , x_N)$ where $x_i  ∈ \{A,C,G,T\}$ for each $i$.  Define the distance between two DNA molecules $x$, $y$ as the number of elements $i ∈ {1, . . . ,N}$ such that $x_i \neq y_i$. Prove that this defines a metric on the set of DNA molecules.
109221
Suppose $S$ is a closed surface with genus greater than $1$. Give an example of two loops on $S$ which are not homotopic, but are homologous to each other.   I need help solving this question. I have read the Wikipedia page on it and I realize that it does not contain the necessary knowledge to visualize this problem.  And I was also wondering the relation between the fundamental group $\pi_1(S)$ and the first homology group $H_1(S)$? Some restrictions is that $S$ is a closed surface and the genus is greater than $1$.
82519
it seems like it... should be? In that I can't think of any counterexamples off the top of my head. I was looking up these  and saw the quaternion group, but the subgroups of the quaternion group aren't abelian...
86239
The tail of RNA polymerase II is flexible, not folded into a fixed structure , but does each repeat have more &quot;rigid&quot; structure (i.e. fold into a structure that has less rotation freedom inside a repeat)? If not, then how can the proteins bind some repeat with high specificity? (you can't make lock and key with soft material)
510
What were the criteria devised for the numbering convention employed in human chromosomes? When was it fixed?  Correct me if I am wrong; it appears that chromosome pairs 1 to 22 were originally ordered in terms of perceived structural size, which ended up fitting neatly with the quantity of base pairs (but not with the quantity of genes).  The sex chromosomes in turn were arbitrarily assigned as "pair 23".  Is this sound?  Thanks in advance.