Due to crucial roles in gene regulation, noncoding small RNAs (smRNAs) of 20–30 nucleotides (nt) have been intensively studied in mammals and plants, and are known to be implicated in significant diseases and metabolic disorders. Elucidation of biogenesis mechanisms and functional cha ...

MicroRNAs (miRNAs) play important roles in development in plants, and some miRNAs show developmentally regulated organ- and tissue-specific expression patterns. Therefore, in situ detection of mature miRNAs is important for understanding the functions of both miRNAs and their ta ...

Northern blotting is a valuable method for detection and quantification of RNA in the field of virology. Although many methods including a various versions of polymerase chain reaction have been developed over the years, Northern blotting has been still considered as a useful and effective ...

The complexity of molecular diagnostic assays is a significant barrier to employment in point-of-care diagnostics, despite the growing need for such technologies. We have developed a sensitive, accurate, rapid, and simple DNA amplification scheme that shows potential for transla ...

A multiple primer extension (MPEX) was originally developed for the hybridization, extension, and amplification of a DNA template on a planar substrate by Kinoshita et al. in 2006. Herein we present a modified MPEX method refined by our group for single nucleotide polymorphism (SNP) detecti ...

The increasing need for large-scale genotyping applications of single nucleotide polymorphisms (SNPs) in model and nonmodel organisms requires the development of low-cost technologies accessible to minimally equipped laboratories. The method presented here allows effi ...

Progress in single nucleotide polymorphism (SNP) detection technologies has provided information for SNP-based studies, such as identification of candidate genes for the complex genetic diseases, pharmacogenetic analysis, drug development, population genetics, evol ...

A microarray-based method for detecting single nucleotide polymorphisms (SNPs) using solid-phase polymerase chain reaction (PCR) on magnetic nanoparticles (MNPs) was developed. In this method one primer with a biotin label is captured by streptavidin-coated MNPs (SA-MNPs), and t ...

Single nucleotide polymorphisms (SNPs) are the most common form of polymorphisms present in the human genome. The single base primer extension (SBE) method is an effective and sensitive tool that can type over 30 known loci scattered throughout an organism’s genome in a single reaction. It all ...

Choosing a single nucleotide polymorphism genotyping method that suits specific research needs is not much less of a challenge than determining the genetic components underlying the disease and/or trait being investigated. This is especially true with a long list of tempting methodo ...

A new method suitable for single nucleotide polymorphism (SNP) detection using differential oligonucleotide probe extension has been developed. Sulfur-linked laser-cleavable trityl labels are implemented in this protocol. The method is based on mass spectrometry and utili ...

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has developed over the past decade into a versatile tool for the analysis of nucleic acids and especially as a reliable genotyping platform. This chapter summarizes its use in the context ...

Single nucleotide polymorphisms (SNPs) are common DNA sequence variations that occur at single bases within the genome. SNPs have been instrumental in elucidating the genetic basis of common, complex diseases using genome-wide association studies, candidate gene case-control a ...

Population genetics studies play an increasingly important role in the management and conservation of nonmodel organisms. Unlike studies with model organisms, a typical population genetics study of a nonmodel organism may be conducted by analyzing thousands or hundreds of thousa ...

In the last decade, molecular beacons have emerged to become a widely used tool in the multiplex typing of single nucleotide polymorphisms (SNPs). Improvements in detection technologies in instrumentation and chemistries to label these probes have made it possible to use up to six spectra ...

Single nucleotide polymorphisms (SNPs) are ideal markers for identifying genes associated with complex diseases for two main reasons. Firstly, SNPs are densely located on the human genome at about one SNP per approximately 500–1,000 base pairs. Secondly, a large number of commercial pla ...

Simple, low-cost mutation detection assays that are suitable for low-throughput analysis are essential for diagnostic applications where the causative mutation may be different in every family. The mismatch oxidation assay is a simple optical absorbance assay to detect nucleoti ...

Methods to rapidly scan large regions of DNA that are not dependent on highly specific melting temperatures or suitable only for large-scale discovery are important to reduce the amount of sequencing required for DNA samples that appear to contain a mutation. This protocol describes the che ...

Excimer formation is a unique feature of some fluorescent dyes (e.g., pyrene) which can be used for probing the proximity of biomolecules. Pyrene excimer fluorescence has previously been used for homogeneous detection of single nucleotide polymorphism (SNP) on DNA. 1-Phenylethynylp ...

The single strand conformation polymorphism (SSCP) method is a sensitive technique used to detect subtle sequence differences in PCR-amplified DNA fragments as separated peaks in electrophoretic analysis. In this chapter, we focus on SSCP analysis for quantifying polymorphic al ...