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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Free Radicals for aging

From my understanding free radicals play a slight role in ageing. In what ways are they so damaging, and can a restricted diet reduce production of free radicals?
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Possible reasons for DNA getting stuck in well

I am in the process of Library preparation for Illumina MI-Seq using mtDNA. Using NEB Hotstart LongAmp Polymerase, I was able to obtain upto 10kb amplicons of mtDNA. However, when I switched to a ...
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What distinguishes “coding” and “noncoding” DNA from each other?

I've been reading a bit about "junk DNA" and how much of our genome consists of this "non coding DNA" in comparison to "coding DNA". I'm just an interested layperson but I thought all combinations of ...
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How does one measure the length of telomeres?

My questions are: What techniques are available for doing so? Are they destructive ? What is their accuracy ?
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810 views

Does extracted DNA degrade after a certain time period?

For direct use as template in PCR runs. Chelex 100 5-10% w/v extraction. Without listing the whole protocol, in the end the supernate is decanted off and then stored at 4°C. I was under the impression ...
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How can I produce milligram quantities of an isotope-labeled DNA oligomer?

I'd like to produce a specific DNA sequence on a milligram-scale and 13C15N-label it. The sequence is around 35 nucleotides long, so chemical synthesis is out due to the exorbitant costs. I'm also ...
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73 views

How do nuclear receptors locate each other to form a DNA loop?

Nuclear receptors can influence transcription far up- or downstream from their own binding sites by looping DNA (Rubina et al.; J Mol Bio 2004). I am not sure how exactly the receptors first attach ...
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Difference in length of Okazaki fragments

The length of Okazaki fragments in the lagging strand is about 100-200 nucleotides in eukaryotes and about 1000-2000 nucleotides in prokaryotes. What (molecular mechanism, enzyme type ) ...
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95 views

What are the costs associated with carrying lots of genetic material

What are the costs (if any) associated with carrying lots of genetic material? energy for copying? raw material for copying? space in the cell? Maintenance cost (matter and energy)? time to copy is ...
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85 views

is it possible to completely reconstruct a family tree by DNA comparison alone?

Having DNA samples of all or almost all members of a population of, say, a few hundred or thousand individuals, is it possible to draw the entire family tree of those individuals? (Let's not assume ...
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239 views

How many transcription factors are there?

In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to ...
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539 views

Looking for a DNA sequence

I am not a biologist. Please pardon me, if my question does not make sense. I am trying to obtain a DNA sequence for pattern analysis in Matlab. I used to generate random sequence ...
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Does our DNA change during our lives?

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 ...
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Are there any DNA base sequences that are fully conserved between the genomes of all humans?

That is, they don't differ throughout the entire population. I understand of course that we can't DNA sequence every human, so by "fully" I mean there's an incredibly small probability of there being ...
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340 views

What's the use of DNA sequencing results?

Suppose I sequence DNA of some organism (a human perhaphs) and now I have the entire DNA "string" - the sequence of nucleotides. What's the use of that? It's just a "string" where nucleotides encode ...
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96 views

DNA extraction from agarose gel

Because DNA is soluble in water, is it possible to extract PCR product by dissolving excised gel containing the DNA band of desired length in water, mashing the gel piece with a pestle, centrifuging ...
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390 views

Does RNA polymerase move around DNA or does DNA rotate benath the polymerase?

I'm thinking of the human genome specfically, but more general answers are welcome. As RNA polymerase moves along the DNA helix it follows a single strand. The two DNA strands are unwound locally ...
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988 views

Why do DNA and RNA have the functions they have?

I know that there are two most important directions of genetic information transfer in living organisms: DNA->DNA and DNA->RNA. The first is replication, and the second is transcription. I wonder if ...
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185 views

What is the origin of “melting” in molecular genetics?

I'm reading some papers about prokaryotic transcription mechanisms, and I've come across a term I haven't heard before: DNA melting or promoter melting. After reading a bit, it's pretty clear that ...
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37 views

What regulates the timing of the motion of molecular machines during DNA Replication?

This question is about this video I found on Youtube. I just want to know what is the mechanism which regulates the timing of motion of the parts of these molecular machines. I know that those big ...
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177 views

How do scientists create specific mutations?

Suppose I want to create a mutant like Antennapaedia how will I go about accomplishing it ? I know that radiation and certain chemicals are mutagenic. So do scientists subject animals to such ...
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322 views

How can I predict DNA binding affinities from a protein sequence?

Are there any computational tools to predict the binding affinity to specific DNA motifs from protein domain sequence information?
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838 views

Basic Amino Acid Residue Binding Mechanism to DNA

I understand that many protein DNA binding domains bind to DNA via basic residues such as Arginine and Lysine. But what is the mechanism used to bind to DNA and where on the DNA would these residues ...
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260 views

Mitochondrial DNA and recombination

Firstly I could do with a brief description of mitochondrial DNA. How does the structure of DNA in mitochondria compare to animal DNA (for the sake of simplicity let's say human - some animals might ...
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What is a good Non Fluorescent DNA Dye?

Can anyone suggest a dye which specifically targets DNA, but is not fluorescent? (We plan to mark DNA before observing it with RAMAN-Spectroscopy. Because of the weak Signal even a low emission would ...
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55 views

Is telomere shortening consistant over consecutive cell divisions from zygote to a differentiated cell?

Considering the complexity of embryogenesis, a temporal referance would be helpful to coordinate the developmental sequences during embryogenesis and fetal development which is to be completed within ...
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361 views

How does Topoisomerase II inhibition affect cancer cells?

Topoisomerase II poisons represent some of the most important and widely prescribed anticancer drugs currently in clinical use. These drugs encompass a diverse group of natural and synthetic ...
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What is the oldest example of DNA identified?

What is the oldest sample of genetic material (presumably DNA) identified? What are the prospects of pushing back much further into the geologic record?
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(Rough) Model for DNA evolution in E. coli genes

I need a model of in-gene DNA drift. I'm not interested in bacterial phylogenies alone. Here is what I understand: Sequences corresponding to genes have both exons and introns, but in bacteria the ...
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DNA modifications other than 5-mC/5-hmC/5-fC/5-caC in vertebrate genomes?

Other than 5-Methylcytosine and the more recently discovered 5-Hydroxymethyl, 5-formil and 5-carboxylcytosine DNA modifications found in DNA sequences, what are other DNA modifications present in ...
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Do somatic cells alter their own nucleotide sequence?

I seem to remember reading that embryonic cells will frequently replicate the section of their genome containing rDNA by splicing in duplicate genes. The cells use this to produce ribosomes at a rate ...
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166 views

Are there other mechanisms for mutation besides imperfect DNA replication?

I was reading http://www.askamathematician.com/2012/05/q-is-quantum-randomness-ever-large-enough-to-be-noticed/ and saw: [...] the evolution of entire species can be changed by a single mistake ...
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How do we know that everybody's DNA fingerprint is unique?

How do we know that everybody's DNA fingerprint is unique? I know, I know, everybody's DNA is unique. But when we do DNA fingerprinting, we're looking at very specific regions of high variability. ...
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How much DNA of mitochondrial origin is incorporated in main cell's DNA?

And especially three points : in which chromosomes is it located (especially for the human case) ? how do we know about it ? does the proportion and composition vary a lot from one eukaryot to ...
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168 views

How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: ...
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What are the limitations of commercial-grade DNA genotyping compared to full sequencing?

I've heard about services like 23andme, which offer genetic testing to the general public. As a person who knows very little about genetics, I'm interested in the subject and would like to know what ...
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Synthetic biology using existing cells

I was watching the video at this link: http://www.bbc.co.uk/news/science-environment-17436365 The speaker says that a cell is taken and its original DNA content is stripped out and replaced with ...
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What conditions should I use for Gel Red staining?

What are the optimal staining conditions when using Gel Red? So far, since we have started using it, the gels ran in our lab have been of very poor quality. The bands are very blurred and often ...
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There are linear and rotary molecular motors in the cells. Do any of them have a fixed or stable frequency or speed?

Are there any linear, rotary or oscillatory molecular motors in the cells which can have fixed frequeny and which can be used as a reference for elapsed time timer? This question is with relevence to ...
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127 views

Do thymine and uracil ever appear in the same strand of RNA?

Wikipedia says that "in RNA, thymine is replaced with uracil in most cases." I'm curious what are the cases when this does not happen? Does this ever occur in normal functioning, or is it an error? ...
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Is there a DNA test to identify dog mixes?

We adopted a dog at the age of two. Our vet said it was a mix of an Australian Shepherd and Border Collie, which we've told everyone. Based on markings, I think it's likely. I am wondering, however, ...
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How to find Exons in mRNA Computationally

I'm having trouble finding a method to find exons in the original DNA sequence used to create the mRNA, even given the sequence of the mRNA, as I cannot find a way to reliably identify the beginning ...
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What causes DNA to skew in gel electrophoresis?

In gel electrophoresis, what causes effects like these (see collumn 11 in the first one, an collumn 6 in the second). ? (These images were samples that I took from an online activity we did for ...
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202 views

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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237 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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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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400 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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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 ...