Sequence variation

DNA microarrays, or DNA chips consist of thousands of individual DNA sequences arrayed at a high density on a single matrix, usually glass slides or quartz wafers, but sometimes on nylon substrates. Probes with known identity are used to determine complementary binding, thus allowing the analysis of gene expression, DNA sequence variation or protein levels in a highly parallel format. 

Tilib SV, Mirzabekov AD (2001) Advances in the analysis of DNA sequence variations using oligonucleotide microchip technology. Curr Opin Biotechnol 12 53-58... 

Shi J, Hui L, Xu Y, et al Sequence variations in the mu-opioid receptor gene (OPRM1) associated with human addiction to heroin. Hum Mutat 19 459 60, 2002 Shinderman M, Maxwell S, Brawand-Arney M, etal Cytochrome P4503A4 metabolic activity, methadone blood concentrations, and methadone doses. Drug Alcohol Dependence 69 205-211, 2003... 

Aulisa L, Dong H, Hartgerink ID (2009) Self-assembly of multidomain peptides sequence variation allows control over cross-linking and viscoelasticity. Biomacromolecules 10 2694-2698... 

A third class of sequence elements can either increase or decrease the rate of transcription initiation of eukaryotic genes. These elements are called either enhancers or repressors (or silencers), depending on which effect they have. They have been found in a variety of locations both upstream and downstream of the transcription start site and even within the transcribed portions of some genes. In contrast to proximal and upstream promoter elements, enhancers and silencers can exert their effects when located hundreds or even thousands of bases away from transcription units located on the same chromosome. Surprisingly, enhancers and silencers can function in an orientation-independent fashion. Literally hundreds of these elements have been described. In some cases, the sequence requirements for binding are rigidly constrained in others, considerable sequence variation is... 

T. Vallaeys, E. Topp, G. Muyzer, V. Macheret, G. Laguerre, A. Rigaud, and G. Soulas, Evaluation of denaturing gradient gel electrophoresis in the detection of I6S rDNA sequence variation in rhizobia and methanotrophs. FEMS Microbiol. Ecol. 24 279 (1997). 

A wide variety of techniques can now be employed to detect DNA sequence variation in above-ground and below-ground ecto- and endomycorrhizal fungal populations (17,18,19,24). 

Sequence variation could in principle result in differences in disease pathology, but no such link has been proven to date and the progression of the disease is generally independent of genotype. There is a strong association of particular subtypes with different modes of transmission. The high prevalence genotype lb infection in the developed world is attributed mostly to the use of contaminated blood in transfusions. Subtypes la and 3a currently... 

Gatlin, C.L., Eng, J.K., Cross, S.T., Detter, J.C., and Yates, J.R III, Automated Identification of amino acid sequence variations in proteins by HPLC/mi-crospray tandem mass spectrometry, Anal. Chem., 72, 757, 2000. 

The standard RNAs were used to test the ability of the bDNA assay to quantify accurately target RNAs regardless of size or slight sequence variation. Standard RNA preparations of 1.3,2.2, and 3.2 kb showed no detectable effect on quantitation. The quantitation of standard transcripts prepared from clones of HCV sub-type la and 3a differed by a factor of 1.6-fold with one probe design and were indistinguishable with another probe design. These two 475-mer transcripts differed at 30 positions. 

The accurate analysis of genetic variation in nematodes has major implications for parasite identification and for investigating population genetic structures (Lejambre, 1993 Grant, 1994). Conventional DNA methods have been valuable and their application has provided a wealth of molecular data (reviewed by McManus and Bowles, 1996), but little attention has been paid to their capacity to resolve sequence variation (reviewed by Gasser, 1997). For instance, PCR-RFLP analysis using (multiple) restriction endonucleases is useful, but sequence variation may go undetected as... 

Gasser, R, Nansen, P. and Guldberg, P. (1996a) Fingerprinting sequence variation in ribosomal DNA of parasites by DGGE. Molecular and Cellular Probes 10, 99-105. 

Gasser, R.B., Zhu, X.Q. and McManus, D.P. (1998c) Display of sequence variation in PCR-amplified mitochondrial DNA regions of Echinococcus by single-strand conformation polymorphism. Acta Tropica 71, 107-115. 

Stothard, J.R., Frame, IA. and Miles, MA. (1997) Use of polymerase chain reaction-based single strand conformational polymorphism and denaturing gradient gel electrophoresis methods for detection of sequence variation of ribosomal DNA of Trypanosoma cruzi. International Journal for Parasitology 27, 339-343. 

Zhu, X.Q. and Gasser, R.B. (1998) SSCP-based mutation scanning approaches to fingerprint sequence variation in ribosomal DNA of ascaridoid nematodes. Electrophoresis 19, 1366-1373. 

Hoffmeyer, S., Burk, O., von Richter, O., Arnold, H. P., Brockmoller, J., Johne, A., Cascorbi, I., Gerlo, T., Roots, I., Eichelbaum, M., Brinkmann, U., Functional polymorphism of the human multidrug resistance gene multiple sequence variations and correlation of one allele with P-glycoprotein expression and activity in vivo, Proc. Natl. Acad. Sci. USA 2000, 97, 3473-3478. 

Rapid sequencing and single nucleotide polymorphisms (SNPs) will play a major role in associating sequence variations with heritable clinical phenotypes of drug or xenobiotic response. SNPs occur approximately once every 300-3,000 base pairs if one compares the genomes of two unrelated individuals [13, 14]. Any two individuals thus differ by approximately 1-10 million base pairs, i.e., in < 1% of the approximately 3.2 billion base pairs of the haploid genome (23 chromosomes). 

The International SNP Map Working Group 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 2001 409 928-933. 

Clark AG, Weiss KM, Nickerson DA, Taylor SL, Buchanan A, Stengard J et al. Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am J Hum Genet 1998 63 595— 612. 

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