Polymers/Oligomers of mononucleotides. Nucleotides are composed of heterocyclic bases such as Adenine, Guanine, Thymine, Cytosine, Uracil, Hypoxanthine, Pseudouridine, Methylcytosine etc, linked to a backbone moeity such as Ribose (RNA), Deoxyribose (DNA), N-(2-aminoethyl)-glycine (PNA) etc. These ...
2
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1answer
49 views
Does bleach destroy RNAse activity, and if so, how does it do it?
I am working with RNA samples, and I'm trying to be very careful about RNAse contamination.
I have some questions about bleach, though. Some people say that a solution of bleach is enough to destroy ...
4
votes
3answers
97 views
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 ...
3
votes
1answer
46 views
Nucleotide frequencies in Kimura's two-parameter model
Here's an excerpt about Kimura's two-parameter model from Felsenstein's Inferring Phylogenies:
"The model is symmetrical, and one can immediately see that, after
enough time has elapsed, it ...
3
votes
1answer
44 views
How are atoms in benzopyridines and benzopurines numbered?
I am well-aware of the numbering system used for the traditional bases, as seen below.
My question is how are the atoms in the size-expanded bases seen in xDNA and xRNA numbered?
2
votes
1answer
31 views
What are the distinctive structural features of single- or double-stranded xRNA, or where can I find them?
I am interested in the structural differences caused by benzopurines and benzopyrimidines at the oligonucleotide level between RNA and xRNA, both in single-stranded and double-stranded form.
I am ...
8
votes
1answer
160 views
Does DNA react in all of the ways most other acids do?
As I understand it from my basic chemistry, there are some fundamental reactions that exist between any acid and other substances for example acid-base reactions that form a salt, and the existence of ...
6
votes
2answers
297 views
For how long and how cold should I perform ethanol/isopropanol precipitations of RNA or DNA?
Precipitating nucleic acids using either isopropanol or ethanol is a very common operation, and I've read some very different protocols on the duration and temperature the precipitation should be ...
8
votes
2answers
647 views
Alternatives to ethidium bromide for staining small nucleic acids?
While ethidium bromide works well for staining larger single-stranded RNA or double-stranded DNA molecules, it doesn't stain smaller nucleic acids very well. I observed that at around 20 bases and ...
