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 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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2answers
62 views

DNA sequence from the middle of a gene

Someone gives you a short DNA sequence that comes from the middle of a gene. 5'- TCTAACTGATTAGC -3' 3'- AGATTGACTAATCG -5' From this sequence, determine the ...
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1answer
12k views

Why do we add salt when precipitating DNA?

All the DNA extraction protocols I have seen involve adding salts to the extraction buffer. What is the purpose of the salts? What happens if they aren't included?
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1answer
57 views

Do “transcription factor binding site” and “operator” mean the same thing?

Can the terms "transcription factor binding site" and "operator" be used interchangeably in all contexts when referring to a DNA sequence, e.g. regardless of a cell type, whether or not the binding ...
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2answers
725 views

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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1answer
44 views

The contribution of stem cells to life extension technology [closed]

What do you think is the most powerful method to extend human lifespan? I want to extend human life span significantly (hopefully extra 50 years or more), so I was expecting that stem cell technology ...
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0answers
58 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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1answer
43 views

Can a certain part of human dna can be replaced with other animals dna?

Human DNA consists of adenine, thymine, guanine and cytosine. Can thymine of other animal can be placed with humans thymine?
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0answers
30 views

Is a single x-ray photon capable of doing enough damage to the dna of a cell to kill that cell?

Ionizing radiation is damaging to DNA, but is there such a thing as a safe dose below which no DNA damage could occur? I'm not asking about a minimum safe dose overall, just whether or not there's an ...
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1answer
39 views

In vitro transcription, contamination problem

I am using a RNA which is in vitro transcripted before I started my project. It turned out it is not prepared properly and has DNA contamination. Instead of perform the in vitro transcription again, ...
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2answers
106 views

Question about Autosomal Recessive Alleles

I had a homework question that I could not figure out. It states: A woman has cystic fibrosis in her family and did not want to have a child that suffered from the disease. She and her spouse ...
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1answer
342 views
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1answer
179 views

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 ...
3
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1answer
76 views

Real-time PCR delay in Cq due to insertion SNP in primer

I am collecting evidence, even anecdotal, how does single nucleotide deletion or insertion in primer region affect the outcome of real-time PCR. I am most interested in how much there is a delay in ...
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2answers
54 views

Detecting cancer or a genetic predisposition based on DNA sequencing

I am not by any means a biologist - so go easy. What would be a method for determining whether or not a patient has cancer based only on a genomic sequence? Update Thanks for the help in revising ...
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2answers
37 views

Removing a restriction site and introducing other at its place

What would you do if you want to remove an EcoRI restriction site and introduce BamHI restriction site at apprx. the same location ? One of the answers in my textbook was : To construct a DNA ...
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0answers
41 views

DNA content in seeds vs. fruit flesh

Is there a publication comparing DNA yield and / or PCR-amplifiability after extraction from fruit flesh (like apples, oranges, cherries etc) in comparison to seeds of the same fruits ? I would prefer ...
5
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1answer
580 views

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 ) ...
2
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1answer
276 views

Telomere shortening during replication

It is widely know that each cell cycle during DNA replication some fraction of the telomeres is lost, and this phenomenon is called the end replication problem. Well this is due to the fact that the ...
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0answers
12 views

Phylogentic Footprinting Project

I'm working on performing phylogentic footprinting to figure out how many TRE sequences there are in the TWIST1 gene. (Sequence motifs). I'm trying to use ENSEMBL to gather orthologues of species in ...
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1answer
32 views

Need help distinguishing between a primary and secondary source

I am trying to figure out if the following article is a primary or secondary source. I'm leaning towards secondary but here are my cases for both. Primary: Published in a peer-reviewed ...
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1answer
60 views

What is this image?

What I understand is- I think this is picture of DNA. But why is it in this conformation ? What types of cells have this type of DNA ?
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2answers
65 views

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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1answer
43 views

DNA ligase mechanism

I am unable to understand what happens to the phosphates from ATP. What are they used for ?Charging 3' end or 5'end ?
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1answer
44 views

SNP genotyping using PCR

I read this wikipedia article on SNP genotyping and wasn't able to understand this part : In examining the results, if a genomic sample is homozygous, then the PCR products that result will be ...
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2answers
146 views

Gel electrophoresis after RNAse treatment

I do not understand how to solve this question. I know that RNAse will cut smaller pieces of RNA. The answer given is A
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2answers
82 views

Stay young by reinserting own DNA from years ago?

As far as I know, the DNA sequence becomes shorter every time a cell divides. A shorter sequence results in information loss and aging characteristics. As a countermeasure, shouldn't one stay young ...
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1answer
55 views

A basic example of the interactions of 2 or more non-identical alleles leading to an advantageous outcome for an individual organism

Could someone help me out with a basic example of the interactions of 2 or more non-identical alleles leading to an advantageous outcome for an individual organism? Based on empirical research OR on a ...
4
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1answer
129 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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35 views

How is the number of histones being related to the number of chromosomes [closed]

Please name me at least one reason. I am referring to rats and to humans, as well.
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3answers
20k views

Why is uracil used in RNA rather than thymine?

What is the advantage gained by the substitution of thymine with uracil? I have read previously that it is due to thymine being "better protected" and therefore more suited to the storage role of ...
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0answers
36 views

DNA fingerprinting

I would like to make my own DNA fingerprint - just for fun to have my "autoportrait":). I was looking around a bit and all the commercial kits you can have are very expensive. Can you suggest me a ...
3
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1answer
73 views

Transposons and the net amount of DNA

The retrotransposons and certain DNA-transposons, are "jumping" sequences which may be incorporated elsewhere in the genomic DNA of an organism, through varying mechanisms. This insertion is almost ...
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3answers
49 views

What is the datatype of dna sample?

What is the type of data you get when analyzing dna of a person? If you want to store them in a database, what type of field you will need (text,number,hex)? And what should be it's length?
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2answers
290 views

What are the limitations to current nucleotide sequencing technologies?

Using the Illumina platform, it is cheap and (relatively) easy to sequence huge amounts of DNA or RNA. There are various other platforms out there (Roche/454, SOLiD, PacBio, Ion Torrent) each with ...
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1answer
99 views

Codon alignment via Python? [closed]

I have pairs of coding DNA sequences which I wish to perform pairwise codon alignments via Python, I have "half completed" the process. So far.. I retrive pairs of orthologous DNA sequences from ...
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2answers
87 views

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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67 views

Transcription takes place from the 5’ to the 3’ end of the m-RNA. Why?

Only one side of the DNA ladder is copied (the sense side). The sense side starts with a 3’ end. This means the corresponding mRNA will have to assemble starting from the 5’ end. This is my initial ...
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1answer
105 views

DNA degradation rate

Usually DNA sample manipulation is realized with an ice box at hand in order to avoid degradation, and also its storage is set at -20ºC. Nevertheless, DNA has been obtained from really ancient samples ...
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3answers
108 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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2answers
103 views

Would it be correct to state that any biological difference between the sexes has to be found in the Y chromosome?

If the reason Why Men Don't Listen and Women Can't Read Maps is genetic, then one of the genes in the Y chromosome is to blame and in theory could be identified. Correct or incorrect?
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3answers
150 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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1answer
109 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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1answer
46 views

Clarification of the procedures to amplify cDNA needed

The typical procedure to obtain cDNA from genomic extracted DNA is the following: RNA is extracted from desired tissue, RNA/DNA hybrid is obtained by virtue of reverse transcriptase RNA dependent DNA ...
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0answers
20 views

Mitotic crossover happens in G1?

I was reading this article in wikipedia and came across this : It has been suggested that recombination takes place during G1, when the DNA is in its 2-strand phase, and replicated during DNA ...
4
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1answer
115 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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2answers
1k views

Altering the human genome

I recently had a conversation with a rather unusual gentleman who was, let's say, more than a little partial to conspiracy theories. He has this idea that governments are lowering "nanowires" from ...
2
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1answer
79 views

Should the length of the electrodes in the electrophoresis chamber be proportional to chamber's size?

I am trying to build a small horizontal electrophoresis chamber from scratch. I want to use it for comet assay and I will be using only 1 slide, so it's going to be about 3cm wide, 10cm long and 4cm ...
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0answers
10 views

what are hyperbranched amplicons in DNA sequencing?

I am reading an article about single-cell sequencing: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2720.html And came across the concept of "hyperbranched amplicons". I googled for it but ...
6
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2answers
711 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 ...