The scientific study of the structure and function of genes at the molecular level, particularly chromosomes and DNA.

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Do you have a comprehensive protocol using xGen blocking oligo? [closed]

Specifically used with genomic DNA and to help prevent non-specific binding
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Mosaic segregation in C. elegans

How can mosaic segregation be used in C. elegans? Can it tell us where a given gene is expressed, or needs to be expressed for worm survival?
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97 views

What is two-start or zigzag model of 30 nm chromatin fibre?

I read some webpages describing the two-start model but could not get it. I'll be obliged if someone helped me understand the topic. The websites I have been through are: 1.http://www.nature.com/nrm/...
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129 views

What is positive and negative supercoiling?

Is the following correct? Positive supercoiling = the coiling of DNA helix (B-DNA) on itself during intesified coiling of the two DNA stands in right handed direction negative supercoiling = the ...
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1answer
69 views

How do the major and minor grooves in the DNA helix arise?

I understand that they arise due to the pairing of bases of two opposite stands and are sites through which important proteins needed for replication and transcription of DNA interact. But I don't get ...
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43 views

Mitochondrial Genetic code

We know that the genetic code is universal. My query is why the mitochondrial genetic code is different from universal genetic code?
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Why is mRNA used as a biomarker for cancer over tRNA or rRNA?

I cannot find a clear explanation for why mRNA is used as cancer biomarker and not tRNA or rRNA. Is there something peculiar about mRNA which cannot be fulfilled by tRNA or rRNA?
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23 views

What are in common between transcription factors?

In terms of their structures (primary to tertiary) and locations? Why do they have these commonalities? Or are any of these commonalities critical to their functions?
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Hydrogen bonding and the blocking thereof in nucleic acids during nuclear processes

In transcription, RNA polymerase unwinds the DNA double helix and begins attaching RNA nucleotides to the template strand. In its wake, the DNA double helix closes back—this is only natural, seeing as ...
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Does DNA polymerase I require a $3^\prime$ end?

DNA polymerase III adds nucleotides in the $5^\prime \rightarrow 3^\prime$ direction because it can only add nucleotides to the $3^\prime$ end of the previous nucleotide. This is why it requires a ...
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What type of point mutation and chromosomal mutation cause Albinism in humans?

First of all, I know that OCA1 (Oculocutaneous Albinism Type 1) is autosomal recessive which means that both parents-who are unaffected-have to pass down one copy of a mutated gene in order to ...
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42 views

What separates gene loci?

Introns are sections of noncoding DNA that separate exons within a gene locus. However, between different gene loci, I also would assume there to be noncoding regions of DNA. What are these regions ...
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Crossing over and exon shuffling?

Campbell Biology 10e, in discussing the functions of introns, writes: The presence of introns in a gene may facilitate the evolution of new and potentially beneficial proteins as a result of a ...
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XNAs as a Genetic material [closed]

I heard there is a new genetic material called XNAs.I wanted to know more about this.Does anyone about XNAs as genetic material?
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94 views

What came first? The DNA or the DNA polymerases?

I know this sounds a lot like chicken and egg question and while the latter has an answer, I am intrigued about the former. A modified form of the question would be, in the course of abiogenesis, ...
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Amplified Fragment Length Polymorphism (AFLP) primers

I am trying to blast AFLP primer sequences to the genome to find the locations of the AFLP markers. However, I can't seem to find full alignments for the primers on the genome. For example, in the ...
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2answers
90 views

Explain allelic complementation at molecular level

I know that Allelic complementation is a phenomenon where two recessive loss-of-function allele generate a functional gene product by compensating each others' defect. But I don't get how do they ...
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1answer
52 views

How does a test like the Natera Panorama distinguish the child's genome from the mother?

Blood tests on an expectant mother, like the Natera Panorama, are now being used regularly to screen fetuses for chromosome abnormalities. At my wife's recent prenatal visit, she wasn't really even ...
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343 views

Gene and alleles

This is a multiple choice question: Consider a gene, ABC, which codes for an enzyme involved in the metabolism of sugars. There are two known alleles of this gene, ABC1 and ABC2. Which statement ...
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1answer
55 views

How was gene therapy able to cure diseases through the transformation of actively dividing cells?

I thought that gene therapy, when performed on target cells that regenerate themselves constantly, can be effective for a limited time only. I.e., the effect gradually wears off after a while, ...
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Is DNA transcription inactive during mitosis ie no proteins are made? How does the cell survive?

I've read that during mitosis, DNA exists as heterochromatin, a form that is unable to be accessed for transcription. Does this mean no new proteins are made during what can be 20% of a cell's life? ...
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2answers
52 views

ChIP-seq for histone modification not in agreement with RNA-seq for expression

I have ChIP-seq for H3K79me2 and H3K36me3 and RNA-seq data for treated and untreated samples. Those two histones mark active genes. Lets say, hypothetically, a peak caller finds differential sites at ...
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1answer
38 views

Constant or variable number of chiasmata during recombination?

During recombination, is the number of chiasmata consistent for each gamete and are the chiasmata regions consistent within a single organism?
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1answer
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Are the genes for transcriptional factors close to their targets in the genome?

Transcriptional factors (activators and repressors) are proteins which regulate transcription. Being proteins, they themselves are also made from expression of certain DNA sequences/genes. For ...
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1answer
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probe amplification in MLPA

I'm reading an article about MLPA (Multiplex ligation-dependent probe amplification) and I got stuck on this sentence: The advantage of splitting the probe into two parts is that only the ...
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61 views

Chromosomomal walking

I'm having a great deal of trouble understanding chromosomal walking, especially in regards to this article: Control of male sexual behavior and sexual orientation in Drosophila by the fruitless ...
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98 views

Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
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Degenerate primer designing software

Can any one provide online free degenerate primer designing software. I have tried couple of them like CODEHOP is one where BLOCK formatting step finding difficulty, can anyone help me out....
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How many genes does D. melanogaster have?

Obviously there is no 100% exact number, but I came across this on flybase, the gold standard for annotation. I am confused now. "Genes located to the genome", is that what I am looking for? If so, ...
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“Signal Advance”: Unsure of meaning or contextual use

I am reading through Recombinant DNA; Genes and Genomes - A Short Course - Third Edition by James D. Watson, et. al. and I came across this paragraph in the discussion about discrete factors of ...
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43 views

How to find conserved residues across species?

I want to identify if certain phosphorylation sites are conserved for protein X across humans and yeast. I know from MS data that there are 4 phosphorylation sites in Human protein X. In order to ...
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37 views

gene transformation from plant to plant - transgenic plant

I want to know if the expression of a transfered gene depends on source of the gene, if e.g.: 1] I isolate a gene from plant and transfered it to the same plant? 2] I isolate a gene that is highly ...
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1answer
25 views

Degree of complementarity

Apologies in advance for asking bit naive question. I have looked up for this concept a lot but didn't find anything. The wikipedia (I know its not authentic all the time, but I think works well for ...
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1answer
123 views

What does it mean to clone a gene?

When I look up information related to the identification of disease genes, texts will often refer to the gene being "first cloned." What does "clone" mean in this context? Is it simply a synonym for ...
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PCR that worked previously is now only showing primer dimers and a smear on gel

PCR amplification of a promoter sequence for gel extraction worked beautifully using Phusion HF enzyme with GC (higher error but less picky) buffer. However, DNA concentration from the gel extraction ...
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genetic complementation problem

I've attached the picture of the problem. SO, based on the information I managed to assemble two large cistrons. (if the combination of two mutants yield (-) mutations are on the same chromosome) A)...
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Can genes be expressed sequentially?

As I understand it, any gene on an exposed/unpacked region of a chromosome is continuously being expressed. Regulatory genes may increase or decrease the amount of protein synthesised due to its ...
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416 views

Lac operon: How can lactose enter the cell in the absence of lactose permease?

My textbook states that lactose permease...transports lactose into the cell and When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor ...
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2answers
126 views

Alternatives to PCR

PCR uses cycles of heating and cooling to denature the strands, calling for special thermostable DNA polymerases. In a cell, during replication, Helicase unwinds the DNA without the requirement of ...
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When performing mutagenesis for an assay, how do you decide on the sample size of individuals to be mutated such that all genes are covered?

If I want to study, say, gustatory response of salmons to a bile acid, I need to mutagenize a sample of salmon males. However, given that there are many genes involved in this response, what is ...
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recombination between DNA segments question

In the diagram shown above, segments A and C are copies of a repeated DNA sequence, flanking a unique stretch shown as B. A and C are in an inverted orientation relative to each other, as indicated by ...
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mutations induced by transposons

Question: In contrast to chemically-induced mutations, mutations induced by transposons are more likely to ... be lethal de dominant be stable revert to wild types be a gain of function The ...
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59 views

tandem repeat sequence; causes of contraction and/or expansion question

Question: Which of the following events, occurring within a tandem repeat sequence, will cause an expansion or contraction of the array? A) Endoduplication B) homologous recombination C) ...
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3answers
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Abbreviations for molecules: What are CheW, CheA, CheY?

I've encountered the abbreviations such as "CheW" and "CheA" for certain organic molecules. For example: Proteins associating with the Tar complex include the autophosphorylating protein kinase ...
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ATP to disassembly of nucleotide ratio

DNA Helicase, the enzyme that is responsible for tearing apart the strands before DNA replication, requires ATP to rip apart nucleotides. I have asked this question to several professors and they ...
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Double stranded breaks in E. coli

What could be a possible reason why no enzymes have been found that make double stranded breaks in the RecBCD pathway?
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Genomic DNA isolation from wheat

Can I use dry seed, wheat for example, in place of young leaves for isolation and purification of genomic DNA for PCR amplification? The goal of my experiment is to validate a novel gene which is ...
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2answers
119 views

how do I find the number of bp in chromosome 3 by knowing number of bp in chromosome 1?

If i have a number of bp in chromosome 1 for example(298,295,559 bp) can I use this number to find the number of bp in chromosome 3.
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How does RNA transcription determine which half of the DNA to use?

I feel that I might have a complete misunderstanding here. If DNA has two strands, how does the machinery of RNA transcription determine which one to transcribe?
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DNA Replication And Primer [duplicate]

Why does nature rely on RNA primer for the start of DNA Replication? Why not simply use DNA primer and make life simple !