Conformation and dynamics of an RNA internal loop.

Biochemistry
G VaraniI Tinoco

Abstract

The conformation and the dynamics of an RNA oligonucleotide (26 nucleotides) which is a model for loop E in eukaryotic 5S RNA have been investigated by one- and two-dimensional NMR. The central portion of the oligonucleotide contains two G A oppositions, a common feature of ribosomal RNAs. The exchangeable proton spectrum indicates that an internal loop separates two stems of four and five base pairs. This observation is not consistent with structures for loop E containing mismatched G.A base pairs proposed from chemical and enzymatic studies on Xenopus laevis 5S RNA. The nonexchangeable proton spectrum has been assigned by two-dimensional NMR. Scalar couplings from correlated experiments and interproton distances from NOESY experiments at short mixing times have been used to determine glycosidic angles, sugar puckers, and other conformational features. The conformation of the stems is very close to standard A-form RNA, and extensive base stacking continues into the internal loop. This result provides a structural basis for the large favorable enthalpy of duplex formation determined in thermodynamic studies. Unusual structural and dynamic features are localized in the nucleotides connecting the loop to the stems.

References

Aug 1, 1977·Nucleic Acids Research·H Donis-KellerW Gilbert
Jun 1, 1976·Nucleic Acids Research·D B Arter, P G Schmidt
Dec 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·S M FreierD H Turner
Nov 20, 1988·Journal of Molecular Biology·S SternH F Noller
Dec 5, 1988·Journal of Molecular Biology·H LeffersR A Garrett
Feb 1, 1985·Journal of Biomolecular Structure & Dynamics·J L LeroyM Guérón
Jun 28, 1988·Biochemistry·P RombyB Ehresmann
Nov 11, 1987·Nucleic Acids Research·J F MilliganO C Uhlenbeck
Oct 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·A D BranchH D Robertson
Aug 5, 1973·Journal of Molecular Biology·J Gralla, D M Crothers
Jan 1, 1984·Annual Review of Biochemistry·H F Noller

❮ Previous
Next ❯

Citations

Oct 1, 1996·Plant Molecular Biology·P KlaffG Steger
May 20, 1991·Journal of Molecular Biology·I L de StevensonP J Romaniuk
Nov 11, 1991·Quarterly Reviews of Biophysics·G Varani, I Tinoco
Jul 25, 1990·Nucleic Acids Research·A A SzewczakP B Moore
Feb 15, 1997·Nucleic Acids Research·R J Cain, G D Glick
Nov 20, 2001·Nucleic Acids Research·T J MackeR Sampath
Jan 1, 1997·Annual Review of Biophysics and Biomolecular Structure·P J Hagerman
Jul 28, 2010·RNA·Evgenia N Nikolova, Hashim M Al-Hashimi
Nov 1, 2013·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Shuntaro Takahashi, Naoki Sugimoto
Jul 30, 1990·Journal of Molecular Biology·J D PuglisiI Tinoco
May 11, 1990·Biochemistry·J D PuglisiI Tinoco
Apr 12, 1991·Biochemistry·G VaraniI Tinoco
Feb 2, 1993·Biochemistry·B WimberlyI Tinoco
Nov 23, 1993·Biochemistry·J A Jaeger, I Tinoco
Feb 1, 1990·Nature·A BhattacharyyaD M Lilley
Jul 17, 2001·Journal of Molecular Biology·T ElgavishR R Gutell
Nov 25, 2000·Journal of Molecular Biology·R R GutellM J Serra
Jul 3, 1992·Science·J D PuglisiJ R Williamson

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.