PCR products with heterozygous mutations containing two types of heteroduplexes / 浙江大学学报·医学版

<p><b>OBJECTIVE</b>To confirm that PCR products with heterozygous mutations contain not only wide-type and mutant homoduplexes, but also two types of heteroduplexes.</p><p><b>METHODS</b>An insertion-deletion mutation in the exon 1 of KRT9 gene (497delAinsGGCT), which caused Chinese epidermolytic palmoplantar keratoderma (EPPK) was investigated by polymerase chain reaction (PCR), polyacrylamide gel electrophoresis (PAGE) and denaturing high-performance liquid chromatography(DHPLC).</p><p><b>RESULTS</b>Two heteroduplexes and two homoduplexes in the PCR product from the heterozygous mutation of the exon 1 of KRT9 (497delAinsGGCT) were detected.</p><p><b>CONCLUSION</b>PCR products from KRT9 gene with heterozygous mutations contain two types of heteroduplexes. It is without the need to perform heating and cooling PCR products obtained from heterozygous mutations in advance before the mutation screening steps such as denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), conformation-sensitive gel electrophoresis (CSGE), DHPLC and heteroduplex analysis (HA), etc.</p>

Analysis of the factors affecting the accuracy of detection for single base alterations by oligonucleotide microarray

The oligonucleotide microarray, a high-throughput polymorphism detection technology, holds great promise for the characterization of complex genetic variance. To achieve greater sensitivity and specificity for it to be an effective platform technology we present results and discuss some of the factors influencing signal intensities and single-mismatch discrimination in array-based mutation/SNP detection. Probes with a series of concentrations were spotted onto the slide in order to find the optimal concentration with the identifiable satisfying signals and the stable ratios between matched and mismatched probes. It was found that under our experimental conditions, when the initial probe concentration is higher than the maximum immobilization capability of the slide (7.5 micrometer), the hybridization signal will be saturated and the ratio between matched and mismatched probes will be more stable than at a lower probe concentration. Considering the cost of probes and the systematic stability, a constant spotting concentration of 10 micrometer was selected. The stability of different types of mismatched oligo-DNA duplexes on the glass surface was also confirmed. The results show that the order of stability of mismatched oligo-DNA duplexes on a glass surface is in general agreement with previous reports conducted using liquid and polyacrylamide gel pads. This suggests that the influence of the mismatched base pair on the stability of the duplex in a solid hybridization system is similar to that in the solution hybridization environment.

Molecular characterization of echovirus 11 isolates from India.

BACKGROUND & OBJECTIVES: Echovirus 11 (ECV11) is one of the most frequent non-polio enteroviruses isolated from stool samples of children with acute flaccid paralysis in north India. The present work was undertaken to study the sequence variability in the 440 bp of 5'-non-translated region of ECV11 genome using heteroduplex mobility assay (HMA). METHODS: Twelve ECV11 isolates were studied for sequence variability in the 5'-non-translated region (5'NTR) using the HMA followed by nucleotide sequencing. HMA was used to determine sequence diversity between Indian ECV11 isolates and prototype Gregory strain. HMA results were confirmed by 5'NTR nucleotide sequencing of five Indian ECV11 isolates. RESULTS: HMA results showed high genomic diversity between the prototype Gregory strain and Indian ECV11 isolates. All isolates were grouped into five different types of heteroduplex mobility patterns with respect to Gregory strain. A 440 bp 5'NTR fragment of five ECV11 isolates representing different heteroduplex patterns, was sequenced. The sequence alignment showed that 5'NTR of Indian isolates was different from prototype Gregory strain and identical to the ECV11 isolates of Finland and Hungary. Phylogenetic analysis including ECV11 isolate sequences from different parts of the world showed that Indian ECV11 isolates represented a different subgroup. INTERPRETATION & CONCLUSION: The results of the present study suggested that the HMA could be successfully used as a preliminary screening method for sequence variability determination of enterovirus field isolates. The sequence data generated on ECV11 isolates from India will be useful for future studies of endemic genotypes of echovirus.

MutS recognition: multiple mismatches and sequence context effects.

Escherichia coli MutS is a versatile repair protein that specifically recognizes not only various types of mismatches but also single stranded loops of up to 4 nucleotides in length. Specific binding, followed by the next step of tracking the DNA helix that locates hemi-methylated sites, is regulated by the conformational state of the protein as a function of ATP binding/hydrolysis. Here, we study how various molecular determinants of a heteroduplex regulate mismatch recognition by MutS, the critical first step of mismatch repair. Using classical DNase I footprinting assays, we demonstrate that the hierarchy of MutS binding to various types of mismatches is identical whether the mismatches are present singly or in multiples. Moreover, this unique hierarchy is indifferent both to the differential level of DNA helical flexibility and to the unpaired status of the mismatched bases in a heteroduplex. Surprisingly, multiple mismatches exhibit reduced affinity of binding to MutS, compared to that of a similar single mismatch. Such a reduction in the affinity might be due to sequence context effects, which we established more directly by studying two identical single mismatches in an altered sequence background. A mismatch, upon simply being flipped at the same location, elicits changes in MutS specific contacts, thereby underscoring the importance of sequence context in modulating MutS binding to mismatches.

HIV-1 subtyping by heteroduplex mobility assay in patients with bleeding disorders

O vírus da imunodeficiência humana do tipo 1 estabelece uma infecçäo presistente que na maioria dos casos evolui para a Síndrome de Imunodeficiência humana do tipo 1 tem sido geneticamente classificado em maior ou em outros grupos. Ogrupo maior é subdivido em nove subtipos baseados em evidências seqüênciais. A infecçäo pelo vírus da imunodeficiência humana do tipo 1 foi transmitida aos hemofílicos principalmente pelos concentrados de coagulaçäo no final da década de 70 e meados da de 80 e a síndrome da imunodeficiência adquirida tornou-se a principal causa de morbidade e morte entre estes pacientes. O Objetivo deste estudo foi o de determinar os subtipos do vírus da imunodeficiência humana em oito pacientes soropositivos com moléstias hemorrágicas de Belo Horizonte, Brasil, utilizando o ensaio de mobilidade heteroduplex, um método näo seqüêncial, que tem a propriedade de separar os portadores do vírus. Realizamos a reaçäo da cadeia de polimerase seguida pelo ensaio de mobilidade heteroduplex e obtivemos em todos os oito pacientes a confirmaçäo que os mesmos pertenciam ao subtipo B do vírus da imunodeficiência humana que é a mais prevalente nos Estados Unidos, Europa e Brasil. Os pacientes hemofílicos provavelmente foram infectados de concentrados provenientes da Europa, Estados Unidos, Säo Paulo e Rio de Janeiro (Brasil), utilizados em período anterior ao do conhecimento do vírus da imunodeficiência humana adquirida, e do uso de plasmas e concentrados näo testados, ou inativados, para o mesmo. O ensaio da mobilidade de heteroduplex e amplificaçäo do ácido desoxiribonucleico pela reaçäo de cadeia da polimerase provaram ser um modo rápido de subtipar o vírus da imunodeficiência humana adquirida em indivíduos infectados por transfusäo. O teste pode ser útil como rastreamento e detecçäo da origem e procedência do vírus da imunodeficiência adquirida.

Kat G mutations in isoniazid resistant Mycobacterium tuberculosis isolates from Thai patients.

Isoniazid resistant mechanisms in Mycobacterium tuberculosis have been shown to involve at least two genes, kat G and inh A. Alteration in the kat G gene has been found in a great number of resistant isolates. Percentage of resistant isolates harboring alteration in this gene varied among laboratories suggesting that different mutations were presented in different geographic areas. Fourteen isoniazid resistant and five multidrug resistant isolates from the Central Chest Hospital, Thailand, were examined for the kat G gene mutations in the region between base position 17 to 299. No different pattern of mutations were found between these two groups. Among nineteen isolates, there were nine isolates which showed point mutations and five isolates with base insertions of the kat G gene. The remaining five isolates revealed gene deletion. Heteroduplex formation technique also confirmed base alterations in these nine mutants.