Advanced Clinical Molecular Diagnostics - Review of Molecular Laboratory Techniques

This set of vocabulary flashcards covers the fundamental concepts of molecular biology, nucleic acid characteristics, laboratory techniques for isolation and amplification, and sequencing methods based on the MLSC 4053 Lecture 1 transcript.

DNA (Deoxyribonucleic acid)

A double helix molecule consisting of two sugar-phosphate backbones with four attached bases: cytosine (C), guanine (G), adenine (A), and thymine (T).

Purine

A category of nitrogenous bases that includes Adenine and Guanine.

Pyrimidine

A category of nitrogenous bases that includes Thymine and Cytosine in DNA, and Uracil in RNA.

Phosphodiester bonds

Bonds that link repeating nucleotide units by joining the $5'$ carbon of one sugar to the $3'$ carbon of the next.

Nucleosomes

Structures formed when double-strand DNA is wound around an octamer core of histone proteins.

Solenoid

A helical structure formed by the further compaction of histones.

Chromatin

Nuclear DNA in conjunction with its associated structural proteins.

Centromere

The primary construction of a chromosome.

Telomeres

The specialized structures located at the ends of a chromosome.

Translation

The process in the ribosome that builds polypeptide chains using $20$ different amino acids in a sequence dictated by three-base codons.

Electrophoresis

A separation technique where negatively charged DNA travels towards the positive pole (anode) in a gel matrix such as agarose or polyacrylamide.

Southern blot

A technique involving restriction enzyme cutting, gel electrophoresis, transfer to a membrane, and probe hybridization to detect specific DNA fragments.

Restriction Fragment Length Polymorphism (RFLP)

A variation in the length of restriction fragments produced by a given restriction enzyme in a sample of DNA.

Polymerase Chain Reaction (PCR)

An in vitro method for exponentially amplifying DNA using cycles of denaturation ($94^\text{o}C$), annealing ($55^\text{o}C$), and extension ($72^\text{o}C$).

Transcription-mediated amplification (TMA)

An amplification method using RNA polymerase and DNA reverse transcriptase to produce RNA amplicons from a target nucleic acid.

Nucleic acid sequence-based amplification (NASBA)

An amplification process similar to TMA, but specifically targeting only RNA for amplification.

Strand displacement amplification (SDA)

A technique using two types of primers, DNA polymerase, and a restriction endonuclease to produce single-strand amplicons asynchronously.

Branched-chain signal amplification (bDNA)

A molecular probe technique that uses branched DNA as a means to amplify the hybridization signal rather than the target.

Serial invasive signal amplification

A signal-enhancing technique that combines two invasive reactions in series, resulting in more than $7$ orders of magnitude of signal amplification.

Ligase chain reaction (LCR)

A probe amplification process that amplifies the probes themselves rather than the target DNA sequence.

Real-time PCR

A PCR method that uses fluorescent methods, such as FRET, TaqMan, SYBR Green, or Molecular Beacons, to monitor amplification as it occurs.

Sanger sequencing

Also known as dideoxy-termination sequencing; a method where DNA polymerase extends a primer until a dideoxynucleotide ($ddNTP$) is incorporated.

Next-generation sequencing (NGS)

A technology that provides highly parallel sequencing with a separate sequence result for every sequence of interest.

Pyrosequencing

A sequencing method based on the generation of a light signal through the release of pyrophosphate ($PPi$) upon nucleotide addition.