Molecular Diagnostics Overview

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Questions and Answers

What is the primary focus of molecular diagnostics?

  • Detecting and measuring genetic material or proteins related to diseases (correct)
  • Analyzing demographic data in health care
  • Studying cellular structures and functions
  • Identifying environmental impacts on health

Which term describes the approach that tailors medical treatment to individual characteristics?

  • Generalized medicine
  • Epidemiological medicine
  • Preventive medicine
  • Personalized medicine (correct)

What is the role of companion diagnostics in molecular diagnostics?

  • To monitor long-term health outcomes for all patients
  • To provide general health advice
  • To enhance the effectiveness of a specific therapy for a patient (correct)
  • To diagnose diseases unrelated to genetic material

How can molecular diagnostics aid in family planning?

<p>By identifying carriers of genetic mutations related to certain conditions (B)</p> Signup and view all the answers

What recent trend has been observed in the field of molecular diagnostics?

<p>Increasing application in infectious diseases (C)</p> Signup and view all the answers

Which of the following best describes molecular diagnostics' application in blood banks?

<p>To screen for infectious diseases in donated blood (C)</p> Signup and view all the answers

What is one of the benefits of molecular diagnostics in cancer treatment?

<p>Helping to identify the likelihood of cancer recurrence (A)</p> Signup and view all the answers

Which statement about molecular diagnostics is correct?

<p>They can identify multiple strains of viruses in a single test. (A)</p> Signup and view all the answers

What is the proper incubation temperature for lysing cells?

<p>56°C (D)</p> Signup and view all the answers

What is the purpose of adding ethanol to the lysate?

<p>To precipitate the DNA (C)</p> Signup and view all the answers

What should be done if residual solution is visible in the purification column after the second wash?

<p>Re-spin the column for 1 minute at maximum speed. (B)</p> Signup and view all the answers

How is DNA concentration estimated?

<p>By measuring absorbance at 260 nm and adjusting for turbidity. (C)</p> Signup and view all the answers

What is the expected A260/A280 ratio for pure dsDNA?

<p>1.8 (C)</p> Signup and view all the answers

What is the maximum speed for centrifuging the GeneJET Genomic DNA Purification Column during the second wash?

<p>12000 x g (C)</p> Signup and view all the answers

What should be done with the purification column after eluting the DNA?

<p>Discard the purification column. (D)</p> Signup and view all the answers

How does reducing the volume of Elution Buffer affect the final quantity of eluted DNA?

<p>It decreases the final quantity. (A)</p> Signup and view all the answers

What is the purpose of adding a concentrated salt solution during DNA extraction?

<p>To make cellular debris clump together. (C)</p> Signup and view all the answers

Which method involves the denaturation of proteins to facilitate the separation of nucleic acids?

<p>Phenol–chloroform extraction. (B)</p> Signup and view all the answers

What role does EDTA play in the lysis solution?

<p>It chelates divalent cations and inactivates nucleases. (B)</p> Signup and view all the answers

Why is Proteinase K used during protein removal in DNA extraction?

<p>It digests a wide range of native proteins. (C)</p> Signup and view all the answers

What is the primary purpose of using ice-cold ethanol or isopropanol in DNA purification?

<p>To precipitate DNA by making it insoluble. (D)</p> Signup and view all the answers

What is the function of SDS in cell lysis?

<p>It breaks apart membranes by interacting with lipids and proteins. (D)</p> Signup and view all the answers

How does minicolumn purification separate nucleic acids from other components?

<p>By adsorption of nucleic acids to a solid phase. (A)</p> Signup and view all the answers

Which of the following is NOT typically part of a common lysis solution?

<p>Sodium acetate (C)</p> Signup and view all the answers

What is the primary focus of the molecular diagnostic laboratory as outlined in the introduction?

<p>Diagnostic testing and identification of molecular markers (A)</p> Signup and view all the answers

Which of the following is critical for ensuring lab safety in molecular biology?

<p>All of the above (D)</p> Signup and view all the answers

What is the key purpose of preparing solutions in molecular diagnostics?

<p>To dilute substances to specific concentrations (A)</p> Signup and view all the answers

What is the first step in the experimental protocol for genomic DNA preparation from blood?

<p>Blood collection (B)</p> Signup and view all the answers

Why is the measurement of DNA concentration important in molecular diagnostics?

<p>To ensure adequate amounts for subsequent testing (A)</p> Signup and view all the answers

Which of the following components is NOT typically included in the preparation of genomic DNA from blood?

<p>Reagents for protein synthesis (D)</p> Signup and view all the answers

What is the significance of measuring the purity of DNA after extraction?

<p>To ensure the absence of contaminants (A)</p> Signup and view all the answers

In which section of the molecular diagnostic lab notebook would you find the experimental protocol?

<p>Preparation of Genomic DNA from Blood (A)</p> Signup and view all the answers

What is the primary purpose of the lysis step in silica-based DNA extraction?

<p>To break down cells and access DNA (C)</p> Signup and view all the answers

Which component is added during the purification-bind step to enhance the binding of DNA to the silica membrane?

<p>Ethanol (B)</p> Signup and view all the answers

What is the result of not removing all ethanol during the elution step?

<p>The DNA cannot fully rehydrate (D)</p> Signup and view all the answers

During the wash step, what is the purpose of the two different washes with buffers?

<p>To remove impurities and residual proteins and salts (D)</p> Signup and view all the answers

What is the recommended storage condition for blood samples prior to DNA extraction?

<p>At room temperature or 4°C (A)</p> Signup and view all the answers

What role does chaotropic salt play in the lysis step?

<p>It disrupts hydrogen bonds and hydrophobic interactions (D)</p> Signup and view all the answers

How can the elution of DNA be maximized during the procedure?

<p>By allowing the elution buffer to sit in the membrane for a few minutes (C)</p> Signup and view all the answers

What is the purpose of including proteinase K in the DNA extraction protocol?

<p>To digest proteins and facilitate lysis (D)</p> Signup and view all the answers

What is the purpose of the cell lysis solution in DNA extraction?

<p>To break down cellular membranes and release DNA (B)</p> Signup and view all the answers

Which precaution is crucial to prevent contamination of isolated DNA?

<p>Employing proper pipetting techniques (B)</p> Signup and view all the answers

How can heme contamination in isolated DNA be detected?

<p>By performing a UV-Vis spectral analysis (B)</p> Signup and view all the answers

What method can be used to confirm the presence of DNA in a stored sample?

<p>Conducting gel electrophoresis (D)</p> Signup and view all the answers

Is it feasible to prove that your DNA is actually in the sample?

<p>Yes, through sequencing analysis (C)</p> Signup and view all the answers

How is DNA extraction significantly beneficial to forensic scientists?

<p>It aids in the identification of individuals through DNA profiling (A)</p> Signup and view all the answers

What role does heme play as a contaminant in DNA isolation from blood?

<p>It can interfere with PCR amplifications (B)</p> Signup and view all the answers

What is one major challenge faced in isolating DNA from blood samples?

<p>Presence of cellular macromolecules (D)</p> Signup and view all the answers

What is a typical strategy to increase DNA purity during extraction?

<p>Incorporating ethanol precipitation (D)</p> Signup and view all the answers

What is the primary goal during the DNA extraction process?

<p>To ensure the DNA is free from any contaminants (C)</p> Signup and view all the answers

Which technique is often used to visualize DNA post-extraction?

<p>Gel electrophoresis (C)</p> Signup and view all the answers

What can cause DNA degradation during the extraction process?

<p>Prolonged exposure to light (B)</p> Signup and view all the answers

What consequence arises from improper pipetting during DNA extraction?

<p>Risk of sample contamination (C)</p> Signup and view all the answers

What aspect of DNA does the purity assessment focus on during extraction?

<p>Presence of contaminants (A)</p> Signup and view all the answers

Flashcards

Molecular Biology

A branch of biology focused on studying life at the molecular level, particularly the workings of genetic material.

Molecular Diagnostics

A type of diagnostic testing that analyzes genetic material or specific proteins related to diseases, allowing for precise and personalized treatment.

Companion Diagnostics

Molecular tests used to identify if a specific therapy (called the 'companion') is likely to be successful for a particular patient.

Biomarkers

Molecules or substances that can be used as indicators of disease or other health conditions.

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Personalized Medicine

The use of molecular diagnostics to understand an individual's genetic makeup and tailor medical care based on their unique characteristics.

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Molecular Pathogen Identification

The process of identifying pathogens (disease-causing agents) by analyzing their genetic material.

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Molecular Diagnostics in Infectious Diseases

An area of molecular diagnostics focusing on the detection and analysis of infectious agents and their genetic variations.

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Molecular Diagnostics in Blood Banks

The use of molecular diagnostics to screen blood donations for infectious diseases, ensuring the safety of blood products for recipients.

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Genomic DNA Extraction from Blood

The process of isolating and purifying DNA from a blood sample.

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Percent Solution

A solution where the concentration of the solute is expressed as a percentage of the total solution weight.

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X Solution

A solution where the concentration of the solute is expressed as a specific number of parts per million.

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Lysis Buffer

A chemical that is used to break down cell membranes and release DNA.

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Electrophoresis

A physical process that separates molecules based on their size and charge.

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Nanodrop Measurement

A technique that measures the ratio of absorbance at 260 nm and 280 nm to assess the purity of DNA.

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DNA Concentration

The concentration of DNA in a solution, typically measured in ng/µl or µg/ml.

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DNA Storage

The process of storing DNA samples at low temperatures to prevent degradation.

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Protein Breakdown

A process that breaks down proteins into smaller peptides by using an enzyme called protease.

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RNase

A type of enzyme that specifically breaks down RNA molecules into smaller fragments.

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Salting Out

A technique used to separate cellular debris (proteins, lipids, and RNA) from DNA by clumping them together using a concentrated salt solution.

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Centrifugation

A process that separates different components of a mixture based on their densities, using a high-speed spinning motion.

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DNA Purification

A technique used to remove impurities (detergents, proteins, salts, and reagents) from DNA samples.

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Ethanol Precipitation

A common method for DNA precipitation that utilizes ice-cold ethanol or isopropanol, causing the DNA to clump together due to its insolubility in alcohol.

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Phenol-Chloroform Extraction

A method for DNA extraction where proteins are denatured by phenol, and the resulting aqueous phase containing DNA is then mixed with chloroform to remove any remaining phenol residues.

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Minicolumn Purification

A technique for DNA purification where DNA binds to a solid phase (like silica) based on pH and salt concentration, allowing for purification of DNA from the solution.

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Lysis

The first step in DNA extraction, where cells are broken down to access the DNA in the nucleus.

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Chaotropic Salts

Chemicals that disrupt the structure of water molecules, weakening interactions between DNA and water, making it easier for DNA to bind to the silica membrane.

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Purification

The process of separating purified DNA from unwanted cellular components and PCR inhibitors.

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Spin Column

A small, porous column containing a silica membrane that binds DNA.

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Washing (DNA Extraction)

The process of removing residual impurities and proteins from the silica membrane after DNA is bound.

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Elution

The final step in DNA extraction, where purified DNA is released from the silica membrane.

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Elution Buffer

A buffer used to elute DNA from the silica membrane. It is slightly basic to ensure DNA stability and solubility.

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What is the purpose of the cell lysis solution?

The solution used to break open cells and release their contents, including DNA.

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How to remove protein and heme contaminants from DNA?

To remove contaminants like proteins and heme, techniques like proteinase K digestion and phenol-chloroform extraction are used.

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How to detect heme contamination in DNA?

Heme, a component of hemoglobin, can be detected by its characteristic absorbance at 415 nm using a spectrophotometer.

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How to prove DNA is present in a sample?

You can confirm the presence of DNA by running an electrophoresis gel, where DNA bands will be visible under UV light.

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Why is DNA extraction important in forensics?

DNA extraction is crucial for forensic scientists because it allows them to identify individuals from biological evidence, like blood or hair.

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Cell Lysis

A process used to break down cell membranes and release DNA, often using specific chemicals and heat.

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Microcentrifuge

A specific type of centrifuge used in laboratories with high speed and force to separate mixtures based on density.

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A260/A280 Ratio

A measure of the purity of DNA, calculated by dividing the absorbance at 260nm (for DNA) by the absorbance at 280nm (for proteins). A ratio of 1.8 indicates pure DNA.

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DNA Dilution

The process of adding a known volume of liquid to a sample to reduce the concentration of the solute, used for preparing DNA for analysis or experiments.

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GeneJET Genomic DNA Purification Column

A type of column used in DNA purification to separate DNA from other cellular components, resulting in a more concentrated and purified DNA sample.

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Study Notes

Molecular Diagnostic Laboratory

  • Molecular biology is the study of biology at the molecular level, focusing on genetic material.
  • Molecular diagnostics is a dynamic field revolutionizing healthcare by detecting and measuring genetic material or proteins associated with specific diseases.
  • This allows for personalized medicine approaches, tailoring care to individual needs.
  • Molecular diagnostics discover biomarkers, leading to treatments designed around these markers.
  • This aids in accurate disease diagnosis, improving the delivery of therapies to the correct patients.
  • Molecular diagnostics are used in hospitals, reference labs, and blood banks.
  • They screen donated blood for infectious diseases and diagnose pathogens.
  • Increasing demand exists for point-of-care molecular diagnostic technologies.

Introduction

  • Molecular diagnostics are crucial in various fields including health, medicine, and forensics.
  • PCR-based technology, Fluorescence in situ hybridization (FISH), nanotechnology, biochips, peptide nucleic acid (PNA), and proteomic technology are used in diagnostics.
  • Electrochemical detection of DNA also is a molecular approach.

Safety Rules

  • Avoid eating, drinking, and smoking in the lab.
  • Wear protective gear (gloves, goggles, lab coat) when handling hazardous chemicals.
  • Always use fresh tips and pipettes for each solution and sample.
  • Maintain a clean work area.
  • Properly label all reagents and samples.
  • Store chemicals and reagents appropriately (freezer or fridge).
  • Do not collect samples if ill.
  • Properly dispose of waste.
  • Inform instructor on accidental chemical spills or concerns.
  • Wash hands thoroughly after lab work.

Preparation of Solutions

  • Molar solutions contain a specific number of grams of a solute per liter of solution.
  • Percentage solutions involve a specific weight of solute per 100ml of solution (w/v).
  • X Solutions are concentrated solutions that need to be diluted for testing.

Genomic DNA Extraction

  • Four main steps for extracting DNA from cells include cell lysis, lipids and proteins degradation, DNA purification, and ethanol precipitation.
  • Cell lysis: breaking down cell membranes to expose DNA.
  • Detergents and surfactants break down cell membranes and nucleus, while protease breaks down proteins.
  • Other processes, such as the removal of RNA using RNase are optional.
  • Centrifugation separates cellular debris from DNA.
  • Ethanol precipitation helps to form a DNA pellet, improving efficiency.
  • Common chemicals: Sodium chloride, tris-HCl, EDTA, detergents, proteins, salts, reagents for cell lysis, ethanol, and isopropanol.

Experimental Protocols (Example)

  • Samples such as blood are mixed with lysis solutions (example).
  • Samples are incubated at 56°C.
  • Ethanol is added to the solution, and the mixture is transferred to a column.
  • Several wash steps are performed.
  • DNA is eluted (released) using a buffer solution.

DNA concentration

  • DNA concentration is estimated using absorbance at 260nm, adjusting for turbidity.
  • A260/A280 ratio is approximately 1.8 for dsDNA. Ratios below 1.7 suggest protein contamination.
  • Turbidity, measured at 320nm, from proteins and organic compounds may affect results.

DNA Storage

  • EDTA is a heavy metal chelator, preventing DNA damage.
  • Storage temperatures are -70°C or 5°C (for short-term).
  • DNA is best stored with high salt (>1M), EDTA (>10mM) and low pH (8.5).
  • Ethidium bromide in CsCl is used for long-term storage, but in the dark.

Applications

  • Scientific: e.g., gene cloning, DNA analysis in cells and organisms.
  • Medicine: diagnosis of diseases, determination of virulence of microorganisms.
  • Forensics: identification of individuals in cases such as rape, petty theft, accidents, war victims, and paternity determination.

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