Enzyme that catalyzes the serial addition of monomers to synthesize a polymeric biomolecule. This term usually applies to DNA/RNA polymerases which synthesize these nucleic acid polymers from mononucleotides.

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18
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4answers
118k views

Why is DNA replication performed in the 5' to 3' direction?

DNA replication goes in the 5' to 3' direction because DNA polymerase acts on the 3'-OH of the existing strand for adding free nucleotides. Is there any biochemical reason why all organisms evolved to ...
10
votes
1answer
225 views

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

DNA synthesis in E. coli is 20x faster than RNA synthesis at 1000nt/s vs 50nt/s. (Mirkin'05) I find that perplexing since DNA polymerization has better proofreading than the RNA variety, which ...
9
votes
2answers
381 views

First RNA polymerase-mRNA

We know that RNA polymerase produces mRNA by reading DNA strand. Which enzyme produces the first RNA polymerase if other RNA polymerases are synthesized in the same way like other enzymes(proteins) ?
6
votes
1answer
217 views

Why do some bacteria have most genes on the leading strand of the genome?

Genes in the (+) strand are black and genes in the (-)strand are red. The gene distribution in E. coli genome is somewhat expected: transcribed regions would tend to alternate with non transcribed ...
6
votes
1answer
93 views

number of RNA pol II molecules in a given human nucleus?

Does anybody have any estimate on the number of RNA pol II molecules in the nucleus of a given human cell? For example, how many RNA polymerase type II protein complexes would there be on average at a ...
5
votes
1answer
235 views

How are DNA polymerase error rates measured?

It is well known that the first DNA polymerase, Taq, is quite error prone. Newer generation commercial enzymes that have either been isolated from different thermophile species or have been improved ...
5
votes
2answers
305 views

How can E. coli proliferate so rapidly?

The E. coli has a genome with approximately 5×106 bp. The main DNA polymerase involved in its chromosome duplication (DNA pol III , the one with highest processivity) can polymerize ~103 nucleotides ...
4
votes
3answers
275 views

Why do we need deep sequencing?

Why do we need deep sequencing? Why cannot the sequencing technologies read all the nucleotides correctly at the first read? Sorry since this question is too trivial, I don't have a biological ...
3
votes
1answer
71 views

Why does Taq polymerase add 3' adenine overhangs?

Is there a mechanism for the preference of Taq polymerase to add a non-templated 3' adenine (overhang) instead of other bases?
3
votes
1answer
715 views

Open protocol for Ligase Independent Cloning

Ligase Independent Cloning is a protocol that allow an insert to be integrated into a vector without ligation. It uses T4 DNA polymerase with only ATP to first chew back from blunt ends to create ...
3
votes
1answer
535 views

Storing Taqman plates with polymerase in fridge before running

I'm going to be running some Taqman assays on cDNA generated from RNA collected from various samples, and will end up running a bunch of plates (right now the setup is 1/2 a plate per sample, ...
3
votes
0answers
169 views

Has anyone ever sucessfully translated xRNA or yRNA? [closed]

I've recently been researching the subject of size-expanded nucleobases in alternative genetic sets. Many papers describe the, at least, partial success in replicating xDNA and yDNA, as well as ...
2
votes
1answer
670 views

Where does Taq polymerase migrate during electrophoresis?

Assuming a 1% Agarose gel with TAE. Follow up questions: Is there a way to stain for it? Could the polymerase be captured and reused?
2
votes
1answer
167 views

A question about IPTG induction

I have found the information: `In the absence of lactose, the lac repressor binds to the operator sequence on DNA and bends the DNA by 40 degrees. This blocks access of T7 RNA polymerase to the ...
2
votes
1answer
3k views

How is the transcription direction of RNA polymerase determined?

When transcription factors attach to the DNA strand - How do they know in which direction they have to initialize the transcription by rna polymerase? Is it always read in the same direction anyway? ...
1
vote
2answers
3k views

Stop codons and exons?

If we had a hypotheical gene called gene exampleGene and this gene had 5 exons, labeled A, B, C, D, and E in that order on the chromosome, could it be the case that the stop codon for this gene be on ...
1
vote
2answers
265 views

What happens when we re-start a PCR reaction?

Recently when my PCR reaction was running there was power fluctuation and the entire lab was blacked out for a few minutes and unfortunately PCR that I was running got switched off. So, would it be ...
1
vote
1answer
56 views

Are there U-rich transcriptional pause sites?

I've heard a statement in a talk that U-rich sequences cause transcriptional pausing. The intuitive explanation for this was that the UTP concentration is lower in the cell than the ATP concentration. ...
1
vote
1answer
186 views

DNA Replication

I just wanted to understand the basic steps behind the replication of the lagging strand of DNA: Have helicase unwind it first DNA Primase lays down RNA primers in fragments, called Okazaki ...
1
vote
0answers
28 views

Estimating RNA concentration from Specific Activity of Labeled RNA

The question reads, Using T7 RNA polymerase to transcribe in vitro a 100-nt RNA off a DNA template. This RNA contains 19 Adenosines. In your 100 uL transcription reaction you added 1.00 µL of α32P•[...
1
vote
0answers
23 views

Infer type of nucleic acid based on number of nucleosides

Lets say we analysed a nucleic acid and found out that it had 20% Adenosine, 25% Guanosine, 40% Thymine and 15% Cytosine. We know that A always pairs with T and G with C. So, based on these numbers, ...
1
vote
0answers
6 views

Does the assembly of the PLC transcription complex utilize phosphorylation in binding of the GTFs?

in the recruitment of general transcription factors during transcription initiation is phosphorylation utilized?
1
vote
0answers
30 views

What are the reasons which make intron detection uncertain?

Intron/exon sequence detection seems to involve statistical prediction which can at best deliver a guess (until experimentally confirmed) as to where the splice site is. What are the reasons why ...
1
vote
0answers
23 views

Will bacterial promoter without either -10 or -35 sequence allow no transcription?

I have a strong constitutive promoter on a plasmid inside of E.Coli, which expresses a gene. Having either -10 or -35 sequence modified to random sequence, will it ensure zero transcription from that ...
0
votes
0answers
26 views

DNA replication: in which direction does the DNA polymerase 3 work?

In a couple of sites I have seen, it states that it reads in 3' to 5' direction (upstream) though the daughter strand is made in the 5'-3' direction. How does that work?