Analysing DNA

What is the most likely outcome if the annealing temperature in a PCR reaction is set too high?

What is the function of DNA polymerase in PCR?

Why is Taq polymerase used in PCR instead of other DNA polymerases?

What is the purpose of the primers in PCR?

Deoxynucleoside triphosphates (dNTPs) serve what crucial role in PCR?

What might be a consequence of setting the annealing temperature too low during PCR?

A researcher is using PCR to detect the presence of a specific gene in a sample. What components are essential for the PCR to work?

What is the primary reason that PCR is useful in detecting disease markers or in forensics?

Which of the following best describes the role of 'template DNA' in the PCR process?

What is the role of temperature in the different steps of a PCR cycle?

A scientist aims to amplify a specific gene with primers that have a high GC content. What adjustment to the PCR process might be necessary?

Besides amplifying specific DNA sequences, what is another application of PCR?

In the context of PCR, what are 'thermocyclers'?

Consider a PCR reaction designed to amplify a gene conferring antimicrobial resistance (AMR). What would be the most concerning outcome if the annealing temperature was too low?

How do gene-specific primers facilitate the extraction and amplification of target DNA sequences?

You are designing primers for a PCR reaction. Which of the following primer sequences has the most appropriate length and GC content for efficient amplification?

What is the relationship between primer design and the specificity of PCR amplification?

If a PCR reaction yields multiple bands in gel electrophoresis, what is the most probable cause?

What role does the initial denaturation step play in PCR?

In gel electrophoresis, what property of DNA fragments primarily determines their rate of migration through the agarose gel?

What is the purpose of applying an electrical current during agarose gel electrophoresis?

How are DNA fragments visualized within an agarose gel after electrophoresis?

What information can be gathered from the position of a DNA band after gel electrophoresis?

If a PCR product appears as a band higher up the gel than expected after electrophoresis, what is a likely explanation?

What type of information does DNA sequencing provide that PCR and gel electrophoresis do not?

Besides determining the exact order of nucleotide bases, what other application is commonly associated with DNA sequencing?

What is a key characteristic of Dideoxy (Sanger) sequencing compared to Next Generation Sequencing (NGS)?

What is a defining feature of Next Generation Sequencing (NGS) technologies?

Which DNA sequencing method is known for producing long reads with increased accuracy, and single-molecule sequencing?

What is the first step typically performed after obtaining sequence data to understand the origin of the sequenced DNA?

In comparing Sanger sequencing to PacBio SMRT sequencing, what is a key trade-off to consider?

If a researcher aims to identify the specific bacterial strain causing an infection, what is the most appropriate application of DNA sequencing?

A lab is on a tight budget and needs to sequence a short, well-known region of a plasmid to confirm its identity. Which sequencing method would be the most cost-effective?

In a scenario where a researcher is investigating the full spectrum of microbes present in a soil sample, which sequencing approach would be the most appropriate?

When analyzing a newly discovered genetic mutation in a human genome, what would be the advantage of using PacBio SMRT sequencing over other methods?

What potential problem can arise when comparing DNA sequence data to a database to identify the closest match?

A researcher finds that multiple distinct bands appear after gel electrophoresis of a PCR product, despite using highly specific primers. What follow-up step is most likely to provide insight into this issue?

In a diagnostic lab, which approach would be most suitable for rapidly screening a large number of patient samples for the presence of a specific, known viral mutation?

Considering the applications of PCR, gel electrophoresis, and DNA sequencing, how does the information from gel electrophoresis enhance the results obtained from PCR?

What key structural difference between ddNTPs and dNTPs causes termination of DNA synthesis during Sanger sequencing?

In Sanger sequencing, what is the direct role of the randomly incorporated ddNTPs?

How are the DNA fragments of varying lengths, produced during Sanger sequencing, typically separated?

In Sanger sequencing, what is the purpose of reading the sequence 'from shortest to longest' fragments?

What role does PCR amplification play in both Sanger sequencing and Next Generation Sequencing (NGS)?

In Next Generation Sequencing (NGS), what is the significance of attaching DNA fragments to a flow cell surface?

During Next Generation Sequencing (NGS), why are specialized dNTPs with reversible chemical modifications used?

How is the nucleotide sequence determined in Next Generation Sequencing (NGS) after each round of synthesis?

What is the purpose of removing the fluorescent marker and chemical blockers in Next Generation Sequencing (NGS)?

How are overlapping DNA sequences reconstructed in Next Generation Sequencing (NGS)?

Which of the following is a key advantage of Next Generation Sequencing (NGS) compared to Sanger sequencing?

What is the primary reason Sanger Sequencing typically takes longer to complete than Next Generation Sequencing (NGS)?

In the context of Sanger sequencing, why are 'DNA fragments of different lengths ending in labeled ddNTP' essential?

Before Next Generation Sequencing (NGS), 'genome/DNA broken into smaller fragments' is performed. What is the significance of this step?

In Sanger sequencing, what would be the most likely consequence of using dNTPs that are contaminated with ddNTPs?

What is the primary reason that Next Generation Sequencing (NGS) is now used more commonly than Sanger sequencing for sequencing large genomes?

During Next Generation Sequencing (NGS), what is the effect of having 'each have 2 reversible chemical modifications: uniquely coloured fluorescent marker + 3' chem'?

A researcher is using Next Generation Sequencing (NGS) to analyze a metagenomic sample from a soil environment. Given the high diversity of organisms, what aspect of NGS is most beneficial for this type of study?

You perform a Sanger sequencing reaction and notice that the resulting electropherogram shows a clear sequence but with significantly reduced signal strength after approximately 500 base pairs. What is the most likely cause of this?

A clinical lab is transitioning from Sanger sequencing to Next Generation Sequencing (NGS) for detecting mutations in a panel of cancer-related genes. What is one key consideration they must address in data analysis when using NGS compared to Sanger sequencing?

Which of the following is a direct application of using genomic databases?

What is a primary function of BLAST (Basic Local Alignment Search Tool) in bioinformatics?

In the context of DNA sequencing and bioinformatics, which of the following tasks is most directly facilitated by comparing sequences?

What role do bioinformatics and DNA sequence analysis play in addressing antibiotic resistance?

In PacBio SMRT sequencing, what is the purpose of attaching a single DNA polymerase to the bottom of a tiny well?

During PacBio SMRT sequencing, why are the dNTPs fluorescently labeled?

In PacBio SMRT sequencing, what happens after a nucleotide is incorporated and its fluorescence is read by the machine?

What is a significant advantage of PacBio SMRT sequencing that distinguishes it from other sequencing methods?

For which of the following applications would sequencing unamplified samples be most advantageous?

How does aligning a PCR sequence (Query) with an E. coli plasmid DNA (Subject) provide useful information?

If you are using bioinformatics tools after sequencing a PCR product, what might the presence of identical bases aligned with an E. coli plasmid sequence indicate?

Why are genomic databases considered 'public online repositories'?

What does a BLAST search primarily accomplish in the context of DNA sequence analysis?

How can bioinformatics tools that compare sequences aid in identifying organisms and mutations?

How is DNA sequence analysis, including BLAST searches against genomic databases, used in the context of antibiotic resistance?

What is the significance of terminal phosphates being removed during nucleotide incorporation in PacBio SMRT sequencing?

What is a key advantage conferred by the ability of SMRT sequencing to sequence very long DNA fragments?

Why would the ability to sequence unamplified samples be particularly advantageous in metagenomic studies of environmental samples?

In PacBio SMRT sequencing, what is the function of the 'excitation and fluorescence detection' system?

How does the use of tiny wells in PacBio SMRT sequencing contribute to its efficiency?

What is the primary purpose of using a thermostable DNA polymerase in PCR?

During the annealing step of PCR, what primarily determines where primers bind to the template DNA?

What is the major difference between the functions of dNTPs and ddNTPs in DNA sequencing?

Why is it essential to remove the fluorescent marker and chemical blockers after each cycle in Next Generation Sequencing (NGS)?

In the context of bioinformatics, what does a high Expectation (E) value in a BLAST search suggest?

Following DNA sequencing, you use bioinformatics tools to compare your sequence with known genes. You identify a gene with 99% identity but notice several gaps in the alignment. What is the most likely explanation for these gaps?

What is the main advantage of using PacBio SMRT sequencing over Sanger sequencing for analyzing a newly discovered bacterial genome?

When using BLAST to analyze a DNA sequence, you find a hit that aligns with a known antibiotic resistance gene. What can you infer from this result?

After performing Sanger sequencing, the resulting electropherogram shows ambiguous peaks beyond a certain point in the sequence. What is the most likely cause of this issue?

Why is the thermostability of DNA polymerase a critical factor in PCR?

How does gel electrophoresis assist in assessing the success and specificity of a PCR reaction?

In Sanger sequencing, what is the role of dideoxynucleotides (ddNTPs) in determining the DNA sequence?

During Next Generation Sequencing (NGS), what is the purpose of attaching DNA fragments to a flow cell?

In a BLAST search, what does the term 'sequence identity' refer to?

How can analyzing PCR products using gel electrophoresis and subsequent DNA sequencing provide insights into antibiotic resistance?

What is the consequence of the terminal phosphates being removed during nucleotide incorporation in PacBio SMRT sequencing?

In contrast to Sanger sequencing and Next Generation Sequencing (NGS), how does PacBio SMRT sequencing minimize amplification bias?

How does the ability to sequence native, unamplified samples improve metagenomic studies using PacBio SMRT sequencing?

What insight does comparing sequencing results of different isolates of the same bacterial species offer in the context of disease outbreaks?

You perform a PCR on a sample and run the products on a gel. The gel shows a smear instead of distinct bands. What is the most likely cause?

What is the main purpose of a 'cycle' in PCR involving denaturation, annealing, and extension?

Which factor primarily determines the migration rate of a linear DNA fragment through an agarose gel during electrophoresis?

What is the purpose of performing a 'reverse transcription' step when detecting an RNA virus using PCR?

What is the general workflow after obtaining DNA sequence data from a PCR product?

What information is gleaned from the use of bioinformatics tools, such as BLAST search, of DNA sequences?

Why is the identification of an AMR gene in a sequence useful?

When can PCR be used to obtain cDNA clones?

When would PCR primarily be needed to obtain a genomic clone?

What does the location of where the PCR product aligns to along the Subject indicate?

Why do we see gaps in DNA alignments?

The E value states...

How does determining AMR gene presence in a database translate to phenotype?

What do fluorescent signals with detection of a single color reveal to the user?

In a BLAST interface, what will the ‘query’ entry mean?

What aspect of gel electrophoresis relies on the physical principles primarily?

Why does the presence of contaminants, in an amplicon during Sanger sequencing, interfere with successful DNA strand synthesis?

What is the main challenge that can arise when interpreting results in Next Generation Sequencing compared to Sanger sequencing?