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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In the life-cycle of the HIV virus, how does the created DNA enter the nuclear membrane?

I am in a high school biology class, so I cannot truly attest to how accurate the information I am given is, but as far as I know only RNA and very small molecules can enter the nuclear membrane ...
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48 views

Do snRNAs exit the nucleus or not?

In Molecular Biology of The Cell (Alberts, et al., 2015), it lists the various RNAs that are trafficked through the Nuclear Pore Complex (NPC) into the cytoplasm. The list includes snRNAs, but I ...
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43 views

curly braces in sequence motifs

what do curly braces in sequence motifs stand for? e.g. in RTCRYBN{4}ACG what is N{4}? moreover, i notice that in TRANSFAC ...
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76 views

Why is the quality range of fastq format so broad?

Referring to fastq format, it is clear that in fastq format, there are 94 quality value for a sequenced Nucleic Acid of a DNA sequence read and they are: ...
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45 views

Why are nucleic acids negatively charged at physiological pH? [closed]

Why do nucleic acids and mononucleotides have a negative charge physiological ph?
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15 views

How cells began to encode their proteins to the nucleic acids? [duplicate]

I mean how exactly cytosine, uracil, thymine, guanine and adenine was created?
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1answer
88 views

Anomalous base pairing of nucleotide tautomers

What tautomers base pair with what bases? I know that adenine pairs with thymine and guanine pairs with cytosine normally. My question is what does the imino form of adenine base pair with? Regular ...
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51 views

Why is A-U bond less stable than A-T bond?

I have encountered the following fact many times, but have not yet encountered a possible explanation for it. Will you please help me understand the molecular mechanism by which the bond between ...
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3answers
202 views

Why does all life use the same macromolecules in their genetic code?

There is no biochemical constraint of any sort, so why doesn't some other code work? Why is it specifically RNA/DNA?
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1answer
55 views

How to synthesize and isolate single stranded cDNA from an RNA template?

I would like to have pure single stranded cDNA of my choice. I am thinking of reverse transcription from RNA (obtained by in vitro transcription), degrading RNA from RNA-DNA hybrid with RNase-H, ...
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2answers
164 views

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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638 views

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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1answer
55 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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24 views

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
3k 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
157 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 ...
6
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1answer
195 views

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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3answers
345 views

How do you merge SNP data with a reference genome?

My Data I have a 23andMe file listing SNPs in the form: ...
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1answer
319 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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3answers
139 views

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
676 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 ...
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3answers
494 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
82 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 ...
2
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1answer
87 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 ...
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1answer
89 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?
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1answer
629 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
928 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 ...
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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 ...