Molecular Diagnostics: Glossary

BACK

Glossary of Terms

Acrylamide gel	See Page
Amplicons	The double stranded DNA fragments produced by PCR amplification of a segment of DNA using specfific PCR primers.
Antisense	A nucleic acid molecule (RNA or DNA) which is complementary to an mRNA transcript, thus able to bind the transcript and prevent if from being translated into a protein.
ASO Allele Specific Oligo Hybridization	Hybridization using two different oligonucleotides, usually one which is perfectly matched to the wild-type sequence and a second which is perfectly matched to the mutant sequence. The probes must be designed to be specific to their homologue see acrylamide
Differential PCR	A specific type of mutiplex PCR reaction where the relative amounts of amplicons generated from each of the targeted sequences are compared, and a relative quantitation of the amount of starting target DNA is made.
Ethidium Bromide	The most common fluorescent dye used to stain DNA gels. Also binds to single stranded nucleic acids (RNA and single stranded DNA). After staining, with ethidium, DNA will fluoresce when illuminated with a UV light. Many of the gels documented on this web site are Ethidium Bromide stained. Ethidium Bromide is a mutagen and must be used with appropriate care.
Frameshift mutation	The insertion or deletion of nucleotides in the coding region of a gene causes the reading fram to shift. Shifting of the reading fram results in a change in the translation of the mRNA transcript. Therefore, a one or two base change results in a frameshift, while a three base change does not shift the reading frame, but can change the amino acid added by that codon (see missense mutation)
Heterozygote	A person who has two different alleles at a given gene locus.
Homozygote	A person who has two identical alleles at a given gene locus. A homozygote can be either a wild-type homozygote or a mutant homozygote.
Microsatellite	Areas of repetitive DNA within the genome where the repeating unit is very small, usually 1-6 nucleotides. These are generally polymorphic within a population and can be used for bone marrow transplant engraftment, forensics, identity testing, paternity testing, etc. Synonymous with STR
Missense mutation	Any mutation that alters a codon so that it codes for a different amino acid.
Multiplex PCR	A PCR reaction where more than one primer set is included in the reaction pool allowing 2 or more different DNA targets to be amplified by PCR in a single reaction tube.
Nonsense mutation	Any mutation that alters a codon so that it codes for a stop codon (translation termination) resulting in a truncated protein.
Oligonucleotides	Short segments of DNA ("oligo" is the frequently used and abbreviated term)
PAGE PolyAcrylamide Gel Electrophoresis	One of the two major types of gels used for the electrophoretic separation of DNA molecules. PAGE, in contrast to agarose gel electrophoresis, is generally used when the DNA fragments to be separated are small. When used in a sequencing gel format, it is capable of single nucleotide resolution.
Palindrome	A region of DNA which reads the same in the forward and backward directions. An example is 5'-CATG-3' which when both strands are considered is: 5'-CATG-3' 3'-GTAC-5' So if the top strand is read, it reads 'CATG' in the forward 5' to 3' direction. If the bottom strand is read in the 5' to 3' direction, it also reads 'CATG' and so is hence a palindrome.
PCR Polymerase Chain Reaction	A technique, discovered by Dr. Kary Mullis in 1985, which is revolutionizing Molecular Pathology. It permits the amplification of one specific region of DNA from a complex mixture of DNA (e.g. A single gene from the entire mixture of genomic DNA). It is a chain reaction because the DNA target is exponentially amplified. A single DNA template molecule can be detected. Two primers are chosen which hybridize to the gene of interest and define the ends of the PCR product (see techniques)
Polymorphism	Any genetic difference (e.g. A single nucleotide difference, a difference in microsatellite length, etc.) which is different from person to person. Often refers to genetic changes which do not cause functional change.
Primer(s)	An oligonucleotide or pair of oligonucleotides used to direct an activity to a region of nucleic acid. With PCR, a pair of primers defines the area of the genome to be amplified. With RT-PCR, the primer anneals to messenger RNA and direct the reverse transcriptase produces cDNA from that site back in the 5' direction.
Purine	A basic compound, composed of two fused heterocyclic rings, occuring in nucleic acids. The purines occuring in RNA and DNA are adenine(A) and guanine(G).
Pyrimidine	A basic compound, composed of one heterocyclic ring, occuring in nucleic acids. In DNA, the pyrimidines are cytosine(C) and thymine(T). In RNA, uracil(U) is substituted for thymine.
Recognition site	The site which restriction endonucleases recognize within a piece of DNA. Most recognize 4, 6, or 8 base pair palindromic sequences. The size of the recognition site generally correlates with the frequency of cutting. They are sometimes referred to as "frequent cutters" or "rare cutters". The actual cut site is generally within the recognition sequence but may be adjacent to or only nearby. Sometimes two different enzymes will recognize the same recognition site, they are known a isoschizomers.
Restriction Enzyme Restriction Endonuclease	An enzyme which cuts DNA at a specific site called the recognition site. They are endonucleases in that they cut within the DNA rather than cutting at the ends. There are three types of restriction endonucleases, the most useful are the type II endonucleases. Most recognition sites are palidromic.
RFLP Restriction Fragment Length Polymorphism	A technique which detects polymorphisms between two people, such as single base changes or different sized minisatellites. The common feature is that when digested with a restriction endonuclease, DNA products are generated which are different lengths.
STR Short Tandem Repeat	Areas of repetitive DNA within the genome where the repeating unit is very small, usually 1-6 nucleotides. These are generally polymorphic within a population and can be used for bone marrow transplant engraftment, forensics, identity testing, paternity testing, etc. Synonymous with microsatellite
Transition	One purine or one pyrimidine base is substituted in a DNA sequence by the other purine or pyrimidine (e.g. A is replaced by G or C is replaced by T, and vice-versa).
Transversion	A purine base replaces a pyrimidine or a pyrimidine replaces a purine (e.g. A is replaced by T or T by A).

< Go Back >

Homepage \| Site Info \| Contact Us \| Links \| Search
Pathology Homepage Copyright © 1999 - 2005 The Johns Hopkins University All rights reserved. No part of this website may be reproduced in any form or by any means or incorporated into any information retrievel system, electronic or mechanical, without the written permission of JHU.