Electrophoresis and Nucleic Acid Migration

These flashcards cover the key concepts and details from the lecture on electrophoresis and nucleic acid migration to aid in exam preparation.

Electrophoresis is defined as the movement of molecules (DNA or RNA) by __________.

applying a specific voltage (electric current).

Under an electric current, DNA and RNA migrate toward the __________ pole.

positive pole (anode).

DNA and RNA migrate at speeds inversely related to the __________ of the polymer.

size or length.

Gel electrophoresis uses __________ gels to separate nucleic acids.

agarose and polyacrylamide.

The two types of orientation of gel electrophoresis are vertical and __________ gels.

horizontal.

The purpose of gel in gel electrophoresis is to provide __________ to the movement of the molecules.

resistance.

Agarose gel is mostly used to separate __________ DNA molecules.

large.

Higher agarose concentration in a gel impedes __________ of larger molecules.

migration.

Pulsed-Field Gel Electrophoresis (PFGE) is a modification of __________ gel electrophoresis.

agarose.

The primary purpose of buffers in electrophoresis is to maintain __________ and protect the samples.

pH.

The buffer Tris borate EDTA (TBE) has a greater buffering capacity than __________.

Tris acetate EDTA (TAE).

Capillary electrophoresis uses __________ glass capillaries for separation.

fused silica.

Capillary electrophoresis separates molecules based on size and __________.

charge (charge/mass ratio).

Electrokinetic injection is commonly used for __________ analysis.

nucleic acid.

Tracking dyes in gel electrophoresis help in monitoring the __________ of the run.

progress.

The most commonly used tracking dye for small fragments is __________.

Bromophenol blue.

An example of a fluorescent dye used for DNA detection is __________ bromide.

Ethidium.

Polyacrylamide gels are best for very __________ DNA fragments.

small.

The addition of denaturing agents such as formamide and urea helps to maintain __________ structure in nucleic acids.

single-stranded.

To avoid pH drift during electrophoresis, it is important to use a __________ pump.

peristaltic.

The movement of tracking dye is monitored; when the dye reaches the desired distance, electrophoresis is __________.

terminated.

Ficoll, sucrose, and glycerol are examples of __________ agents used to increase sample density.

density.

The main advantage of polyacrylamide over agarose is its __________ resolution capability.

higher.

The stability of the buffer pH is crucial to prevent damage to __________ molecules.

sample.

Agarose concentration should be higher for __________ DNA fragments.

smaller.

The DNA molecule will move toward the anode due to its __________ charge.

negative.

The components of polyacrylamide include acrylamide and __________ bisacrylamide.

methylene.

Detection systems like fluorescent dyes visualize bands formed during the __________ process.

migration.

Sodium phosphate and __________ are common buffers used for RNA electrophoresis.

MOPS buffer.

In PFGE, the migration direction of DNA is altered to enhance __________ of large fragments.

separation.

Gel loading tips are used to avoid __________ in the gel.

scratches.

The purpose of a buffer system in electrophoresis is to carry __________ and protect samples.

current.

Tracker dye serves as a __________ to monitor the progress of electrophoresis.

guide.

The migration of DNA in gel occurs because of the application of an __________ current.

electric.

Electrophoresis equipment is categorized into __________ and horizontal setups.

vertical.

The process of electrophoresis separates biological molecules based on their __________ and charge.

size.

Bromophenol blue is used for monitoring migration, especially for __________ fragments.

small.

Methods such as __________ are used to inject samples into the capillary.

electrokinetic injection.

The pH control of a gel protects sample molecules from __________ during electrophoresis.

damage.

E.g. Agarose and Polyacrylamide are types of __________ used as matrices in electrophoresis.

polymers.

Sodium Acetate is part of the composition in __________ buffers.

TAE.

The size of the DNA fragments is determined by the __________ of the agarose concentration.

appropriateness.

Polyacrylamide gels can be very thin, between __________ and 4 mm.

0.05.

The __________ of the gel influences the migration speed of the nucleic acids.

thickness.

Monitoring the progress of the electrophoresis run is essential to prevent __________ migration.

over.

The characteristics of a good gel matrix include being __________ by electrophoresis.

unaffected.

The technique of silver staining is mainly for detecting __________ in gel analyses.

proteins.

Voltage application in PFGE occurs in __________ orientation to enhance migration.

alternating.

For very large pieces of DNA, __________ is used for separation.

Pulsed-Field Gel Electrophoresis (PFGE).

Formamide and Urea are denaturing agents that prevent __________ in nucleic acids.

folding.

Capillary electrophoresis is often preferred due to its incorporation with __________.

computer technology.

Gel loading involves the careful placement of samples into the __________ within the gel.

wells.

The main disadvantage of powdered forms of polyacrylamide is that they are __________.

neurotoxic.

Detection methods like SYBR Green are ____ times more sensitive than Ethidium bromide.

25 to 100.

Electrophoresis conditions should maintain constant thickness and __________ of the gel.

volume.

Polyacrylamide gels have a higher resolution for separating fragments based on a difference of __________.

1 base pair.

During electrophoresis, larger DNA fragments migrate __________ than smaller fragments.

slower.

The migration of nucleic acids is particularly influenced by their __________ and the matrix used.

size.

Ethidium bromide is no longer preferred for routine testing due to its __________ properties.

mutagenic.

Additives to buffers can influence sample molecules' __________.

migration.

Capillary tubes separate particles by their size and __________ in electric current.

charge.

Intercalating agents like Ethidium bromide bind to DNA and are visualized under __________ light.

UV.

The mobility of DNA during electrophoresis is affected by the __________ of the agarose gel.

concentration.

To prevent fragmentation of RNA, it must be completely __________ when preparing for electrophoresis.

denatured.

For analysis of proteins, a technique widely applied is __________ staining.

silver.

The most transparent material used in capillary electrophoresis is __________ silica.

fused.

To check the appropriate separation capacity during electrophoresis, ensure the DNA fragments are within the __________ range.

size.

In polymerization processes, the presence of __________ can inhibit the formation of gels.

excess oxygen.

During electrophoresis, each sample well should have an appropriate amount of __________ for accurate loading.

volume.

When monitoring migration, the tracking dye serves as a __________ for guidance.

reference.

In gel electrophoresis, fragments can be monitored visually by the __________ they produce.

bands.

The concentration of agarose affects the __________ of the gel and thus the separation of DNA.

thickness.

The preferred dye for real-time PCR methods is __________ Green.

SYBR.

In gel recirculation, pH levels must be maintained to avoid __________ drift.

pH.

Agarose gels are used primarily for the separation of __________ nucleic acids.

large.

Before loading into the wells, samples must be prepared with the correct __________.

density.

This type of gel is free to modify: __________ Gel.

Polyacrylamide.

To prevent distortions during gel casting, it is important to avoid __________ formation.

bubbles.

During electrophoresis, larger molecules tend to migrate __________ compared to smaller ones.

slower.

The technique called CHEF is part of the __________ category for separating large DNA fragments.

PFGE.

A common buffer additive that helps maintain single-stranded structure in nucleic acids is __________.

formamide.

Tracking dyes allow researchers to monitor __________ during the process of electrophoresis.

migration.

E.g., typical acrylamide concentration for protein analysis ranges from __________%.

5-20.

When using agarose gels, be cautious of __________ that can compromise the gel structure.

temperature.

Buffers must serve as carriers for __________ charges and must remain stable in pH.

electrical.

The process of denaturation aids in keeping RNA __________ during electrophoresis.

single-stranded.

The two commonly used gels for electrophoresis are agarose and __________.

polyacrylamide.

The need for __________ in electrophoresis is to prevent pH imbalances from affecting the samples.

buffers.

During migration in gel, DNA is primarily monitored for its __________ size.

fragment.

The layers of the gel should provide sufficient __________ for accurate migration of molecules.

support.

Harmful substances in laboratory procedures, such as __________, can pose risks during electrophoresis.

neurotoxins.

The two common shapes of gels are __________ and vertical plates.

horizontal.

When preparing polyacrylamide gels, it’s essential to consider the percentage of __________ used.

cross-linker.

To optimize separation in electrophoresis, the amount of buffer and __________ must be controlled.

current.

One method to fix proteins before staining is using __________ and acetic acid.

methanol.

Monitoring the gel’s casting temperature is important to avoid __________ during polymerization.

distortions.

To increase separation efficiency in PFGE, alternating __________ of the electric field are applied.

orientations.

Polyacrylamide gels are often __________ in nucleic acid sequencing due to their resolution.

preferred.

Upon loss of stability, the buffer in electrophoresis may become __________ and must be replenished.

depleted.

The migration direction in PFGE involves altering pathways, enhancing the separation of __________.

large fragments.