scholarly journals Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures

Biochemistry ◽  
2019 ◽  
Vol 58 (8) ◽  
pp. 1094-1108 ◽  
Author(s):  
Kyle D. Berger ◽  
Scott D. Kennedy ◽  
Douglas H. Turner
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Base Pairs ◽  
Internal Loops ◽  
Nuclear Magnetic

Nuclear Magnetic Resonance reveals a two hairpin equilibrium near the 3'-splice site of Influenza A segment 7 mRNA that can be shifted by oligonucleotides

RNA ◽  
2022 ◽  
pp. rna.078951.121
Author(s):  
Andrew D. Kauffmann ◽  
Scott D. Kennedy ◽  
Walter N. Moss ◽  
Elzbieta Kierzek ◽  
Ryszard Kierzek ◽  
...  
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Splice Site ◽  
Influenza A ◽  
3D Nmr ◽  
Hairpin Loop ◽  
Base Pairs ◽  
Internal Loop ◽  
Hairpin Secondary Structure ◽  
Nuclear Magnetic

Influenza A kills hundreds of thousands of people globally every year and has potential to generate more severe pandemics. Influenza A’s RNA genome and transcriptome provide many potential therapeutic targets. Here, nuclear magnetic resonance (NMR) experiments suggest that one such target could be a hairpin loop of eight nucleotides in a pseudoknot that sequesters a 3' splice site in canonical pairs until a conformational change releases it into a dynamic 2X2 nucleotide internal loop. NMR experiments reveal that the hairpin loop is dynamic and able to bind oligonucleotides as short as pentamers. A 3D NMR structure of the complex contains four and likely five base pairs between pentamer and loop. Moreover, a hairpin sequence was discovered that mimics the equilibrium of the influenza hairpin between its structure in the pseudoknot and upon release of the splice site. Oligonucleotide binding shifts the equilibrium completely to the hairpin secondary structure required for pseudoknot folding. The results suggest this hairpin can be used to screen for compounds that stabilize the pseudoknot and potentially reduce splicing.

A cooperative conformational change in duplex DNA induced by Zn2+ and other divalent metal ions

1993 ◽  
Vol 71 (3-4) ◽  
pp. 162-168 ◽  
Author(s):  
Jeremy S. Lee ◽  
Laura J. P. Latimer ◽  
R. Stephen Reid
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Metal Ions ◽  
Conformational Change ◽  
Divalent Metal ◽  
Proton Nuclear Magnetic Resonance ◽  
Duplex Dna ◽  
Divalent Metal Ions ◽  
Base Pairs ◽  
Nuclear Magnetic

Zn2+ and some other divalent metal ions bind to duplex DNA at pHs above 8 and cause a conformational change. This new structure does not bind ethidium, allowing the development of a rapid fluorescence assay. All duplex DNAs, regardless of sequence or G∙C content, can form this structure. The rate of formation shows a strong dependence on temperature, pH, and Zn2+ concentration; at 20 °C, 1 mM Zn2+, and pH 8.6 the dismutation is half complete in 30 min. Addition of EDTA causes rapid reversion to 'B' DNA, showing that the new conformation retains two strands that are antiparallel. Unlike the ultraviolet or circular dichroism spectra, the nuclear magnetic resonance spectrum was informative since the imino protons of both A∙T and G∙C base pairs are lost upon addition of a stoichiometric amount of Zn2+. The pitch of the helix was estimated from gel electrophoresis of circular DNAs in the presence of Zn2+ and it contains at least 5% fewer base pairs per turn than 'B' DNA. The transformation is cooperative and shows hysteresis, suggesting that this is a distinct structure and not simply a minor variant of 'B' DNA. It is proposed to call this new structure 'M' DNA because of the intimate involvement of metal ions.Key words: DNA conformation, cooperative transition, ethidium binding, divalent metal ions, proton nuclear magnetic resonance.

Comparison of the structures of operator DNA free and in complex with λ repressor

1991 ◽  
Vol 69 (2-3) ◽  
pp. 202-205 ◽  
Author(s):  
James D. Baleja ◽  
Brian D. Sykes
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Dna Sequence ◽  
Protein Recognition ◽  
Base Pairs ◽  
Dna Structures ◽  
X Ray ◽  
X Ray Crystallography ◽  
Operator Dna ◽  
Nuclear Magnetic

The structures of operator DNA unbound and in complex with λ repressor protein are compared. The conformation of the left 10 base pairs of a λ right regulatory operator DNA sequence has been previously determined in solution using nuclear magnetic resonance techniques and the structure of a homologous left regulatory operator DNA bound to λ repressor N-terminal domain had been previously solved using X-ray crystallography. The DNA adopts an overall linear B-form DNA both in the absence and presence of λ repressor. Superimpositioning of the DNA structures reveals small differences between them that are due to the binding of protein and not to the different techniques used for their determination.Key words: DNA structure, λ repressor, DNA–protein recognition, nuclear magnetic resonance.

High-resolution nuclear magnetic resonance determination of transfer RNA tertiary base pairs in solution. 1. Species containing a small variable loop

Biochemistry ◽  
1977 ◽  
Vol 16 (10) ◽  
pp. 2086-2094 ◽  
Author(s):  
Brian R. Reid ◽  
N. Susan Ribeiro ◽  
Lillian McCollum ◽  
Joseph Abbate ◽  
Ralph E. Hurd
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
High Resolution ◽  
Transfer Rna ◽  
Base Pairs ◽  
Variable Loop ◽  
Nuclear Magnetic

An emerging technology: Nuclear magnetic resonance microscopy

1988 ◽  
Vol 46 ◽  
pp. 1000-1001
Author(s):  
M.J. Hennessy ◽  
E. Kwok
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Relaxation Times ◽  
Basic Research ◽  
Local Environment ◽  
Magnetic Resonance Images ◽  
Nmr Microscopy ◽  
Mri Scans ◽  
Temperature Relaxation ◽  
Nuclear Magnetic

Much progress in nuclear magnetic resonance microscope has been made in the last few years as a result of improved instrumentation and techniques being made available through basic research in magnetic resonance imaging (MRI) technologies for medicine. Nuclear magnetic resonance (NMR) was first observed in the hydrogen nucleus in water by Bloch, Purcell and Pound over 40 years ago. Today, in medicine, virtually all commercial MRI scans are made of water bound in tissue. This is also true for NMR microscopy, which has focussed mainly on biological applications. The reason water is the favored molecule for NMR is because water is,the most abundant molecule in biology. It is also the most NMR sensitive having the largest nuclear magnetic moment and having reasonable room temperature relaxation times (from 10 ms to 3 sec). The contrast seen in magnetic resonance images is due mostly to distribution of water relaxation times in sample which are extremely sensitive to the local environment.

Sign in / Sign up

Export Citation Format

Share Document