Single-nucleotide polymorphisms (SNPs) are the most common type of genetic variation in man. Genes containing one or more SNPs can give rise to two or more allelic forms of mRNAs. These mRNA variants may possess different biological functions as a result of differences in primary or higher order structures that interact with other cellular components. Here we report the observation of marked differences in mRNA secondary structure associated with SNPs in the coding regions of two human mRNAs: alanyl tRNA synthetase and replication protein A, 70-kDa subunit (RPA70). Enzymatic probing of SNP-containing allelic fragments of the mRNAs revealed pronounced allelic differences in cleavage pattern at sites 14 or 18 nt away from the SNP, suggesting that a single-nucleotide variation can give rise to different mRNA folds. By using phosphorothioate oligodeoxyribonucleotides complementary to the region of different allelic structures in the RPA70 mRNA, but not extending to the SNP itself, we find that the SNP exerts an allele-specific effect on the accessibility of its f lanking site in the endogenous human RPA70 mRNA. This further supports the allelespecific structural features identified by enzymatic probing. These results demonstrate the contribution of common genetic variation to structural diversity of mRNA and suggest a broader role than previously thought for the effects of SNPs on mRNA structure and, ultimately, biological function.Single-nucleotide polymorphisms (SNPs) are single base-pair substitutions that occur within and outside genes (1-3). SNPs account for many well characterized human phenotypes, including disease susceptibility and resistance (4, 5) and drug response (6, 7). As a result, SNP discovery efforts have markedly expanded over the past 2 years. The frequency of SNPs varies between genomic regions and between coding and noncoding sequences. The extent of nucleotide diversity ranges from 0.0003 to 0.005; in other words, there are from 3 to 50 SNPs per 10 kilobases when two chromosomes are compared (for review, see ref.2).Genes containing one or more SNPs can give rise to two or more allelic forms of mRNAs. mRNAs containing different bases at SNP sites may vary in their interactions with cellular components involved in mRNA synthesis, maturation, transport, translation, or degradation. It has been documented that a number of single base-pair substitutions alter or create essential sequence elements for splicing, processing, or translation of human mRNA (1). These SNPs are associated with altered length and/or steady-state level of cytoplasmic mRNA. On the other hand, SNPs that do not affect RNA consensus and protein sequences have not been analyzed in detail. It is conceivable that such SNPs could also lead to phenotypic effects, most likely through non-consensus-dependent mechanisms.A growing body of evidence shows that the folding of mRNA influences a diverse range of biological events such as mRNA splicing (8, 9) and processing (10-12), and translational control (13-16) and regulation (17)...