Abstract: This document provides methods and materials for determining the identity of the terminal nucleotide (e.g., the 3? terminal nucleotide) of a nucleic acid molecule. For example, methods and materials for using RNA-DNA chimeric primers during a primer extension reaction followed by treatment with one or more RNAse enzymes to prepare nucleic acid molecules that can be analyzed to identify the terminal nucleotides added to the RNA-DNA chimeric primers during the primer extension are provided.

Abstract: This document relates to methods and materials involved in detecting Fragile X mutations and assessing the methylation state of Fragile X alleles. For example, methods and materials for detecting Fragile X alleles using polymerase chain reaction and a hybridization probe (e.g., a non-radioactively labeled hybridization probe) are provided.

Abstract: Detection of probe fragment products of basepair mismatch cleavage indicate the presence and sequence of target DNA. Detection of the target is enhanced by amplification through recycling targets by maintaining an assay temperature between the melting point of the target/probe DNA duplex and that of the target/product complex, in the presence of an amplifier comprising ammonium acetate or an amine derivative (for example, diethylamine, piperidine or ammonium carbonate). Cleavage reduces the size of the duplex, and thus lowering its melting point. The amplifier releases the target from the complex, thereby permitting further catalysis of cleavage and effectively amplifying the signal to be detected.