13

Short answer: Yes Long answer: Depends what you are working with. DNA: If you are working with DNA, its pretty stable and you can usually get away with a 70% ethanol wash/autoclave (mainly to prevent contamination and obtain consistent results). EDIT: Read Chris's answer also below RNA: If you are working with RNA well.. whatever you did for DNA doesnt ...


9

The pKas of (neutral) guanine and thymine are 9-10 (ref). At high pH (>~10), those bases will be deprotonated and exist as negatively charged conjugate bases. As the deprotonated species, part of the G/C and A/T hydrogen bonding networks are eliminated. In the figure below, green dotted lines represent the hydrogen bonds that explain the observed base ...


9

First of all, sterility is not necessary. It takes much more effort to reach this than just to wipe down everything with ethanol. What you need is a clean and controlled work environment (but this is something you need anyway to get reproducible results) and good and clean equipment. You will need more precautions for RNA work as RNA is more sensitive and ...


8

Initially, there were several quality encodings that used to follow different ranges of ASCII characters to denote the quality of read. The range that you mention is a union of all those encoding formats. Nowadays, the most common encoding is Phred+33 (used by Illumina, Sanger, Ion Torrent and other popular sequencers) which uses these characters: !"#$%&...


8

Phosophoester is a valid term. There are at least a 1000 peer-reviewed articles that use this term. IUPAC Goldbook defines nucleotides as: Compounds formally obtained by esterification of the 3 or 5 hydroxy group of nucleosides with phosphoric acid. They are the monomers of nucleic acids and are formed from them by hydrolytic cleavage." Phosphoester or ...


7

Preamble Any answer regarding the origins of our biochemical evolutionary origin will be reasonably speculative given that this is a very hard question to scientifically test and this field is generally understudied to say it is pretty much the most fundamental biochemical question. But there are a few reasons why RNA makes sense as the prime genetic ...


7

There is indeed a repulsive force between the phosphates in the DNA backbone. (The pK of the phosphate is very low so it will be ionised at all physiologically-relevant pH.) This is why DNA behaves like a stiff rod over short distances. However cations in solution will help to shield some of this repulsion. This is why DNA melting temperature decreases as ...


7

I have crawled through google and many, many journal articles. What I can make of it, is: "It is generally agreed that from mammalian cells (as, for example, calf thymus..." are capable of yielding high molecular weight DNA from cells, with very little protein present to decrease purity. [From Welsh and Vyska] Additionally: "Calf thymus gland is a fairly ...


5

Alkaline denaturation neutralize the charge of acids but also cause hydrolysis of bases upon prolonged treatment. Strong bases will raise pH until the H+ shared between the N-base electronegative centers (N-H and O=) is stripped from the H-bond, effectively breaking them. Organic solvents such as dimethyl sulfoxide and formamide, or high pH, could break the ...


5

Correct, all but one step in pyrimidine synthesis occurs in the cytosol, and purine synthesis occurs in the cytosol only. Nucleotides freely diffuse through nuclear pores but are actively transported through mitochondrial membranes via embedded membrane transport proteins (i.e. ATP-ADP translocators, GTP transporters, and pyrimidine nucleotide transporters)...


5

Well it turns out that when nucleotides are bonded together in a strand of DNA/RNA (nucleic acid) they ALWAYS HAVE only one phosphate group attached to their nucleoside (nucleoside = sugar + nitrogenous base (without phosphate)). However, when they are by themselves, they are more often found with two or three phosphate groups as oppose to just the one. For ...


5

General approach to identifying non-standard bases in organisms Purify from source material with standard separation methods Identify using chemical methods and comparison with known compounds Establish the biochemical pathway for synthesis etc. — the specific reaction(s) required to produce (and handle) the compound and the enzymes responsible for ...


4

B-form DNA is wrapped around histones in a left-handed manner resulting in a left-handed solenoidal superhelix (see that, that and this). The reason for this wrapping is that it reduces the helical tension. This post has more information about DNA helical tension. Also note that exceptions exist (i.e. right-ended direction) especially for histone at the ...


4

A methylated nucleotide is the same nucleotide, for the purposes of base-pairing events. The methylated base will be paired with its Watson-Crick opposite after replication, for instance (and methylation will even persist after replication).


4

DNA sequence is what we call a string of nucleotides in the DNA polymer, such as GATTACA, representing a chemical structure wherein each letter ("G", "A", "T", "T", "A", "C", "A") represents a nucleotide that has a chemical bond to the next nucleotide. Possible nucleotides in DNA are ...


3

Everyone is giving you a hard time for this question. But it's a great question! Good for you for asking it. The answer is that we really don't know why nucleic acids are composed of ribose, as opposed to any other sugars. We don't even know why life on earth only uses L-ribose instead of D-ribose. Or if instead of being carbon-based, we don't know if ...


3

It sounds like you are confused about how Darwinian evolution "works". For example, as we survey the current life forms in this biosphere there is absolutely no evidence that these species (or their molecules, which you refer to) are optimized in any way, shape, or form. All we can state with any certainty is that at some time in the past, during one, or ...


3

N is the IUPAC code for any nucleotide, so in DNA sequence an N signifies any one of the four bases could be in that position. The {4} means 4 of the previous character in the pattern, or NNNN. In Perl regular expressions \d{4} means match 4 digits in a row, so the notation is quite similar.


3

Sure that will work, or gel purify the ss cDNA, or treat the rxn with alkali to degrade RNA. The real questions in my mind are: What will you use as a primer for the RT? What are you going to do with this pure ss cDNA? If you already have the target cloned (how else would you transcribe it in vitro?), then why not just do a linear PCR where you cut the ...


3

First, you need to know which genome sequence does the SNP file refer to. They must have mentioned the reference sequence that they used. As others mentioned the case of CT is heterozygosity. If you just want to mark the changes then discard the residue that is already present in the reference genome and use the other allele. However, you want to keep a ...


3

As user137 said, the general base abstracts a proton from the 2'OH and subsequently the 2'O- renders a nucleophilic attack on the δ+ Phosphorous, leading to the hydrolysis of the phosphodiester bond. There can be slight variations in the mechanism and the intermediates; for details see this review.               After hydrolysis both 2'- and 3'- phosphates ...


3

I think the situation you showed should be called mirror-everted repeats: to my knowledge they occur very rarely, and I only found references in this and this articles, even though no graphic explanation is provided.


3

The term: ‘reverse tandem repeat’ has been used by a few authors, but the Google search engine retrieves only 28 instances, of which no more than 20 are unique. There are about three times as many hits for: ‘reverse tandem duplication’ which would be a more precise term in the current instance.


3

If you want experimental papers, we should be precise about what we're measuring. "The dimension of a nucleotide" is rather imprecise, as a nucleotide is a rather oblong, knobbly thing. 0.34 nm is a relevant measurement related to nucleotides, but it's specifically the distance between consecutive bases in a standard B-form DNA helix - that is, what's the ...


3

There follows an attempt to answer my own question, which I think is important to consider in the general context of postings on SE Biology concerning uracil and thymine in DNA and RNA synthesis. There seems to be little misincorporation because of the low concentrations of dUTP in cells. Any small amount of misincorporation can be handled by the DNA ...


2

As to why they don't recognize RNA-DNA heteroduplexes (which are present during transcription, for example), I suspect that the methylation which protects bacterial genomic dsDNA (see the DNA modifying enzyme section of this Columbia University lecture for more info) also protects RNA-DNA hybrids, as the genomic DNA would still be methylated. Note that most ...


2

This paper found that these enzymes recognize RNA:DNA heteroduplexes. Such duplexes are unlikely to be encountered in vivo. They are present when DNA is primed for replication, but these duplexes are relatively short and thus are less likely to randomly contain a recognition sequence. Furthermore, if the recognition sequence is found in the primer, the gDNA ...


2

Just to fully document the IUPAC advice on this, here is the relevant section from the Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences as reproduced here in the link provided by @Hamish McWilliam. 5.2. Modified nucleotides In a number of organisms DNA and RNA are modified at certain positions. For instance, the DNA of Escherichia ...


2

The tautomers are rare but they can form and it is suggested that tautomerization can lead to mutations because of non-cognate base pairing. Khuu & Ho (2009), have inferred the presence of adenine and thymine tautomers from the crystal structure of an in-vitro assembled holliday junction. They infer that imino-Adenine base pairs with amino-cytosine (...


2

As mentioned by @WYSIWYG in his answer the quality scores in FASTQ file format are encoded in ASCII characters, and there has been several ways to encode this information. The wikipedia FASTQ page that you link in your question describes some (not sure if all) the different alternatives. Now, why do we have this wide range of characters for the quality ...


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