Deoxyribonucleic acid (DNA) is the carrier of genetic information, including for all known living organisms. The only known exceptions are RNA viruses.

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Why deoxyribose for DNA and ribose for RNA?

Why is DNA made out of deoxyribose and RNA made of ribose? Why can't they both use ribose or deoxyribose? I think that the deoxyribose gives an advantage in storing genes, the job of DNA and ribose is ...
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How are DNA polymerase error rates measured?

It is well known that the first DNA polymerase, Taq, is quite error prone. Newer generation commercial enzymes that have either been isolated from different thermophile species or have been improved ...
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263 views

What is the benefit for cells having the ATP production regulated in mitochondria compared to being from the nucleus?

Mitochondria have their own DNA and appear to be loosely connected to the nucleus and it role. Why are the functions of mitochondria not in the nucleus? Why doesn't the nucleus control the ...
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enzymes that stabilize DNA loops

As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops. I have read that cohesin is one of ...
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Tool for nucleotide alignment with all nucleotide codes (e.g. R, Y, W, S, etc.)?

I have a vector sequence and would like to find the following nucleotide sequence in it. AASYWSRA This query sequence uses several degenerate symbols, defined ...
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How does formaldehyde cause protein-DNA crosslinking?

How does formaldehyde cause protein-DNA crosslinking? I would guess it's because the strongly polar water molecule interacts strongly with polar residues on a protein-DNA complex, and adding a less ...
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446 views

Primer Dimer / Hairpin Algorithms

What are the algorithms / methods in use for the calculation of primer dimers and hairpins? As an example, IDT's OligoAnalyzer tool will generate these analysis given particular sequences. The ...
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688 views

How long is DNA stable in a freezer?

Inspired by the post about extracting pet DNA, how long would genomic DNA be stable for in a -20°C freezer? It is common practice to store DNA (double-stranded, plasmid) in a -20°C freezer in ...
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If DNA has a half life of about 500 years, how can old seeds be planted?

According to this article, DNA has a half life of 512 years Wikipedia claims that there are seeds planted as old as 31000 years Doing the basic math $100 / (2^{30000/512})$ we get that only about ...
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Biodiversity is restricted by genome combinatorics?

Me and some friends are interested in opinions for the following: Conjecture The maximum number of species must be limited by the maximum combinatorial/permutational space that can be occupied ...
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What makes DNA helical?

Why isn't DNA like RNA; why isn't RNA like DNA, that is, helical? Why are RNA chains straight?
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Why do we need deep sequencing?

Why do we need deep sequencing? Why cannot the sequencing technologies read all the nucleotides correctly at the first read? Sorry since this question is too trivial, I don't have a biological ...
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where to find the relative frequency distribution of synonymous codons

Most amino acids can be encoded by more than one codon. For example, Serine can be encoded by any one of ...
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DNA of the human body?

If our DNA determines certain patterns within the human body such as hair color and eye color, if scientists were able to "turn off" such as the gene for eye color after the pattern was established, ...
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227 views

Is there a PSI-BLAST for nucleotide sequences?

I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs ...
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Is solving cancer required in order to avoid aging?

When the telomerase enzyme is not active the telomere shortens every time the cell duplicates leading to a reproductive limit (Hayflicks limit). On one hand this is a believed reason for aging. On the ...
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DNA as an acid? [duplicate]

Possible Duplicate: Does DNA react in all of the ways most other acids do? Even if DNA is made up of nucleotide bases, it is said to be an acid. Why is this?
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Stability of helical strands of DNA?

The DNA molecules contain phosphate groups involved in $3'\rightarrow 5'$phosphodiester linkages. These groups, in the bonded state with deoxyribose, contain 1 negative charges ($\ce{3'-PO4^{-}-5'}$). ...
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Does the genetic material the sperm carries affect it's physical properties

Basically, what I'm asking is, is the actual sperm cell built from the blueprint in the DNA of the man or is it itself also a consequence of the DNA it carries? I'd like to know a few more things ...
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190 views

What is the minimum length required for a circular DNA ligation?

What is the minimum length of a DNA molecule for the ends to come in close enough contact that they can ligate. Assume there are free divalent cations in solution. Does anyone have any idea?
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How do mutations come to be shared by all cells?

It's my understanding that various hazards can damage the DNA in our cells, causing mutations. But whenever I picture this, I see the damage being done to one of our tissues (for example, our lungs ...
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Which organisms have introns?

From Wikipedia: For example, introns are extremely common within the nuclear genome of higher vertebrates (e.g. humans and mice), where protein-coding genes almost always contain multiple introns, ...
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Why are 3 nucleotides used as codons for amino-acid mapping in DNA?

DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length? A related question can be ...
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141 views

How does “inheritance of methylation” of DNA and/or histones work?

What are the current models/ideas describing the mechanisms explaining inheritance of methylation on DNA resp. histone level? Is there evidance of this "setup" information being really ...
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Finding exons in DNA problem

My attempt: I looked for the TACs because I thought this would be AUG in mRNA and ultimately Methionine (the start codon). But apparently, that's not how you do this problem. Im confused because ...
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Effect of single nucleotide deletion or insertion on primer annealing

How is primer annealing, and, consequently, PCR amplification affected by single nucleotide deletion or insertion inside the primer ? Imagine a primer like this: GCGTCATAAAGGGGACGTG (primer) and ...
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Redundancy of the genetic code

One particular codon codes only for one amino acid, but an amino acid can be coded for by several different codons. Now according to the genetic code, the codon UUU ...
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relative-rate of evolution

I am supposed to calculate the relative rate of evolution of two sequences (human and sheep) with a chicken serving as the outgroup. The sequences are pretty long, so I will just create a short ...
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Reference sequence for defining single nucleotide polymorphisms

Single nucleotide polymorphism (SNP) or genetic variation in general, by definition are relative to a reference sequence. When we talk about databases of SNP as in ("dbSNP—Database for Single ...
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Microarray data and analysis tools

Microarray has various uses, and to analyse the data a main function classification is used. There are many methods used to classify the data but what are the best and most frequently used methods? ...
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Telomerase in tetrahymena

In this amazing video, at 26:03 we see this image We now know that the telomerase contains a sequence complementary to the telomere sequence and so is able to do what it is capable of doing in this ...
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255 views

How much does the Hayflick limit/telomere length vary across taxa and within humans?

Since they seem to be quite connected, I'm curious if anyone knows of research comparing the Hayflick limit (and presumably by extension telomere length) between different taxa. I've heard the ...
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361 views

Why Only DNA can Contain Hereditary Material?

Well I'm well aware that it is proven that DNA contains genetic material via transformation and Hershey-Chase Experiment of T2 bacteriophage. Still I was wondering what is the reason only DNA ...
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What triggers DNA to produce proteins?

What is the trigger for DNA to produce proteins or RNA? I have found enough material to study the inner workings of the cell and DNA; but, I can't find an explanation of the mechanics the cell uses ...
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Evolutionarily speaking, why do humans have 46 chromosomes

In humans, each cell normally contains 23 pairs of chromosomes, for a total of 46. Monkeys, chimpanzees, and Apes have 24 pairs (twenty-four pairs), for a total of 48. What caused humans to have 46? ...
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What does 5' and 3' mean in DNA and RNA strands?

What are 5' and 3' in DNA and RNA strands? Please clarify with some images and please use simple English.
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Difference between mice and rats

What is the actual biological difference between mice and rats? Are they actually the same thing with two different names depending on appearance (are they all mice for instance and we call the larger ...
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High sequence similarity but start codon isn't methionine

I have noticed in a particular genome sequence of a prokaryote that various regions in a sequence share similarity which is high(>80%) with known proteins. However, the start is not a methionine. Is ...
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More entropy: Atom or Macromolecule? [closed]

A question that appeared on my last exam was : Which of the following has greater entropy A) An atom B) A macromolecule The question doesn't specify anything else(i.e. type/size of atom or ...
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444 views

Is there variation of AT/CG ratio along species?

Chargaff's rules say that the number of Adenine of the number of Thymine in a genome are equal (nA=nT) and similarly nC=nG. This makes obvious sense knowing that C binds to G and A to T. But what ...
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Separating DNA Fragments by Gel Electrophoresis. Are all the strands for one size the same?

My apologies if my question is too basic, and please point me to a more appropriate forum. I am reading the textbook "Essential Cell Biology" by Alberts et al, and am consulting other sources as ...
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What risk to DNA does long-term exposure to low-dose radiation pose?

A new study from MIT scientists suggests that long-term exposure to low-radiation poses no risk of DNA damage for mice (it is also important to note that mice are unusually susceptible to cancer). So ...
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How to measure quality and quantity of DNA?

I would like to mesure DNA. I quantify the concentration with Qubit fluorometer, but I would like to know also quality of DNA. I try BioAnalyzer (Agilent),but without success. Bioanalyzer measure DNA ...
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How to learn molecular biology through pubmed research articles?

Instead of using a textbook, is there an alternative curriculum, that simply lists a set of pubmed research articles for each topic covered in a typical undergrad molecular biology course? I am ...
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265 views

How much DNA of Albert Einstein is recoverable?

Since there seem to be five biological descendants of Albert Einstein, and the original chromosomes of him distributed among them ... Is it possible to recover enough DNA of an individual from his ...
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dsDNA translation

Since DNA is double stranded and each strand is complementary to the other, the codons on each strand will come out to be different after transcription(depending on the reading frame). Does this mean ...
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125 views

What is the most genetically simple organism except viruses?

What is the most genetically simple organism (except viruses) on this planet? By simple I mean the least number of genes.
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What is DNA binding domain? It is not clear what the domain means

I am confused about the term DNA binding domain. Does it mean that there are some parts of the DNA that tends to coil up? Does it happen because some proteins tend to stick around that area? Also it ...
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Self pairing in DNA

I know that ssRNA molecule can fold over itself (e.g. in t-RNA). Can DNA do the same? Is there any example of this in nature? Why is this phenomenon more common in RNA than in DNA?
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Importance of Double Helix DNA Structure

Gene expression involves transcribing only one strand of DNA molecule. So i was wondering what are some biological advantages of the double stranded DNA?