Polymers/Oligomers of mononucleotides. Nucleotides are composed of heterocyclic bases such as Adenine, Guanine, Thymine, Cytosine, and Uracil linked to a backbone moeity such as ribose (RNA), deoxyribose (DNA), N-(2-aminoethyl)-glycine (PNA), etc. These monomers are usually linked by phosphodiester ...

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Cleavage of RNA by restriction enzymes?

Six restriction enzymes discussed in Sequence-specific cleavage of RNA by Type II restriction enzymes (Murray et al.) have the ability to detect and cut RNA strands with that enzyme's recognition ...
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How sterile is sterile when working with nucleic acids to prevent contamination?

I am reading up on preparatory work on working with nucleic acids and a lot of the instructions speak on excessive procedures on cleaning environments with high %ethanol and making sure the equipment ...
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43 views

Nucleosome wrapping direction

Does anyone know which direction the nucleosomes are wrapped? I wonder: Relative to the B-DNA double helix twist direction (right-hand) Relative to the neighbor nucleosomes. Do they alternate to ...
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Inter-codon mutations statistical analysis

I am looking for a statistical approach to inter-codon mutations. For example a 64*64 (64*63 actually) table, that contain the possibility of mutation from one codon to another codon (CCA to CAA or ...
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1answer
442 views

Why does high pH result in the denaturation of DNA?

In the Southern blot method, for example, a solution of NaOH is used to denature the DNA in the sample. I find this counterintuitive since I expected that $\text{Na}^+$ cations would neutralize the ...
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1answer
69 views

Examples of how the presence or absence 2'-hydroxyl groups influence physicochemical properties of DNA and RNA

I know, for instance, that RNA is much more succetible to alkaline hydrolysis than DNA and this difference is determined by the presence of 2'-hydroxyl group in ribose. I have also heard that "DNA is ...
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1answer
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Location of nucleotide synthesis and transport

I couldn't find this question directly asked so I thought I would ask it In Fundamentals of Biochemistry 3e (Voet et al), it has a small small little comment about pyrimidine synthesis: (In a diagram ...
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1answer
224 views

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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Standard letter for 5-methylcytosine

I'm working on a piece of software that computes melting temperatures for nucleic acid duplexes, and I'm about to add support for 5-methylcytosine as a nucleotide base. At the moment, the bases ...
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2answers
537 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 ...
5
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3answers
414 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
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1answer
78 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 ...
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1answer
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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 ...
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1answer
74 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?
9
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1answer
466 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 ...
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2answers
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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 ...
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2answers
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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 ...