Works (50)

Updated: July 16th, 2023 21:18

2012 journal article

Human tRNA(UUU)(LYs3) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism

JOURNAL OF MOLECULAR BIOLOGY, 416(4), 467–485.

By: F. Vendeix n, F. Murphy*, W. Cantara n, G. Leszczynska*, E. Gustilo n, B. Sproat, A. Malkiewicz*, P. Agris n

author keywords: modifications; wobble decoding; anticodon structure; tRNA(LYs3)
MeSH headings : Anticodon / chemistry; Base Pairing; Circular Dichroism; Codon / chemistry; Crystallography, X-Ray; Humans; Hydrogen Bonding; Models, Molecular; Nucleic Acid Conformation; Pseudouridine / chemistry; RNA, Transfer, Lys / chemistry; Thermodynamics; Thiouridine / analogs & derivatives; Thiouridine / chemistry
TL;DR: The results unambiguously demonstrate that modifications pre-structure the anticodon as a key prerequisite for efficient and accurate recognition of cognate and wobble codons. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2011 journal article

YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase

RNA, 17(9), 1678–1687.

By: K. Harris, V. Jones, Y. Bilbille, M. Swairjo & P. Agris

Source: NC State University Libraries
Added: August 6, 2018

2010 journal article

Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA

Nucleic Acids Research, 38(9), 3094–3105.

By: A. Scheunemann, W. Graham, F. Vendeix & P. Agris

Source: NC State University Libraries
Added: August 6, 2018

2009 journal article

Free energy calculation of modified base-pair formation in explicit solvent: A predictive model

RNA, 15(12), 2278–2287.

By: F. Vendeix n, A. Munoz n & P. Agris n

author keywords: modified nucleosides; base pairs in water; wobble recognition; refined molecular dynamics simulation
MeSH headings : Base Pairing; Models, Genetic; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; RNA / chemistry; Thermodynamics
TL;DR: MDS is predictive of the effects of modifications, H(2)O molecule intervention in the formation of base-pair geometry, and energies that are important for native RNA structure and function. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2009 journal article

The structure of the human tRNA(Lys3) anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

NUCLEIC ACIDS RESEARCH, 37(10), 3342–3353.

By: Y. Bilbille n, F. Vendeix n, R. Guenther n, A. Malkiewicz n, X. Ariza n, J. Vilarrasa n, P. Agris n

MeSH headings : Anticodon / chemistry; Base Pair Mismatch; Base Sequence; Carbohydrates / chemistry; Genome, Viral; HIV-1 / genetics; Humans; Models, Molecular; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular; Protons; Pseudouridine / chemistry; RNA, Transfer, Lys / chemistry; RNA, Viral / chemistry; Thermodynamics; Thiouridine / analogs & derivatives; Thiouridine / chemistry
TL;DR: The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. (via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

A Disease-causing Point Mutation in Human Mitochondrial tRNA(Met) Results in tRNA Misfolding Leading to Defects in Translational Initiation and Elongation

JOURNAL OF BIOLOGICAL CHEMISTRY, 283(49), 34445–34456.

By: C. Jones*, C. Jones n, W. Graham n, P. Agris n & L. Spremulli*

MeSH headings : Animals; Base Sequence; Binding Sites; Cattle; Escherichia coli / enzymology; Humans; Mitochondria / enzymology; Mitochondria / metabolism; Mutation; Nucleic Acid Conformation; Nucleic Acid Denaturation; Optic Atrophy, Hereditary, Leber / genetics; Point Mutation; Protein Biosynthesis; RNA, Transfer, Met / chemistry; Thermodynamics
TL;DR: It is shown that the single 8U→C mutation leads to a failure of the tRNA to respond conformationally to Mg2+. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding

BIOCHEMISTRY, 47(23), 6117–6129.

By: F. Vendeix n, A. Dziergowska n, E. Gustilo n, W. Graham n, B. Sproat n, A. Malkiewicz n, P. Agris n

MeSH headings : Anticodon / chemistry; Base Sequence; Binding Sites; Codon / chemistry; Codon / metabolism; Dinucleoside Phosphates / chemistry; Escherichia coli / genetics; Magnetic Resonance Spectroscopy; Nucleic Acid Conformation; Oligoribonucleotides / chemistry; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Transfer / genetics; Ribosomes / metabolism
TL;DR: Results clearly demonstrate that the xo (5)U 34-type modifications order the anticodon loop prior to A-site codon binding for an expanded codon reading, possibly reducing an entropic energy barrier to codonbinding. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications

EMBO REPORTS, 9(7), 629–635.

By: P. Agris n

author keywords: entropy; order; pre-structured; rRNA; tRNA
MeSH headings : Anticodon / metabolism; Genetic Code; Nucleic Acid Conformation; Protein Biosynthesis; RNA Processing, Post-Transcriptional; RNA, Transfer / chemistry; RNA, Transfer / genetics; RNA, Transfer / metabolism; Ribosomes / metabolism
TL;DR: The modified nucleosides of the anticodon domain of tRNA restrict its dynamics and shape its architecture; therefore, the need of the ribosome to constrain or remodel each tRNA to fit the decoding site is diminished, which reduces an entropic penalty for translation and provides a physicochemical basis for the conservation of RNA modifications in general. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNA(Met)

NUCLEIC ACIDS RESEARCH, 36(20), 6548–6557.

By: H. Lusic n, E. Gustilo n, F. Vendeix n, R. Kaiser n, M. Delaney n, W. Graham n, V. Moye n, W. Cantara n, P. Agris n, A. Deiters n

MeSH headings : Anticodon / chemistry; Base Sequence; Codon / metabolism; Cytidine / analogs & derivatives; Cytidine / chemistry; Humans; Molecular Sequence Data; Nucleic Acid Conformation; Protein Biosynthesis; RNA / chemistry; RNA, Mitochondrial; RNA, Transfer, Met / chemical synthesis; RNA, Transfer, Met / chemistry; RNA, Transfer, Met / metabolism; Thermodynamics
TL;DR: The first synthesis and analyses of the tRNA's anticodon stem and loop domain containing the 5-formylcytidine modification are reported, contributing to the tRNAs anticodon domain structure, thermodynamic properties and its ability to bind codons AUA and AUG in translational initiation and elongation. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2008 review

tRNA's modifications bring order to gene expression

[Review of ]. Current Opinion in Microbiology, 11(2), 134–140.

By: E. Gustilo, A. Franck & P. Agris

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

E-coli glutamyl-tRNA synthetase is inhibited by anticodon stem-loop domains and a minihelix

RNA BIOLOGY, 4(2), 85–92.

By: E. Gustilo n, D. Dubois, J. Lapointe & P. Agris*

author keywords: designed inhibitors; RNA fragments; competitive inhibitors; identity elements; modified RNA; translation
MeSH headings : Anticodon / chemistry; Base Sequence; Binding Sites; Enzyme Inhibitors / chemistry; Escherichia coli / enzymology; Escherichia coli Proteins / antagonists & inhibitors; Escherichia coli Proteins / metabolism; Glutamate-tRNA Ligase / antagonists & inhibitors; Glutamate-tRNA Ligase / metabolism; Molecular Sequence Data; Nucleic Acid Conformation; RNA, Transfer / chemistry; Thermodynamics; Transfer RNA Aminoacylation; Uridine / analogs & derivatives; Uridine / chemistry
TL;DR: The modified ASLGlu-s2U34, though having a higher affinity for ERS, may be released more readily and thus, not be as good an inhibitor as the unmodified ASL, but the RNA constructs are effective tools to study RNA-protein interaction. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 14(6), 498–502.

By: A. Weixlbaumer*, F. Murphy*, A. Dziergowska*, A. Malkiewicz*, F. Vendeix n, P. Agris n, V. Ramakrishnan*

MeSH headings : Amino Acid Sequence; Anticodon / genetics; Base Pairing; Base Sequence; Codon / genetics; Crystallography; Models, Molecular; Molecular Sequence Data; Molecular Structure; RNA, Transfer, Val / genetics; RNA, Transfer, Val / physiology; Uridine / chemistry
TL;DR: Structures of an anticodon stem-loop of tRNAVal containing the modified uridine with all four valine codons in the decoding site of the 30S ribosomal subunit are determined and suggest how a modification in the uridine at the wobble position can expand the decoding capability of a tRNA. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Quality assessment of commercial small interfering RNA and DNA: Monoclonal antibodies and a high-throughput chemiluminescence assay

Analytical Biochemistry, 360(1), 172–174.

By: L. Barley-Maloney & P. Agris

Source: NC State University Libraries
Added: August 6, 2018

2007 journal article

Specificity of phage display selected peptides for modified anticodon stem and loop domains of tRNA

PROTEIN JOURNAL, 26(1), 61–73.

By: M. Eshete n, M. Marchbank*, S. Deutscher*, B. Sproat, G. Leszczynska*, A. Malkiewicz*, P. Agris n

author keywords: anticodon domain; protein-RNA interaction; pseudouridine; 2-thiouridine
MeSH headings : Amino Acid Motifs; Anticodon / antagonists & inhibitors; Anticodon / metabolism; Base Pairing; Codon / chemistry; Humans; Models, Chemical; Nucleic Acid Conformation; Peptide Library; Peptides / metabolism; Protein Binding; Pseudouridine / chemistry; RNA, Transfer, Glu / chemistry; RNA, Transfer, Lys / chemistry; Spectrometry, Fluorescence; Thermodynamics; Thiouridine / analogs & derivatives; Thiouridine / chemistry
TL;DR: RNA modifications are potentially important recognition elements for proteins and can be targets for selective recognition by peptides, and exhibited the highest binding affinity for ASLLys3. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2007 review

tRNA's wobble decoding of the genome: 40 years of modification

[Review of ]. Journal of Molecular Biology, 366(1), 1–13.

By: P. Agris, F. Vendeix & W. Graham

Source: NC State University Libraries
Added: August 6, 2018

2006 journal article

A counterintuitive Mg2+-dependent and modification-assisted functional folding of mitochondrial tRNAs

JOURNAL OF MOLECULAR BIOLOGY, 362(4), 771–786.

By: C. Jones n, A. Spencer*, J. Hsu*, L. Spremulli*, S. Martinis*, M. DeRider n, P. Agris n

author keywords: mitochondrial RNA folding; aminoacylation; tRNA(Met); tRNA(Leu)
MeSH headings : Aminoacylation; Animals; Base Sequence; Cattle; Circular Dichroism; Electrophoretic Mobility Shift Assay; Escherichia coli / chemistry; Magnesium / metabolism; Magnesium / pharmacology; Molecular Sequence Data; Nucleic Acid Conformation / drug effects; Nucleic Acid Denaturation; RNA / chemistry; RNA / genetics; RNA Stability / drug effects; RNA, Mitochondrial; RNA, Transfer / chemistry; RNA, Transfer / genetics; Temperature; Yeasts / chemistry
TL;DR: Investigation of functional folding interactions of chemically synthesized and site-specifically modified mitochondrial and cytoplasmic tRNAs finds that Mg2+ is critical for folding of the truncated D-domain of bovine mtRNAMet with the tRNA's T-domain and indicates that conserved modifications assist and stabilize the formation of the functional mtRNA tertiary structure. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2006 journal article

Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling

Journal of Molecular Biology, 362(5), 1025–1042.

By: K. Gagnon n, X. Zhang n, P. Agris n & E. Maxwell n

MeSH headings : Amino Acid Sequence; Archaea / chemistry; Archaea / genetics; Archaea / metabolism; Archaeal Proteins / chemistry; Archaeal Proteins / genetics; Archaeal Proteins / isolation & purification; Archaeal Proteins / metabolism; Base Sequence; Chromatography, Affinity; Circular Dichroism; Methylation; Models, Biological; Molecular Sequence Data; Mutation; Nucleic Acid Conformation; Protein Binding; RNA, Archaeal / chemistry; RNA, Archaeal / genetics; RNA, Archaeal / metabolism; RNA, Guide, Kinetoplastida / chemistry; RNA, Guide, Kinetoplastida / genetics; RNA, Guide, Kinetoplastida / metabolism; RNA, Small Nucleolar / chemistry; RNA, Small Nucleolar / genetics; RNA, Small Nucleolar / metabolism; Ribonucleoproteins, Small Nuclear / chemistry; Ribonucleoproteins, Small Nuclear / genetics; Ribonucleoproteins, Small Nuclear / metabolism; Temperature
TL;DR: RNA remodeling appears to be a common and requisite feature of archaeal dual-guide box C/D sR NP assembly and formation of the mature sRNP can follow different assembly pathways in generating catalytically active complexes. (via Semantic Scholar)
Source: NC State University Libraries
Added: August 6, 2018

2006 journal article

Assessing incomplete deprotection of microarray oligonucleotides in situ

Nucleic Acids Research, 34(19).

By: H. Dressman, L. Barley-Maloney, L. Rowlette, P. Agris & M. Garcia-Blanco

Source: NC State University Libraries
Added: August 6, 2018

2006 journal article

tRNA regulation of gene expression: Interactions of an mRNA 5 '-UTR with a regulatory tRNA

RNA, 12(7), 1254–1261.

By: A. Nelson n, T. Henkin* & P. Agris n

author keywords: gene regulation; Gram-positive bacteria; tRNA; RNA experimental model
MeSH headings : 5' Untranslated Regions / genetics; Bacillus subtilis / genetics; Base Sequence; Electrophoresis, Polyacrylamide Gel; Gene Expression Regulation; Models, Molecular; Nucleic Acid Conformation; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Messenger / chemistry; RNA, Messenger / genetics; RNA, Transfer / chemistry; RNA, Transfer / genetics; RNA, Transfer / metabolism; Spectrometry, Fluorescence
TL;DR: The bimolecular 5'-UTR and ASL(Gly)(GCC) models mimic the RNA-RNA interaction required for T box gene regulation in vivo. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2005 patent

Antibacterial and antiviral agents and methods of screening for the same

Washington, DC: U.S. Patent and Trademark Office.

By: P. Agris & S. Ashraf

Source: NC State University Libraries
Added: August 6, 2018

2005 patent

Methods and compositions for determining the purity of chemically synthesized nucleic acids

Washington, DC: U.S. Patent and Trademark Office.

By: P. Agris

Source: NC State University Libraries
Added: August 6, 2018

2004 review

Decoding the genome: a modified view

[Review of ]. NUCLEIC ACIDS RESEARCH, 32(1), 223–238.

By: P. Agris n

MeSH headings : Animals; Anticodon / chemistry; Anticodon / genetics; Anticodon / metabolism; Base Sequence; Codon / chemistry; Codon / genetics; Codon / metabolism; Genetic Code; Genome; Humans; Protein Biosynthesis; RNA, Transfer / chemistry; RNA, Transfer / genetics; RNA, Transfer / metabolism; Thermodynamics
TL;DR: It is suggested that anticodon stem and loop domain nucleoside modifications allow a limited number of tRNAs to accurately and efficiently decode the 61 amino acid codons by selectively restricting some anticodon-codon interactions and expanding others. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Modified nucleotides in tRNA(Lys) and tRNA(Val) are important for translocation

JOURNAL OF MOLECULAR BIOLOGY, 338(3), 439–444.

By: S. Phelps*, A. Malkiewicz*, P. Agris n & S. Joseph*

author keywords: ribosome; translocation; tRNA; wobble; decoding
MeSH headings : Protein Biosynthesis / genetics; Protein Biosynthesis / physiology; RNA, Transfer, Lys / genetics; RNA, Transfer, Lys / metabolism; RNA, Transfer, Val / genetics; RNA, Transfer, Val / metabolism; Ribosomes / metabolism
TL;DR: It is shown that modified nucleosides at the first, or wobble, position of the anticodon and 3′-adjacent toThe anticodon are important for translocation of tRNA from the ribosome's aminoacyl site (A site) to the peptidyl site (P site). (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Sequence-altered peptide adopts optimum conformation for modification-dependent binding of the yeast tRNA(Phe) anticodon domain

PROTEIN JOURNAL, 23(1), 33–38.

By: P. Mucha*, A. Szyk, P. Rekowski & P. Agris*

author keywords: beta-turn; methylated nucleosides; phage display library; RNA-peptide interaction
MeSH headings : Anticodon / chemistry; Circular Dichroism; Molecular Conformation; Oligoribonucleotides / chemistry; Peptide Library; Peptides / chemistry; RNA, Fungal / chemistry; RNA, Transfer, Phe / chemistry; Saccharomyces cerevisiae / chemistry
TL;DR: The results suggest that peptides with different conformations, but similar affinities, adopt the optimal binding conformation, indicative of a structurally adaptive model of binding in which the modified RNA serves as a scaffold. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus

NUCLEIC ACIDS RESEARCH, 32(9), 2819–2828.

By: R. Guenther n, T. Sit*, H. Gracz*, M. Dolan, H. Townsend*, G. Liu, W. Newman*, P. Agris*, S. Lommel*

Contributors: R. Guenther n, T. Sit*, H. Gracz*, M. Dolan, H. Townsend*, G. Liu, W. Newman*, P. Agris*, S. Lommel*

MeSH headings : Base Pairing; Base Sequence; Computer Simulation; Gene Expression Regulation, Viral; Macromolecular Substances; Models, Molecular; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; Promoter Regions, Genetic; RNA, Viral / chemistry; RNA, Viral / metabolism; Regulatory Sequences, Ribonucleic Acid; Tombusviridae / genetics; Transcription, Genetic
TL;DR: The RCNMV TA structural model is similar to those for the Simian retrovirus frameshifting element and the Human immunodeficiency virus-1 dimerization kissing hairpins, suggesting a conservation of form and function. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

The role of modifications in codon discrimination by tRNA(Lys) UUU

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 11(12), 1186–1191.

By: F. Murphy*, V. Ramakrishnan*, A. Malkiewicz* & P. Agris n

MeSH headings : Anticodon / chemistry; Anticodon / metabolism; Base Pairing; Codon / chemistry; Codon / genetics; Codon / metabolism; Crystallography, X-Ray; Models, Molecular; Nucleic Acid Conformation; RNA Stability; RNA, Transfer, Lys / chemistry; RNA, Transfer, Lys / genetics; RNA, Transfer, Lys / metabolism; Thermus thermophilus / chemistry; Thermus thermophilus / genetics
TL;DR: Crystal structures of modified tRNA anticodon stem-loops bound to the 30S ribosomal subunit with lysine codons in the A site allow the rationalization of how modifications in the anticodon loop enable decoding of both lysines codons AAA and AAG. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2003 journal article

Naturally-occurring modification restricts the anticodon domain conformational space of tRNA(Phe)

JOURNAL OF MOLECULAR BIOLOGY, 334(5), 901–918.

By: J. Stuart n, K. Koshlap n, R. Guenther n & P. Agris n

author keywords: methylation; anticodon dynamics; tRNA position 37; codon recognition; frameshifting
MeSH headings : Anticodon; Base Sequence; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular; Nucleic Acid Conformation; RNA, Transfer, Phe / chemistry
TL;DR: A comparison of the resulting structures indicates that modification of position 37 affects the accuracy of decoding and the maintenance of the mRNA reading frame by restricting anticodon loop conformational space. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2003 journal article

Using capillary electrophoresis to study methylation effect on RNA-peptide interaction

Acta Biochimica Polonica, 50(3), 857–864.

By: P. Mucha, A. Szyk, P. Rekowski & P. Agris

Source: NC State University Libraries
Added: August 6, 2018

2002 journal article

Accurate translation of the genetic code depends on tRNA modified nucleosides

JOURNAL OF BIOLOGICAL CHEMISTRY, 277(19), 16391–16395.

By: C. Yarian n, H. Townsend n, W. Czestkowski*, E. Sochacka*, A. Malkiewicz*, R. Guenther n, A. Miskiewicz*, P. Agris n

MeSH headings : Adenosine / analogs & derivatives; Adenosine / chemistry; Asparagine / chemistry; Base Pairing; Base Sequence; Codon; Genetic Code; Molecular Sequence Data; Nucleic Acid Conformation; Nucleosides / metabolism; Protein Biosynthesis; Protein Structure, Tertiary; RNA / metabolism; RNA, Messenger / metabolism; RNA, Ribosomal, 16S / metabolism; RNA, Transfer / metabolism; Ribosomes / metabolism; Thiouridine / analogs & derivatives; Thiouridine / chemistry; Uridine / analogs & derivatives; Uridine / chemistry
TL;DR: It is concluded that modified nucleosides evolved to modulate an anticodon domain structure necessary for many tRNA species to accurately translate the genetic code. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2002 journal article

Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding

NUCLEIC ACIDS RESEARCH, 30(21), 4751–4760.

By: K. Nobles n, C. Yarian n, G. Liu n, R. Guenther n & P. Agris n

MeSH headings : Base Sequence; Electrophoretic Mobility Shift Assay; Hydrogen Bonding; Lead / pharmacology; Magnesium / pharmacology; Models, Molecular; Nucleic Acid Conformation / drug effects; Nucleosides / chemistry; Nucleosides / metabolism; RNA Stability / drug effects; RNA, Fungal / chemistry; RNA, Fungal / genetics; RNA, Fungal / metabolism; RNA, Transfer, Phe / chemistry; RNA, Transfer, Phe / genetics; RNA, Transfer, Phe / metabolism; Ribonuclease T1 / metabolism; Thermodynamics
Source: Web Of Science
Added: August 6, 2018

2002 journal article

Identification and quantification of protecting groups remaining in commercial oligonucleotide products using monoclonal antibodies

ANALYTICAL BIOCHEMISTRY, 306(1), 135–143.

By: C. Fu n, S. Smith n, S. Simkins n & P. Agris n

author keywords: DNA; RNA; automated synthesis; protecting group detection; quality control
MeSH headings : Antibodies, Monoclonal / immunology; Antibody Specificity; Chromatography, High Pressure Liquid; DNA / chemistry; DNA / immunology; Enzyme-Linked Immunosorbent Assay; Immunoblotting / methods; Molecular Structure; Oligonucleotides / chemistry; Oligonucleotides / immunology; Quality Control; RNA / chemistry; RNA / immunology; Sensitivity and Specificity; Spectrum Analysis
TL;DR: Monoclonal antibodies selectively identify and quantify picomoles of remaining protecting groups on antisense therapeutics and oligonucleotide diagnostics. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2002 journal article

Interaction of RNA with phage display selected peptides analyzed by capillary electrophoresis mobility shift assay

RNA, 8(5), 698–704.

By: P. Mucha n, A. Szyk*, P. Rekowski*, R. Guenther n & P. Agris n

author keywords: anticodon stem and loop; capillary electrophoresis; methylated nucleoside-dependent RNA-peptide; interaction; phage display selected peptides; tRNA
MeSH headings : Amino Acid Sequence; Anticodon / chemistry; Anticodon / genetics; Anticodon / metabolism; Base Sequence; Electrophoresis, Capillary / methods; In Vitro Techniques; Molecular Sequence Data; Nucleic Acid Conformation; Peptide Library; Peptides / chemistry; Peptides / metabolism; RNA, Transfer, Phe / chemistry; RNA, Transfer, Phe / genetics; RNA, Transfer, Phe / metabolism
TL;DR: Capillary electrophoresis was found to be an efficient and sensitive method for the qualitative analysis of RNA/peptide interaction and should be generally applicable to the study of RNA- peptide (protein) interactions. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2002 personal communication

QC in antisense oligo synthesis

By: P. Agris, S. Smith, C. Fu & S. Simkins

Source: NC State University Libraries
Added: August 6, 2018

2001 journal article

Anticodon domain methylated nucleosides of yeast tRNA(Phe) are significant recognition determinants in the binding of a phage display selected peptide

BIOCHEMISTRY, 40(47), 14191–14199.

By: P. Mucha n, A. Szyk n, P. Rekowski n, P. Weiss n & P. Agris n

MeSH headings : Anticodon / antagonists & inhibitors; Anticodon / metabolism; Binding Sites; Cytidine / analogs & derivatives; Guanosine / analogs & derivatives; Models, Chemical; Nucleic Acid Conformation; Nucleosides / metabolism; Peptide Library; Peptides / metabolism; Protein Binding; RNA, Fungal / antagonists & inhibitors; RNA, Fungal / metabolism; RNA, Transfer, Phe / antagonists & inhibitors; RNA, Transfer, Phe / metabolism
TL;DR: Modifications as simple as methylations contribute identity elements that a selected peptide specifically recognizes in binding synthetic and native tRNA and in inhibiting tRNA aminoacylation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2000 journal article

Functional anticodon architecture of human tRNA(Lys3) includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t(6)A

BIOCHEMISTRY, 39(44), 13396–13404.

By: J. Stuart n, Z. Gdaniec n, R. Guenther n, M. Marszalek n, E. Sochacka n, A. Malkiewicz n, P. Agris n

MeSH headings : Adenosine / analogs & derivatives; Adenosine / chemistry; Adenosine / metabolism; Amino Acid Substitution; Anticodon / chemical synthesis; Anticodon / chemistry; Crystallography, X-Ray; Humans; Hydrogen Bonding; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular / methods; Nucleic Acid Conformation; Protein Binding; Pseudouridine / chemistry; RNA, Transfer, Lys / chemical synthesis; RNA, Transfer, Lys / chemistry; Ribosomal Proteins / chemistry; Thermodynamics; Threonine / chemistry; Threonine / metabolism
TL;DR: From these results, it is concluded that ribosome binding cannot simply be an induced fit of the anticodon stem and loop, otherwise the unmodified ASL(Lys3)(UUU) would bind as well as ASL (Lys 3)(UU U)-t(6)A(37), and the ionized carboxylic acid moiety of t(6), possibly neutralizes the positive charge of A(+)(38). (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2000 journal article

Modified constructs of the tRNA T Psi C domain to probe substrate conformational requirements of m(1)A(58) and m(5)U(54) tRNA methyltransferases

NUCLEIC ACIDS RESEARCH, 28(6), 1374–1380.

By: R. Sengupta n, S. Vainauskas, C. Yarian*, E. Sochacka, A. Malkiewicz, R. Guenther, K. Koshlap*, P. Agris*

MeSH headings : Animals; Escherichia coli / enzymology; Kinetics; Magnetic Resonance Spectroscopy; Methylation; Nucleic Acid Conformation; Nucleosides / chemistry; Nucleosides / genetics; Nucleosides / metabolism; RNA Stability; RNA, Transfer, Phe / chemical synthesis; RNA, Transfer, Phe / chemistry; RNA, Transfer, Phe / genetics; RNA, Transfer, Phe / metabolism; Substrate Specificity; Temperature; Tetrahymena pyriformis / enzymology; Thermodynamics; Yeasts / genetics; tRNA Methyltransferases / metabolism
TL;DR: It is reported that RAMT can recognize and methylate a TSL heptadecamer, and local conformation around U(54) was found to be an important determinant for the activities of both RAMT and RUMT. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2000 journal article

Modified nucleoside dependent Watson-Crick and wobble codon binding by tRNA(UUU)(Lys) species

BIOCHEMISTRY, 39(44), 13390–13395.

By: C. Yarian n, M. Marszalek n, E. Sochacka n, A. Malkiewicz n, R. Guenther n, A. Miskiewicz n, P. Agris n

MeSH headings : Adenosine / analogs & derivatives; Adenosine / chemistry; Anticodon / chemistry; Binding Sites; Humans; Nucleic Acid Conformation; Protein Binding; Pseudouridine / chemistry; RNA, Ribosomal, 16S / chemistry; RNA, Transfer, Lys / chemistry; Ribosomal Proteins / chemistry; Structure-Activity Relationship; Thermodynamics; Uridine / analogs & derivatives; Uridine / chemistry
TL;DR: The data suggest that tRNA(Lys)(UUU) species require anticodon domain modifications in the loop to impart an ordered structure to the anticodon for ribosomal binding to AAA and require a combination of modified nucleosides to bind AAG. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2000 journal article

Role of modified nucleosides of yeast tRNA(Phe) in ribosomal binding

CELL BIOCHEMISTRY AND BIOPHYSICS, 33(3), 241–252.

By: S. Ashraf*, R. Guenther n, G. Ansari n, A. Malkiewicz*, E. Sochacka* & P. Agris n

author keywords: tRNA(Phe); anticodon; ASL; nucleoside modification; ribosome
MeSH headings : Nucleosides / genetics; Nucleosides / metabolism; RNA, Fungal / genetics; RNA, Fungal / metabolism; RNA, Transfer, Phe / genetics; RNA, Transfer, Phe / metabolism; Ribosomes / metabolism; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism
TL;DR: Effective ribosome binding of tRNAPhe is a combination of anticodon stem stability and the correct architecture and dynamics of the anticodon loop, and 2′O-methylation of guanosine at wobble position 34 (Gm34) is identified as being responsible for the characteristically enhanced chemical reactivity of C1400 in Escherichia coli 16S rRNA upon ribosomal footprinting of yeast t RNAPhe. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2000 journal article

Synthesis and properties of uniquely modified oligoribonucleotides: Yeast tRNA(Phe) fragments with 6-methyluridine and 5,6-dimethyluridine at site-specific positions

NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, 19(3), 515–531.

By: E. Sochacka*, G. Czerwinska*, R. Guenther n, R. Cain n, P. Agris n & A. Malkiewicz*

MeSH headings : Anticodon; Magnetic Resonance Spectroscopy; Methylation; Molecular Conformation; Oligoribonucleotides / chemical synthesis; Oligoribonucleotides / chemistry; Organophosphorus Compounds / chemistry; RNA, Transfer, Phe / chemistry; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Uridine / analogs & derivatives; Uridine / chemistry; Yeasts / chemistry
TL;DR: Stability when the modified uridine is in a loop is sequence context dependent, and can not, at this time, be predicted from the location in the loop, but decrease in RNA duplex stability is predictable. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

1999 journal article

A distinctive RNA fold: The solution structure of an analogue of the yeast tRNA(Phe) T psi C domain

BIOCHEMISTRY, 38(27), 8647–8656.

By: K. Koshlap n, R. Guenther n, E. Sochacka n, A. Malkiewicz n & P. Agris n

MeSH headings : Anticodon / chemistry; Base Sequence; Crystallography, X-Ray; Models, Molecular; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular / methods; Nucleic Acid Conformation; Pseudouridine / chemistry; RNA, Fungal / chemistry; RNA, Transfer, Phe / chemistry; Saccharomyces cerevisiae / chemistry; Solutions; Uridine / analogs & derivatives; Uridine / chemistry
TL;DR: It is believed that the structure determined may represent an intermediate in the folding pathway during the maturation of tRNA, which has a considerable resemblance to the analogous domain in the crystal structure of the full-length yeast tRNAPhe. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

1999 patent

Antibacterial agents and methods of screening for the same

Washington, DC: U.S. Patent and Trademark Office.

By: P. Agris & S. Ashraf

Source: NC State University Libraries
Added: August 6, 2018

1999 journal article

Experimental models of protein-RNA interaction: Isolation and analyses of tRNA(Phe) and U1 snRNA-binding peptides from bacteriophage display libraries

JOURNAL OF PROTEIN CHEMISTRY, 18(4), 425–435.

By: P. Agris n, M. Marchbank*, W. Newman n, R. Guenther n, P. Ingram n, J. Swallow n, P. Mucha*, A. Szyk* ...

author keywords: phage peptide display library; peptide-RNA binding; tRNA; U1 snRNA
MeSH headings : Amino Acid Sequence; Anticodon; Bacteriophages; Base Sequence; Biotinylation; Circular Dichroism; Molecular Sequence Data; Nucleic Acid Conformation; Peptide Library; Peptides / chemistry; Peptides / metabolism; RNA, Small Nuclear / chemistry; RNA, Small Nuclear / metabolism; RNA, Transfer, Phe / chemistry; RNA, Transfer, Phe / metabolism; Spectrometry, Fluorescence
TL;DR: These methodologies demonstrate the feasibility of rapidly identifying, isolating, and initiating the analyses of small peptides that bind to RNAs in an effort to define better the chemistry, structure, and function of protein–RNA complexes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

1999 journal article

Orientation of the tRNA anticodon in the ribosomal P-site: Quantitative footprinting with U-33-modified, anticodon stem and loop domains

RNA, 5(9), 1191–1199.

By: S. Ashraf n, R. Guenther n & P. Agris n

author keywords: anticodon stem/loops; modified nucleosides; quantitative footprinting; ribosome
MeSH headings : Aldehydes / pharmacology; Anticodon / genetics; Antiviral Agents / pharmacology; Base Sequence; Butanones; Dose-Response Relationship, Drug; Genetic Techniques; Kinetics; Molecular Sequence Data; Mutagens / pharmacology; RNA, Fungal / genetics; RNA, Fungal / metabolism; RNA, Ribosomal, 16S / metabolism; RNA, Transfer / genetics; RNA, Transfer / metabolism; RNA, Transfer, Phe / metabolism; Ribosomes / genetics; Ribosomes / metabolism; Sulfuric Acid Esters / pharmacology; Temperature
TL;DR: Two residues, G926 and G1338, were afforded significantly greater protection by both yeast tRNA(Phe) and the ASL-U33 than other residues, such as A532, A794, C795, and A1339, which are important to efficient P-site binding of tRNA. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

1999 journal article

Single atom modification (O -> S) of tRNA confers ribosome binding

RNA, 5(2), 188–194.

By: S. Ashraf n, E. Sochacka*, R. Cain n, R. Guenther n, A. Malkiewicz* & P. Agris n

author keywords: 2-thiouridine; anticodon conformation; anticodon stem loop analogs; nucleoside modifications; ribosome; translation; tRNA(LyS)
MeSH headings : Aldehydes / metabolism; Anticodon / genetics; Butanones; Escherichia coli / metabolism; Humans; Magnetic Resonance Spectroscopy; Nucleic Acid Conformation; Nucleic Acid Denaturation / genetics; Nucleic Acid Hybridization / genetics; RNA, Fungal / genetics; RNA, Transfer, Lys / chemistry; RNA, Transfer, Lys / genetics; Ribosomes / metabolism; Spectrum Analysis; Temperature; Thiouridine / analogs & derivatives; Thiouridine / metabolism
TL;DR: It is concluded that s2U34 in tRNALysSUU and in other s2 U34-containing tRNAs is critical for generating an anticodon conformation that leads to effective codon interaction in all organisms. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

1999 journal article

Structural and functional roles of the N1-and N3-protons of Psi at tRNA's position 39

NUCLEIC ACIDS RESEARCH, 27(17), 3543–3549.

By: C. Yarian n, M. Basti*, R. Cain n, G. Ansari n, R. Guenther n, E. Sochacka*, G. Czerwinska*, A. Malkiewicz*, P. Agris*

MeSH headings : Anticodon / chemistry; Genes, Fungal / genetics; Magnetic Resonance Spectroscopy; Nucleic Acid Conformation; Protons; Pseudouridine / chemistry; RNA, Ribosomal, 16S / chemistry; RNA, Transfer, Phe / chemistry; Ribosomes / chemistry; Structure-Activity Relationship; Temperature; Thermodynamics; Uridine / chemistry; Yeasts / genetics
Source: Web Of Science
Added: August 6, 2018

1999 journal article

The uridine in "U-turn": Contributions to tRNA-ribosomal binding

RNA, 5(4), 503–511.

By: S. Ashraf n, G. Ansari n, R. Guenther n, E. Sochacka*, A. Malkiewicz* & P. Agris n

author keywords: anticodon conformation; anticodon stem loop analogs; ASL; nucleoside modifications; ribosome; translation; tRNA(Phe) U-turn
MeSH headings : Anticodon / chemistry; Anticodon / genetics; Humans; Models, Molecular; Molecular Structure; Nucleic Acid Conformation; Nucleic Acid Denaturation; RNA, Fungal / chemistry; RNA, Fungal / genetics; RNA, Transfer, Phe / chemistry; RNA, Transfer, Phe / metabolism; Ribosomes / genetics; Ribosomes / metabolism; Temperature; Uridine / chemistry; Uridine / genetics
TL;DR: The results demonstrate that proton donations by the N3-H and 2'OH groups of U33 are not absolutely required for ribosomal binding, and suggest that the overall uridine conformation, including a dynamic (C3'-endo > C2'-endo) sugar pucker, anti-conformation, and ability of uracil to stack between C32 and A35-phosphate, are the contributing factors to a functional U-turn. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

1999 journal article

Thermodynamic contribution of nucleoside modifications to yeast tRNA(Phe) anticodon stem loop analogs

Acta Biochimica Polonica, 46(1), 163–172.

By: P. Agris, R. Guenther, E. Sochacka, W. Newman, G. Czerwinska, G. Liu, W. Ye, A. Malkiewicz

Source: NC State University Libraries
Added: August 6, 2018

1998 journal article

Modified RNAs as potential drug targets

Acta Biochimica Polonica, 45(1), 13–18.

By: R. Guenther, B. Forrest, W. Newman, A. Malkiewicz & P. Agris

Source: NC State University Libraries
Added: August 6, 2018

1997 conference paper

Ribosomal binding of modified tRNA anticodons related to thermal stability

Symposium on RNA Biology II. RNA: Tool and Target (1997: North Carolina Biotechnology Center) Research Triangle Park, North Carolina, USA, October 17-19, 1997 (Nucleic acids symposium series; no. 36), 36, 58–60. Oxford: Oxford University Press.

By: S. Ashraf, R. Guenther, W. Ye, Y. Lee, A. Malkiewicz & P. Agris

Source: NC State University Libraries
Added: August 6, 2018

1997 journal article

Unconventional structure of tRNA(Lys)SUU anticodon explains tRNA's role in bacterial and mammalian ribosomal frameshifting and primer selection by HIV-1

RNA, 3(4), 420–428.

By: P. Agris, R. Guenther, P. Ingram, M. Basti, J. Stuart, E. Sochacka, A. Malkiewicz

Source: NC State University Libraries
Added: August 6, 2018

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