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5 votes

Is it possible to use PCR to test for Machado-Joseph disease?

This paper describes an allele-specific PCR protocol to detect CAG repeat expansion in MJD patients: Maciel P, Costa MDC, Ferro A, et al. Improvement in the Molecular Diagnosis of Machado-Joseph ...
acvill's user avatar
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5 votes

What makes/breaks the hydrogen bonds between DNA and RNA during transcription?

I wouldn't really say RNA polymerase is "creating" the hydrogen bonds so much as it's thermodynamics that creates them. When we talk about an enzyme "creating" a bond, what we're generally referring ...
Stephen B.'s user avatar
5 votes
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DNA replication: How many DNA polymerase molecules work in parallel?

In the (beautifully rendered) video you linked to, the green molecules are DNA polymerases. So you can already see that there are more than two DNA polymerases at work! At each replication fork, ...
leekaiinthesky's user avatar
4 votes
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How do cells determine RNA types?

Well remember that an mRNA, the RNA that is destined for the ribosome, has already been processed by the time it gets there. This is done by the splicing machinery, among other things (capping enzymes,...
CKM's user avatar
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3 votes
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Why does Taq polymerase add 3' adenine overhangs?

Non-templated terminal addition by certain DNA polymerases is apparently dependent on the base stacking between the incoming base and the existing duplex (Fiala et al., 2007*). This was verified by ...
WYSIWYG's user avatar
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3 votes
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Terminology of the sequences of promoters in relation to DNA strands

It appears that this question is one of terminology, so I am answering it as such. Convention for representing features in DNA sequences The convention is that in indicating any sequence feature† in ...
David's user avatar
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3 votes
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Do all RNA polymerase in Eukaryotes share the same transcription factors?

Except for the TATA-binding protein (TBP), there are no common transcription factors for each RNA polymerase. However, there are homologies between many of the factors used by the different enzymes. ...
adjan's user avatar
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3 votes

What makes/breaks the hydrogen bonds between DNA and RNA during transcription?

Although the answer provided by @StephenB is essentially correct, I’d like to supplement this with more visual illustrations — including a link to an animation which the poster requested — as well as ...
David's user avatar
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3 votes

How do molecules find their places?

It depends on the molecule and the type of a chemical reaction. In simple chemical reactions molecules literally randomly collide with the probability proportional to their concentrations, which gives ...
Roger V.'s user avatar
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2 votes

What determines the nucleotides incorporated into RNA by polynucleotide phosphorylase?

There would seem to be two possibilities: The enzyme has differential specificity for different substrate NDPs. or The deciding factor is the relative concentrations of the different NDPs in the ...
David's user avatar
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2 votes
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Definition of nucleotide-associated proteins and RNA-polymerase associated proteins

In short: Nucleotide-associated proteins are DNA-binding proteins that bind DNA. RNA-polymerase associated proteins bind RNA-polymerases and are required for its functionality. In more detail: DNA-...
AlexDeLarge's user avatar
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1 vote
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Polymerase Chain Reaction Specifics

are the primers used in every cycle the same sequence? Yes. You put the whole reaction on the thermocycler, and then walk away until all the cycles are complete. But one could do a second round of ...
swbarnes2's user avatar
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1 vote

Polymerase Chain Reaction Specifics

The primer is incorporated into the start of the new strand. The number of dna strands produced is limited by the number of primers.
Polypipe Wrangler's user avatar
1 vote

a biochemical pathway for evaluating the effect of 3' to 5' exonuclease on the proofreading activity of DNA synthesis

well I tried to implement this pathway in MATLAB and it seems to me that it makes some sense. Here are two versions of the reaction progress simulation, one with low and the other with high affinity ...
e-gabrielyan's user avatar
1 vote
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Origins of transcription factors and RNA Polymerase

This is one of the main features of the RNA World. What I mean by that is, RNA not only acts as a repository of genetic information, it also acts as an enzyme. This enzyme is known as Ribozyme. ...
Vasundhara Gray's user avatar
1 vote

Which DNA polymerase can use a nick as priming site?

It sounds like you are looking for a DNA polymerase that can perform nick translation. NEB maintains a chart listing the properties of their polymerases, including nick translation and extension from ...
acvill's user avatar
  • 8,296
1 vote

How does cell detect if a RNA polymerase II is stalled during transcription and in turn deploy the proper transcription-coupled repair factors?

The beauty of RNA polymerase II is its faculty to act like a sensor towards damage to genetic data. The response of the RNA molecule is variable on the type of DNA lesion which presents itself. DNA ...
Epistemonaut's user avatar
1 vote
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Are bacterial RNA polymerases distributed evenly throughout the cell or localized?

In E. coli most RNA polymerase molecules are bound to DNA, and those that aren't are within easy reach of the DNA. According to Larry Moran A typical E. coli cell contains about 5000 molecules of ...
Alan Boyd's user avatar
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1 vote

Definition of nucleotide-associated proteins and RNA-polymerase associated proteins

Neither of the terms “Nucleotide-associated protein” or “RNA-polymerase associated protein” are standard in molecular biology in so far as they are not defined in the reference Gene Ontology. (In ...
David's user avatar
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1 vote

Why and how is DNA synthesis so much faster then RNA synthesis in bacteria?

I wouldn't call them hypotheses, but the question is intriguing, and, as it seems to be ignored in the literature, I'll make a couple of suggestions. Perhaps it has something to do with recognition ...
David's user avatar
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1 vote

Storing Taqman plates with polymerase in fridge before running

Not sure if this question is still valid, but it was marked as unanswered and frequently viewed, so here's a go :) These days most polymerases (certainly for Real Time PCR) are so-called Hot Start ...
Cabe's user avatar
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