DNA Analysis
Steven H. Y. Wong, Iraving Sunshine in Handbook of Analytical Therapeutic Drug Monitoring and Toxicology, 2017
In humans, the mtDNA genome is 16,569 bp in a closed circular loop. MtDNA codes for 13 proteins, 2 ribosomal RNAs and 22 transfer RNAs. In addition, the genome contains little repetitive or non-coding DNA. The only substantial section of non-coding DNA occurs in one region, of approximately 1000 bp, known as the “control region” or “displacement loop” (or more simply the “D-loop”). The D-loop does, however, contain the origin of replication for one of the two DNA strands, as well as regulatory sites for gene transcription. It is in this generally non-coding region that the greatest variation among people is found and forensic identity testing has focused.26,29,67,72 The polymorphisms consist of scattered single base differences concentrated within two hypervariable regions, each roughly 300 bp in length.
Molecular Biology and Gene Therapy
R James A England, Eamon Shamil, Rajeev Mathew, Manohar Bance, Pavol Surda, Jemy Jose, Omar Hilmi, Adam J Donne in Scott-Brown's Essential Otorhinolaryngology, 2022
DNA mutation may occur as a result of base substitutions, as well as nucleotide insertions and deletions. Insertions and deletions of nucleotides are very rare in coding DNA. Base substitution is a more common form of mutation in coding DNA, which may have a range of consequences on the function of the gene: a loss of function; a gain in function, often due to stabilisation of the active protein or no net functional effect. An example of a silent substitution yielding no functional effect is seen when an amino acid may be encoded by different codons (e.g. GUA, GAC, GUG and GUU all encode valine), so a substitution of the third base results in no change to the amino acid. At the other extreme is the nonsense mutation, whereby a base substitution results in an early stop codon, which leads to truncation of the polypeptide and a dramatic reduction in function.
The Scientific Basis of Medicine
John S. Axford, Chris A. O'Callaghan in Medicine for Finals and Beyond, 2023
Every protein is encoded by a DNA sequence within a gene at a defined locus on a chromosome. Codons of three sequential nucleotides encode a single amino acid or a stop signal. Regulatory regions containing target sites for various DNA-binding proteins flank the coding sequence and control gene expression. These regions form a vital part of the gene and their loss can have profound effects on protein expression. Mutations in control regions can cause disease, as evidenced by some of the haemoglobin gene mutations that cause thalassaemia. An upstream promoter provides binding sites for RNA polymerase and transcription factors. Functionally related enhancer sequences are located further afield and recruit various DNA-binding proteins that can regulate the efficiency of gene transcription. The transcriptional unit contains exons of coding DNA separated by introns, which play no part in the finished protein. A large portion of our genome is composed of repetitive DNA of unclear function.
Playing the genome card
Published in Journal of Neurogenetics, 2020
I suggest that these terms are fundamentally misleading as applied to genome sequencing. The implied analogy is to codes used in spycraft. Once you decode or decipher a coded message, you understand its meaning. The implication is that by sequencing a genome, we understand its meaning. But biologists knew in the 1990s and know now that this is not the case. To understand the meaning of a gene (i.e. a protein-coding DNA sequence), we would need to understand the function(s) of the protein it codes for, if not also how it carries out that function. To understand the meaning of a stretch of DNA that does not code for a protein, we would need to understand its function, such as what gene(s) it alters the expression of, via which nucleic acid and protein partners, and how. In most cases, simply having a DNA sequence does not convey such meaning. It is a sequence of basepairs, which, for protein-coding sequences, is also a sequence of amino acids. This is a starting point for exploring its meaning, which is what the protein does and how. Thus, DNA sequencing is more analogous to writing down a series of letters in a foreign language, without yet knowing what the sentence means, than it is to decoding or deciphering an encoded message.
Heterozygous missense mutation of the RELN gene is one of the causes of epilepsy
Published in Neurological Research, 2022
Xi-Qin Fang, Ran-Ran Zhang, Xue-Wu Liu
The proband’s diagnosis was based on the clinical manifestations and examinations (including magnetic resonance imaging and electroencephalography). Mutations were determined using target sequence capture combined with high-throughput sequencing technology. This method can detect more than 95% of the exon area, and the coverage rate of the target area can reach 99.8%. After obtaining peripheral blood samples from the three family members (proband, his mother, his grandmother), the samples were sent to the Jinzhun Medical Laboratory (Beijing, China). First, the DNA was interrupted to prepare a library, and then the DNA in the coding region of the target gene and the adjacent cutting region was captured and enriched by the chip. A high-throughput platform was used for mutation detection.
Site specific hypermethylation of CpGs in Connexin genes 30, 26 and 43 in different grades of glioma and attenuated levels of their mRNAs
Published in International Journal of Neuroscience, 2019
Jayalakshmi J., Arambakkam Janardhanam Vanisree, Shantha Ravisankar, Rama K.
MethPrimer and Primer Blast were used to design primers for BSP and MeDIP-qPCR (Table 1). Promoter region (Figure 1) and transcription factor binding sites were predicted with PROMO and TESS software (Figure 2). As there is no CpG island in Cx43 promoter region, CpGs in intron were chosen for this study. The first exon that contains the 5′-untranslated region (5′-UTR) with the transcription start site and a second exon that contains a small amount of the 5′-UTR, complete coding region and the 3′-UTR were analysed. These two exons are separated by intron [14–17]. There are four CpG islands in the intron region. The sequence (GenBank Accession No. NG_008308 with respect to the major transcription start site +1) from +3461 to +3623 in the intron was used to design the primer by Methprimer software.
Related Knowledge Centers
- DNA
- Eukaryote
- Exome
- Exon
- Prokaryote
- Protein
- Rna
- Untranslated Region
- Gene
- NON-Coding DNA