Works (6)

Updated: July 5th, 2023 16:01

2007 journal article

Conformational energy and structure in canonical and noncanonical forms of tRNA determined by temperature analysis of the rate of s(4)U8-C13 photocrosslinking

RNA, 13(11), 2000–2011.

By: W. Huggins n, T. Shapkina n & P. Wollenzien n

author keywords: RNA tertiary structure; photocrosslinking rates; activation energy; conformational energy; T-1 excited state lifetimes
MeSH headings : Base Composition; Base Sequence; Buffers; Cytosine / chemistry; Molecular Sequence Data; Nucleic Acid Conformation; RNA, Bacterial; RNA, Transfer / chemistry; RNA, Transfer, Met / chemistry; RNA, Transfer, Phe / chemistry; RNA, Transfer, Val / chemistry; Temperature; Thermodynamics; Uracil / chemistry
TL;DR: Measurements of the temperature dependence of the rate constants for photocrosslinking between the s(4)U8 and C13 have been used to investigate the tRNA conformational energy and structure in Escherichia coli tRNA(Val), tRNA (Phe), and t RNA(fMet) under different conditions. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome

NUCLEIC ACIDS RESEARCH, 32(4), 1518–1526.

By: T. Shapkina n, S. Lappi*, S. Franzen* & P. Wollenzien*

MeSH headings : Base Sequence; Escherichia coli / genetics; Lasers; Molecular Sequence Data; Photons; Purine Nucleosides / radiation effects; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / radiation effects; Ribosomes / radiation effects; Ultraviolet Rays
TL;DR: Cross- linking frequencies obtained with one laser pulse are more correlated to internucleotide distances than arefrequency obtained with transilluminator irradiation, probably due to intensity-dependent photoreversal. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Conformational change in the 16S rRNA in the Escherichia coli 70S ribosome induced by P/P- and P/E-site tRNA(Phe) binding

BIOCHEMISTRY, 42(49), 14386–14396.

By: J. Noah n, T. Shapkina n, K. Nanda n, W. Huggins n & P. Wollenzien n

MeSH headings : Acetylation / radiation effects; Binding Sites / radiation effects; Cytosine / chemistry; Cytosine / radiation effects; Escherichia coli / chemistry; Escherichia coli / genetics; Escherichia coli / radiation effects; Nucleic Acid Conformation / radiation effects; Peptide Chain Elongation, Translational / genetics; Peptide Chain Elongation, Translational / radiation effects; Photochemistry; Poly U / chemistry; Poly U / genetics; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / radiation effects; RNA, Messenger / chemistry; RNA, Messenger / genetics; RNA, Messenger / radiation effects; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / genetics; RNA, Ribosomal, 16S / radiation effects; RNA, Transfer, Phe / chemistry; RNA, Transfer, Phe / genetics; RNA, Transfer, Phe / radiation effects; Ribosomes / chemistry; Ribosomes / genetics; Ribosomes / radiation effects; Transcription, Genetic / radiation effects; Ultraviolet Rays
TL;DR: Results indicate a limited structural change in the small subunit around C967 and C1400 during tRNA P-site binding sensitive to the type of mRNA that is used, and indicates an alternative arrangement in this region in empty ribosomes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2001 journal article

Short-range RNA-RNA crosslinking methods to determine rRNA structure and interactions

METHODS, 25(3), 333–343.

By: D. Juzumiene n, T. Shapkina n, S. Kirillov n & P. Wollenzien n

MeSH headings : Cross-Linking Reagents / pharmacology; DNA Ligases / chemistry; DNA Ligases / isolation & purification; DNA, Complementary / chemistry; Electrophoresis, Polyacrylamide Gel; Models, Molecular; Nucleic Acid Conformation; RNA / chemistry; RNA / ultrastructure; RNA, Messenger / chemistry; RNA, Ribosomal / chemistry; RNA, Ribosomal, 16S / chemistry; RNA, Transfer / chemistry; Ultraviolet Rays
TL;DR: Details of procedures to analyze RNA-RNA crosslinks made by far-UV irradiation (< 300 nm) or made by irradiation with near-UV light on RNA containing photosensitive nucleotides, in the present case containing 4-thiouridine are described. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2000 journal article

Initiation factor 3-induced structural changes in the 30 S ribosomal subunit and in complexes containing tRNA(f)(Met) and mRNA

JOURNAL OF MOLECULAR BIOLOGY, 299(3), 615–628.

By: T. Shapkina n, M. Dolan n, P. Babin n & P. Wollenzien n

author keywords: initiation factor 3; UV-induced crosslinking; 16 S rRNA coformational change; molecular model; 16 S rRNA-tRNA interaction
MeSH headings : Alkalies / metabolism; Anticodon / genetics; Bacterial Proteins / chemistry; Bacterial Proteins / metabolism; Base Sequence; Binding Sites / radiation effects; Escherichia coli / chemistry; Escherichia coli / genetics; Hydrolysis; Models, Molecular; Nucleic Acid Conformation; Peptide Initiation Factors / chemistry; Peptide Initiation Factors / metabolism; Prokaryotic Initiation Factor-3; Protein Binding / radiation effects; Protein Structure, Tertiary; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; RNA, Messenger / genetics; RNA, Messenger / metabolism; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / genetics; RNA, Ribosomal, 16S / metabolism; RNA, Transfer, Met / genetics; RNA, Transfer, Met / metabolism; RNA-Binding Proteins / chemistry; RNA-Binding Proteins / metabolism; Ribosomal Proteins / chemistry; Ribosomal Proteins / metabolism; Ribosomes / chemistry; Ribosomes / genetics; Ribosomes / metabolism; Transcription, Genetic / genetics; Ultraviolet Rays
TL;DR: Initiation factor 3 (IF3) acts to switch the decoding preference of the small ribosomal subunit from elongator to initiator tRNA, indicating they are not mediated through tRNA(f)(Met) or mRNA. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2000 journal article

UV-induced crosslinks in the 16S rRNAs of Escherichia coli, Bacillus subtilis and Thermus aquaticus and their implications for ribosome structure and photochemistry

NUCLEIC ACIDS RESEARCH, 28(19), 3785–3792.

By: J. Noah n, T. Shapkina n & P. Wollenzien n

MeSH headings : Bacillus subtilis / cytology; Bacillus subtilis / genetics; Bacillus subtilis / radiation effects; Base Composition; Base Sequence; Binding Sites; Conserved Sequence / genetics; Conserved Sequence / radiation effects; Escherichia coli / cytology; Escherichia coli / genetics; Escherichia coli / radiation effects; Hot Temperature; Lasers; Molecular Sequence Data; Nucleic Acid Conformation / radiation effects; Nucleotides / chemistry; Nucleotides / genetics; Nucleotides / metabolism; Nucleotides / radiation effects; Photochemistry; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; RNA, Bacterial / radiation effects; RNA, Ribosomal, 16S / chemistry; RNA, Ribosomal, 16S / genetics; RNA, Ribosomal, 16S / metabolism; RNA, Ribosomal, 16S / radiation effects; Ribosomes / chemistry; Ribosomes / genetics; Ribosomes / radiation effects; Thermus / cytology; Thermus / genetics; Thermus / radiation effects; Transcription, Genetic; Ultraviolet Rays
TL;DR: The overall similarity of crosslink positions in the three organisms suggests that the crosslinks arise from tertiary interactions that are highly conserved but with differences in detail in some regions. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

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