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Results for “SNPs”

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At least 505 records · Page 28Linked to original sources
PubMed2003

A novel approach of cell-free peptide synthesis and SNPs detection using nano-circular single-stranded DNA.

Development of peptide/protein synthesis is very important for investigating the functions of peptides and proteins. The advantages of cell-free synthesis, which has been extensively developed, include the ability to synthesize toxic proteins, aggregated proteins and proteins containing unnatural amino acids. However, this promising approach does not have a high reaction yield. In this study, we examine whether the rolling synchronization system, which produces long RNAs with a repeated sequence encoded by very small circular ssDNAs without the promoter sequence for RNA polymerase, can be used for cell-free peptide synthesis to improve the reaction yield. As a result, we have found that rolling synchronization is useful for large-scale cell-free peptide/protein synthesis.

Base Sequence↗
PubMed2000

New method for scanning of single-nucleotide polymorphisms (SNPs): recognition of guanine-guanine mismatches by dimeric naphthyridine.

Dimeric naphthyridine was designed and synthesized as a novel ligand that specifically binds to G-G mismatch, one of four SNP types. In the presence of dimeric naphthyridine, CD spectra of the G-G mismatch containing duplex noticeably changed, being accompanied by the induced CD at 300-350 nm, whereas no CD spectral change was observed for normal duplex. DNaseI footprinting titration indicated a selective binding of dimeric naphthyridine to the G-G mismatch with a dissociation constant of 53 nM.

Base Pair Mismatch↗
PubMed2005

SNPs typing by base-discriminating fluorescence DNA probe.

For the development of a novel SNP typing method using BDF (base-discriminating fluorescent) nucleosides in biological samples, we examined the detection of the single base alteration in BRCA1 gene with PCR products amplified by an asymmetric PCR. A combination of PyU- and PyC-containing BDF probes clearly facilitates the discrimination of not only A/G homozygous samples but also heterozygous samples. The present SNP typing method with BDF probes is a very powerful homogeneous assay that does not require a special device or time-consuming steps.

DNA Probes↗
PubMed2006

Use of abasic site-containing DNA for electrochemical SNPs detection.

In combination with an electrode modified with an abasic site-containing DNA duplex, flavins selectively bind to thymine with a useful electrochemical response, and flavins could be successfully utilized for detection of thymine-related mutations. The abasic site provides hydrophobic microenvironments for the hydrogen bond-forming ligands can recognize the specific target base in the DNA duplex, which is detected by the difference in the electrochemical response.

Biosensing Techniques↗
PubMed2000

Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays.

Most human cancers are characterized by genomic instability, the accumulation of multiple genetic alterations and allelic imbalance throughout the genome. Loss of heterozygosity (LOH) is a common form of allelic imbalance and the detection of LOH has been used to identify genomic regions that harbor tumor suppressor genes and to characterize tumor stages and progression. Here we describe the use of high-density oligonucleotide arrays for genome-wide scans for LOH and allelic imbalance in human tumors. The arrays contain redundant sets of probes for 600 genetic loci that are distributed across all human chromosomes. The arrays were used to detect allelic imbalance in two types of human tumors, and a subset of the results was confirmed using conventional gel-based methods. We also tested the ability to study heterogeneous cell populations and found that allelic imbalance can be detected in the presence of a substantial background of normal cells. The detection of LOH and other chromosomal changes using large numbers of single nucleotide polymorphism (SNP) markers should enable identification of patterns of allelic imbalance with potential prognostic and diagnostic utility.

Adenocarcinoma↗
PubMed2005

Structural interpretation of mutations and SNPs using STRAP-NT.

Visualization of residue positions in protein alignments and mapping onto suitable structural models is an important first step in the interpretation of mutations or polymorphisms in terms of protein function, interaction, and thermodynamic stability. Selecting and highlighting large numbers of residue positions in a protein structure can be time-consuming and tedious with currently available software. Previously, a series of tasks and analyses had to be performed one-by-one to map mutations onto 3D protein structures; STRAP-NT is an extension of STRAP that automates these tasks so that users can quickly and conveniently map mutations onto 3D protein structures. When the structure of the protein of interest is not yet available, a related protein can frequently be found in the structure databases. In this case the alignment of both proteins becomes the crucial part of the analysis. Therefore we embedded these program modules into the Java-based multiple sequence alignment program STRAP-NT. STRAP-NT can simultaneously map an arbitrary number of mutations denoted using either the nucleotide or amino acid sequence. When the designations of the mutations refer to genomic sites, STRAP-NT translates them into the corresponding amino acid positions, taking intron-exon boundaries into account. STRAP-NT tightly integrates a number of current protein structure viewers (currently PYMOL, RASMOL, JMOL, and VMD) with which mutations and polymorphisms can be directly displayed on the 3D protein structure model. STRAP-NT is available at the PDB site and at http://www.charite.de/bioinf/strap/ or http://strapjava.de.

DNA Mutational Analysis↗
PubMed2005

The SNPs of RAF.

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Humans↗
PubMed2006

SNPs in human beta-defensin 1 gene (DEFB1): frequencies in a Mexican population and new PCR-RFLPs assays.

Polymerase chain reaction-restriction fragment length polymorphism assays for two single nucleotide polymorphisms in the human beta-defensin 1 gene have been validated with real-time PCR in 101 healthy individuals from western Mexico. Allele frequencies were 52.5% (692-A) and 98.5% (1836-A). These assays can be confidently used as a cheaper alternative genotyping method for these sites.

Ethnicity↗