The study of the molecular processes of the nucleus and cell function.

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1answer
127 views

How realistic is to use DNA for long term storage?

This is mainly a followup question to the recent paper Next-Generation Digital Information Storage in DNA. Personally, while I agree about the data density of the format, I can't help point out the ...
8
votes
2answers
88 views

Is there a Reverse Transcription optimization for long, 9kb, transcripts?

Has anyone optimized RT for long transcripts (9kb)? The downstream application will be PCR amplification and Illumina library prep. It will be trivial to make internal primers sets for the PCR that ...
7
votes
1answer
298 views

How tolerant are ants to cold?

There was a trail of what are commonly known as sugar ants (small, brown, hyperactive) in my kitchen. Three of them walked onto an ice tray placed in their path. They only walked a short distance on ...
7
votes
1answer
403 views

How do you knockout an E. coli gene without disrupting the rest of the gene cluster?

I'm familiar with the method to build Keio collection using single-gene deletion with an antibiotic cassette. However, what happens when there are gene clusters or overlapping ORFs and you still only ...
7
votes
1answer
2k views

The effect of the start codon GTG on translation in E. coli

Translation in E. coli is initiated at the start ATG codon, which encodes for the amino acid Methionine (Met). In some cases, the start codon can be GTG, which within the open reading frame (ORF) ...
7
votes
2answers
807 views

How do I prepare and clone from E. coli DNA?

I'm looking for a protocol to get genomic DNA from an E. coli sample so that I can clone a small portion of it using PCR into a plasmid. (< 500 bp in this case). It seems OWW (Open Wet Ware) ...
7
votes
2answers
972 views

Bacterial cell lysis - what solution to use?

I am trying to determine how quickly detergents act on bacterial cells (cell lysis). I would like to compare some detergents at difference concentrations for bacteriolytic activity. I don’t care about ...
7
votes
1answer
131 views

PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?

I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors. I do this by predicting the location of Hydrogens on residues and then calculating how far these ...
7
votes
1answer
87 views

Selection on linked loci in a diploid population

Let’s consider two linked loci $A$ and $B$ that are both bi-allelic. In consequence, we have four different possible haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$, which frequencies are $X_1$, ...
7
votes
2answers
455 views

What exactly happens if during translation, an amino acid is not present?

Lets say that the cell wants to make a particular protein. Transcription of the appropriate gene is done and the mRNA is made. mRNA attaches to the ribosome and the translation is initiated in a ...
7
votes
1answer
57 views

Intracellular lipid transport

I know that lipids are carried around the body in the blood either as micelles or by lipid-binding proteins which allow them to be solved. Lipids can't always be integrated in a membrane though, the ...
7
votes
1answer
376 views

How fast do different organs turn over cells?

It is said that the human body turns over all cells or molecules in 7 year cycles. This is not quite correct, because there are different organs changing at different speeds. My interest is what is ...
7
votes
1answer
768 views

What is the mechanism of transgene integration (from expression vector to the host genome)?

How does a transgene (in vector) integrate to the host genome? (e.g. in glass bead method, neither biolistic nor agrobacterium). I already cut some parts (NdeI-PciI) of the vector (pUC18) and ...
7
votes
1answer
2k 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 ) ...
7
votes
1answer
46 views

circulating microRNAs are functional?

In plasma and other body fluids, miRNAs can be found. They not only originate from dying cells but also from active secretion and are usually 'packed' into vesicles/lipo-proteic structures (i.e. ...
7
votes
1answer
173 views

What is the fastest way to build an alanine scanning library?

For interfacial studies, I would like to build an alanine scanning library for one of my proteins examining 20 sites. I will ultimately express the gene using E.coli cell-free protein synthesis. I ...
7
votes
1answer
124 views

Does the MS2 RNA binding protein have any translational repression effects?

Reposted from Quora: http://www.quora.com/Does-the-MS2-RNA-binding-protein-have-any-translational-repression-effects I'm thinking of the MS2 protein binding to its RNA hairpin target. Would the ...
6
votes
4answers
1k views

What are good resources for self-learning modern molecular biology concepts? [closed]

My learning of molecular biology ended in the early 90's (and with early 90's era information). While I don't aspire to be a molecular biologist, I do aspire to better understand modern approaches ...
6
votes
3answers
516 views

Should I dilute DNA with water or elution buffer?

I've extracted DNA using a kit and final step is eluted with buffer. If I must dilute my DNA samples, do I use the same elution buffer or can I use milliq water?
6
votes
2answers
90 views

Can an organism process H₂O into H₂O₂?

In an answer to a recent question on Worldbuilding, I suggested that an organism convert $H_2O$ into $H_2O_2$. I suggested a few processes that yielded the desired final result ($2H_2O \rightarrow ...
6
votes
1answer
2k views

Purpose of poly(A)+ RNA?

I am learning RNA-seq analysis. I always encounter this phase "poly(A)+ RNA". After searching, I got this: "Most messenger RNAs contain a poly(A) tail, while structural RNAs do not. Poly(A) selection ...
6
votes
2answers
759 views

Reverse transcription PCR optimization

What is the ideal amount of RNA to use for the RT? and how much cDNA to use then for the PCR? I did RT with a solution of RNA of 0.36 ug/ul. Then for my PCR I used 1 ul of the cDNA obtained and used ...
6
votes
2answers
109 views

DAM enzyme distances move along the genome

I am fusing a protein with a Dam enzyme (http://en.wikipedia.org/wiki/Dam_(methylase)). The idea is that when the protein binds to the DNA, the Dam enzyme will start methylating nearby GATC sites, ...
6
votes
4answers
539 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 ...
6
votes
1answer
3k views

What causes the colors we see in eyes?

Genetics aside, what are the biochemical reasons the different colours of human irises? Also, related, how does eye colour change, particularly in childhood? (example: my eyes used to be blue, ...
6
votes
1answer
244 views

Why does not the host produce any immune response to antiserum antibodies?

When an antiserum is injected to a person to protect oneself from a certain disease, the antibodies in the antiserum come from another organism. The question is: Why don't the injected antibodies ...
6
votes
2answers
19k views

What is the function of the RNA primer in DNA replication?

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?
6
votes
1answer
215 views

What's the state of the art in designing and creating your own life forms?

What's the state of the art for solving the following problem. You imagine a set of features that you want a life-form to have. Just to take an arbitrary example, say you want your life-form to have ...
6
votes
1answer
272 views

Effect of histidine on the binding affinity of HisP

I was asked the following question by my teacher: A gene regulatory protein called HisP regulates the enzymes for histidine biosynthesis in the bacterium E. Coli. HisP is a protein whoes ...
6
votes
1answer
61 views

How exactly can dsRNA be introduced to a cell?

Is it just by viruses or are there other means by which it gets into cells, such as plasmid uptake?
6
votes
1answer
48 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 ...
6
votes
1answer
389 views

How much does the distance between a transcription factor binding site and a promoter influence transcription?

Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
6
votes
1answer
745 views

Does anyone have any TOPO directional cloning tips? [closed]

I'm just about to start working on a TOPO cloning after I couldn't get it to work with standard restriction/ligation. Does anyone have any tips for TOPO cloning?
6
votes
3answers
670 views

Why does replication require primers while transcription does not?

In transcription, there is no need for any primer. I guess the basic mechanism of DNA polymerase & RNA polymerase is the same. So why does replication have the need for a primer?
6
votes
1answer
2k views

Why is ATP the preferred choice for energy carriers?

Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?
6
votes
2answers
201 views

Can forensic DNA analysis be used to generate a visual approximation of a suspect?

In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
6
votes
1answer
220 views

In C. elegans, why does knock-down of cco-1 in some tissues increase lifespan, and knock-down of cco-1 in other tissues decrease lifespan?

Full question: In C. elegans, why does knock-down of cco-1 via RNA interference in specific tissues like body wall muscle decreases life span, whereas knock-down in the nervous system and intestine ...
6
votes
1answer
109 views

What are the lifetimes of cellular components on organelle or molecular level?

I was thinking that even though I know how generally the cell works, I don't really have a feeling of how volatile it is. I want to know what is the lifetime/turnover rate of different constituents of ...
6
votes
2answers
2k views

Very high 260/230 absorbance ratio of an RNA sample

After my most recent RNA extraction, the RNA samples had very high 260/230 absorbance ratios, (ranging from 5 to 25). I've never gotten numbers like this and I know the ratio is supposed to be ~2 in ...
6
votes
1answer
433 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 ...
6
votes
1answer
110 views

Bicoid regulation of hunchback

I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? ...
6
votes
1answer
419 views

How Do Adherent Cells In Culture Attach To A Plastic Dish?

I am particularly interested in MC3T3-E1 cells (mouse fibroblasts), which are adherent cells. Are hemidesmosomes involved in anchoring the cells to the plastic dish? What (if any) other molecules are ...
6
votes
1answer
81 views

Will eukaryotic RNA fold in the same way in prokaryotes?

As far as I know, there are no specific eukaryotic or prokaryotic factors that aid in RNA folding other than cellular environment (salt and ion concentrations, dissolved molecules, etc). Are there any ...
5
votes
5answers
300 views

What is the lowest common denominator of cancer?

What is the lowest level attribute that all cancers share? Also, what is the highest level attributes that all cancers share?
5
votes
1answer
581 views

How to avoid air bubbles while pipetting?

I get air bubbles while pipetting small volumes. How can I avoid them ?
5
votes
2answers
200 views

Can PCR tubes be made of different materials than plastic?

Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar?
5
votes
1answer
99 views

What are the different ways an exon gets spliced?

Exons are produced by more than one mechanism, e.g. splicing out introns after transcription, if I remember correctly. Please list all mechanisms.
5
votes
1answer
568 views

What is the definition of a stringent/relaxed plasmid?

I have found a publication which proposes some definitions, including a definition for strict and relaxed replication. The definitions are: Relaxed control of plasmid replication. Relaxed control ...
5
votes
2answers
84 views

Alternatives to trypsin for cell detachment?

I have ran out of trypsin and need to passage my cells (immortalized chondrocytes, C28/I2) today or tomorrow. I have been out of town and forgot to order more trypsin. I was wondering if there are ...
5
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3answers
128 views

Finding a template/oligo combination for my first PCR experiment

I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine. Everything is done now and I ...