Nucleic Acid Extraction – Key Vocabulary

Vocabulary flashcards covering major terms, reagents, and procedures involved in DNA and RNA extraction from various biological samples as described in the lecture notes.

Nucleic Acid Extraction

Process of releasing and purifying DNA or RNA from cells for downstream analyses.

Cell Lysis

Disruption of cell and nuclear membranes (and cell wall, if present) to free nucleic acids.

Sample Preparation

Collection and pre-treatment steps ensuring specimens yield intact nucleic acids for testing.

Gram-Negative Bacteria

Early model organisms for recombinant DNA work; thin walls enable lysis with high pH and detergents.

Cell Wall Degradation

Removal of bacterial or fungal walls by enzymes, mechanical force, or detergent/strong base.

Enzymatic Lysis

Use of cell-wall–digesting enzymes to release nucleic acids.

Mechanical Lysis

Physical disruption (e.g., grinding, homogenizing) to break cells or tissues.

Detergent/Strong Base Lysis

Chemical method that dissolves membranes and denatures proteins to free DNA.

Viral DNA Integration

Viral genomes residing integrated in host DNA or within free viral particles.

White Blood Cells (WBCs)

Primary source of nucleic acid in blood or bone marrow samples.

Differential Density-Gradient Centrifugation

Separation of mononuclear WBCs using Ficoll layers and centrifugation.

Differential Lysis

Hypotonic lysis of RBCs while pelleting intact WBCs for nucleic acid extraction.

Ficoll

Branched sucrose polymer forming a gradient that separates blood components by density.

Mononuclear Layer

WBC fraction collected from the Ficoll interface after centrifugation.

Liquid Biopsy

Molecular testing of circulating cell-free nucleic acids for diagnosis or prognosis without surgery.

Plasma Cell-Free Nucleic Acids

DNA/RNA released from tumors, transplants, or normal cells found in plasma.

Tissue Dissociation

Grinding, homogenizing, or mincing fresh/frozen tissue to release nucleic acids.

Deparaffinization

Removal of paraffin from fixed tissue by xylene followed by graded ethanol rehydration.

Buffered Formalin

Fixative causing minimal DNA damage compared with mercury-based reagents.

Salting Out

Inorganic DNA extraction using low pH and high salt to precipitate proteins while DNA stays soluble.

Phenol-Chloroform Extraction

Organic isolation method employing phenol/chloroform to remove proteins and lipids from DNA.

Cetyltrimethylammonium Bromide (CTAB)

Cationic detergent that separates DNA from polysaccharide contaminants in difficult samples.

RNase Treatment

Addition of ribonuclease to DNA preps to eliminate RNA contamination.

Solid-Phase Isolation

Binding of nucleic acids to silica or other matrices on spin columns for wash-and-elute purification.

Spin Column

Small silica-based cartridge inserted in microtubes to capture nucleic acids during centrifugation.

Chelex Extraction

Rapid DNA isolation using a cation-chelating resin mixed with sample and boiled.

Mitochondrial DNA Isolation

Sequential centrifugations and DNase treatments to purify mtDNA from crude mitochondria.

RNase

Heat-stable enzymes that degrade RNA and must be inactivated or excluded during RNA isolation.

RNase-Free (RNF) Area

Designated lab space with gloves and baked glassware to prevent RNA degradation.

Ribosomal RNA (rRNA)

Most abundant cellular RNA; appears as large and small subunits on gels.

Messenger RNA (mRNA)

2.5–5 % of total RNA; carries coding information from DNA to ribosomes.

Transfer RNA (tRNA)

Adaptor RNA molecules present in total RNA preparations along with small nuclear RNAs.

Reticulocyte Lysis

Selective lysis or separation of RNA-rich reticulocytes in blood for RNA extraction.

Guanidine Isothiocyanate

Strong chaotropic agent that denatures RNases during RNA isolation.

Acid Phenol:Chloroform:Isoamyl Alcohol (25:24:1)

Organic mix efficiently extracting RNA while isoamyl alcohol prevents foaming.

Isoamyl Alcohol

Component in organic extractions that minimizes foam formation during phase separation.

Acidic Organic Phase

Lower pH environment ensuring RNA partitions into the aqueous layer in phenol extractions.

Glycogen Carrier

Inert molecule added to aid precipitation and visibility of small RNA pellets.

Chaotropic Buffer

High-salt, denaturing solution enabling nucleic acid binding to silica matrices.

PolyA mRNA

mRNA molecules possessing a 3′ polyadenylated tail unique among RNA species.

PolyT/PolyU Oligomers

Single-stranded T or U sequences immobilized on beads/columns that hybridize to polyA tails.

Fixed Tissue RNA Extraction

Protocols reversing formaldehyde modification and releasing RNA from paraffin-embedded tissue.

Exosome

Small vesicle released into blood carrying nucleic acids reflective of the tissue of origin.

Liquid Nitrogen Tissue Grinding

Cryogenic pulverization of frozen tissue to facilitate nucleic acid isolation.