Chemical approaches for structure and function of RNA in postgenomic era.

In the study of cellular RNA chemistry, a major thrust of research focused upon sequence determinations for decades. Structures of snRNAs (4.5S RNA I (Alu), U1, U2, U3, U4, U5, and U6) were determined at Baylor College of Medicine, Houston, Tex, in an earlier time of pregenomic era.

Thermodynamic analyses of the constitutive splicing pathway for ovomucoid pre-mRNA.

The ovomucoid pre-mRNA has been folded into mini-hairpins adaptable for the RNA recognition motif (RRM) protein binding. The number of mini-hairpins were 372 for pre-mRNA and 83-86 for mature m RNA The spatial arrangements are, in average, 16 nucleotides per mini-hairpin which includes 7 nt in the stem, 5.6 nt in the loop and 3.

A modeling study of co-transcriptional metabolism of hnRNP using FMR1 gene.

Since molecular structure of hnRNP is not available in foreseeable future, it is best to construct a working model for hnRNP structure. A geometric problem, assembly of 700 +/- 20 nucleotides with 48 proteins, is visualized by a frame work in which all the proteins participate in primary binding, followed by secondary, tertiary and quaternary binding with neighboring proteins without additional import. Thus, 40S hnRNP contains crown-like secondary structure (48 stem-loops) and appearance of 6 petal (octamers) rose-like architectures.

Structural elements of dynamic RNA strings.

Short transient secondary structures form while RNA is being transcribed, and these become the initial sites for protein anchoring. The insulin gene transcript (IGT) of chain length 1,430 nucleotides can be folded into 92 stem-loops, at an average of one stem-loop per 15.5 nucleotides (range: 9-35).

Nuclear snRNA and nuclear function (discovery of 5' cap structures in RNA).

In view of the fact that eukaryotic gene expression starts in the nucleus, it is important to have a thorough understanding of nuclear macromolecular structure and function. Newly discovered snRNAs are eukaryotic cell specific and have unique subnuclear compartmental localizations. There are over 200 nucleolar-specific RNAs that include some abundant U3, U8, and U13 RNAs.