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Questions tagged [nucleic-acids]

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 bonds as in the case of DNA and RNA but can be other bonds such as peptide bonds in the case of PNA.

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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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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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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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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 ...
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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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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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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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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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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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Why calf thymus DNA is widely used instead any other body part?

Calf-thymus DNA is widely used as DNA sample. Such as testing anti-dsDNA antibody activity, nuclease activity etc, as well as certain books include calf-thymus-DNA in various examples (such as the ...
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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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Structure of phosphates in nucleotides [closed]

Nucleotides are made up of a heterocyclic nitrogenous base, a sugar (only ribose or deoxyribose), and a phosphate. In nucleotides, obviously the nitrogenous base matters as its variations dictate the ...
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Is nucleoside-triphosphate delivery to RNA or DNA polymerase active or passive?

Are nucleoside triphosphates (NTPs) actively delivered to RNA polymerase (similarly dNTPs to DNA polymerase) through some active chaperoned process, or are they so abundant in the nucleus that they ...
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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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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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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 as:...
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Why don’t different organisms have nucleic acid genomes containing different bases and sugar?

All organisms contain genetic material. Be it DNA or RNA, both of them have a fixed pentose group (deoxyribose and ribose). Also they contain the same types of nitrogenous bases, Adenine, Thymine(or ...
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Misincorporation of dUTP into DNA?

Uracil, the RNA base, has been replaced in DNA by thymine, (which has the same base-pairing with guanine). However the synthesis of dTTP (more usually written TTP) requires dUTP: To what extent is ...
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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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Why is an A-U bond less stable than an 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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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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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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What could I call such nucleic-acid-Sequence? A sort of palindromic sequence? is there any term called mirror repeat?

5'... ATGCC|CCGTA ...3' 3'... TACGG|GGCAT ...5' or say 5'... AAGT|TGAA ...3' 3'... TTCA|ACTT ...5' or in generalised way; on each strand; ABCDEF|FEDCBA Is there any terminology for such-sort ...
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Spectrophotometric Values of Individual Nucleotides

All around the net you will find this list giving 260/280 ratios of individual nucleotides: Guanine: 1.15 Adenine: 4.50 Cytosine: 1.51 Uracil: 4.00 Thymine: 1.47 Yet I cannot find a reliable source ...
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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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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 will ...
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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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Can DNA be denatured at acidic pH?

Some say that DNA is denatured only at basic pH. And some say at both acidic and basic pH. So I want to know clearly why and how if DNA is also denatured by basic pH.
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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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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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Can aptamers be used to identify the terminal amino acid residue of a peptide?

Suppose there were DNA or RNA aptamers that bind specifically to a certain terminal amino acid residue. Let's name it aaSA (amino acid specific aptamer). For example, the aptamer binding to terminal ...
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What is the name of the bond between phosphate and the sugar in a nucleotide?

I am slightly confused about what the name of the bond is between the phosphate and sugar within a nucleotide. All my research comes up with is a phosphodiester bond being the backbone of DNA. But ...
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Why are GC-rich regions less condensed than GC-poor regions?

As far as I know, chromatin consists of two kinds: Heterochromatin is more condensed so translational factors have less access to this region, and this region is poor in GC. Euchromatin is less ...
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What is the actual size of a nucleotide?

I found in this website that the dimension of a nucleotide is 0.34 nm. Is there any experimental paper confirming this statement?
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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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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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211 views

amount of tRNA and its extra arm

How much of the total RNAs is tRNA? Some say 15% and some 20%. Those percentages came from my different teachers. Which is correct? And what are the functions of the extra arm (variable loop) of tRNA? ...
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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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Can we spike with a different enzyme to a SYBR Green Master Mix?

I followed the standard SYBR Green Protocol for doing a qPCR. For which I used 10 uL of 1X SYBR Green Master Mix Forward Primer and Reverse Primer (each at a final conc. = 8.5 uM) Template (unknown ...
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Want reference for a convention

This answer to another question satisfactorily answer one of my major confusion. The convention is that in indicating any sequence feature† in a protein-coding gene on double-stranded DNA, a ...
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Gene located on Which strand? Want reference. [duplicate]

Update: Initially my question (below) was appropriately marked as duplicate/overlapping with two other questions; This and this ; among them a specific part of an answer of the second duplicate/...
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Modifications of free nucleotides

We know that RNA can get modified post transcriptionally (RNA modification). So when the RNA is degraded, is it possible for such modifications to still be present on the individual nucleotides -- ...
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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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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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Notation for repetitive nucleic acids

With regard to nucleic acids with repeating residues, could anyone provide a description of what the following sequences are, and the key differences between them: Poly(dA) Oligo(dA) Poly(A)
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How to choose right volume of DNA and SYBR Green

I'm testing fluorescence level of a sample having dsDNA, SYBR Green and milli q water but I'm facing difficulty in choosing right volume of dsDNA and cons level of SYBR Green. Details of sample: ...
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Size of deoxyribonucleotide

What is the diameter of each type of deoxyribonucleotide (if the types are significantly different in diameter, if they are fairly similar one value would suffice)? I.e., if a hole was to be created ...
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What is the structure of DNA during Interphase? Chromatin Fibre or Beads on a string(nucleosomes)?

During Interphase, does DNA predominantly exist as Chromatin Fibre (30nm fibre) or Chromatin/beads on a string structure(10nm) ?
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Can I ask tip for tissue measuring(especially for RNA preparation)?

I extracted RNA at mouse liver and human blood, but degradation occurs. I think, at mouse liver, too hard to measuring 50mg liver(I am newbie for animal tissue preparation) so spend several minutes. ...
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Function and Characterization of poly(T) and (AT)

I came across three terms; "poly(T)45", "poly(A)45" and "(AT)15". Can anyone explain what they are? I know the number refers to strand length, possibly poly-T is a strand of thymine monomers and that ...