Chemokines I: R&D Systems
5. Upon exposure of gp41 to the macrophage cell membrane, allowing passage of viral nucleic acid into macrophage cytoplasm ( ... 3. Following binding to CD4, plus a change in gp120 conformation, V3 region binds to CKR5. 4. gp120 "dissociates" from gp41, ... One group of the CXC chemokines have the characteristic three amino acid sequence ELR (glutamic acid-leucine-arginine) motif ... showing only one amino acid substitution between the human and mouse proteins. SDF-1 amino acid sequence also shows equal ...
David H. Mathews, M.D., Ph.D. | UR Medicine
The influence of locked nucleic acid residues on the thermodynamic properties of 2-O-methyl RNA/RNA heteroduplexes.. Kierzek ... Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice ... Predicting oligonucleotide affinity to nucleic acid targets.. Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH ... NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.. Turner DH, ...
Structural basis for mismatch surveillance by CRISPR-Cas9 | Nature
Although the canonical kinked guide RNA-DNA duplex conformation facilitates DNA cleavage, we observe that substrates that ... We observed a distinct, linear conformation of the guide RNA-DNA duplex formed in the presence of mismatches, which prevents ... This unusual nucleic acid conformation is stabilized by RuvC and appears to facilitate the binding of this mismatch. The ... Nucleic acid preparation. DNA duplexes (55 nt) were prepared from PAGE-purified oligonucleotides synthesized by Integrated DNA ...
A novel model of molnupiravir against SARS-CoV-2 replication: accumulated RNA mutations to induce error catastrophe | Signal...
The conformations of protein and nucleic acid did not differ significantly between the two structures or from the corresponding ... 3) Favipiravir, a purine nucleic acid analog, could mimics the purines G and A to form non-canonical base pairs and has also ... RNA-dependent RNA polymerase (RdRp), also known as nsp12, is a key component in the synthesis of viral ribonucleic acid (RNA) ... conformations in the structures of RdRp complexed to wild-type or remdesivir-containing RNA. Modeling of M-A or M-G base pairs ...
Publications - Robert Craigie, Ph.D. - NIDDK
Nucleic Acids Res (2011 Nov 1) 39:9009-22. Abstract/Full Text. No interaction of barrier-to-autointegration factor (BAF) with ... FRET analysis reveals distinct conformations of IN tetramers in the presence of viral DNA or LEDGF/p75.. Kessl JJ, Li M, ... Selection of 2-Deoxy-2-Fluoroarabino Nucleic Acid (FANA) Aptamers That Bind HIV-1 Integrase with Picomolar Affinity.. Rose KM ...
Structural Studies Bibliography from Ned Seeman's Laboratory
In: Structure and Conformations of Nucleic Acids and Protein-Nucleic Acid Interactions, ed by M. Sundaralingam and S.T. Rao, ... N.C. Seeman, Single Crystal Crystallography for Nucleic Acid Structural Studies. In: Geometry and Dynamics of Nucleic Acids, ed ... N.C. Seeman, J.L. Sussman, H.M. Berman and S.-H. Kim, Nucleic Acid Conformation: The Crystal Structure of a Naturally Occurring ... S.-H. Kim, H.M. Berman, N.C. Seeman and M.D. Newton, Seven Basic Conformations of Nucleic Acid Structural Units. Acta ...
Frontiers | Human Virus Genomes Are Enriched in Conserved Adenine/Thymine/Uracil Multiple Tracts That Pause Polymerase...
We have previously shown that human virus genomes are enriched in G-rich sequences that fold in four-stranded nucleic acid ... which include DNA or RNA in single-stranded or double-stranded conformations. This heterogeneity improves the possible ... We have previously shown that human virus genomes are enriched in G-rich sequences that fold in four-stranded nucleic acid ... This work expands on the presence and mechanism of nucleic acid secondary structures in human viruses and provides a new ...
Program Publications: Texas A&M University: Comprehensive Tools and Models for Addressing Exposure to Mixtures During...
Nucleic Acids Res 48:1800-1810. doi:10.1093/nar/gkz1172 PMID:31930333 PMCID:PMC7039002 ... Estrogen-induced transcription at individual alleles is independent of receptor level and active conformation but can be ... Using multidimensional separations to distinguish isomeric amino acid-bile acid conjugates and assess their presence and ... Circulating short-chain fatty acids in preterm birth: A pilot case-control study. Reprod Sci 27(5):1181-1186. doi:10.1007/ ...
An antitumor drug-induced topoisomerase cleavage complex blocks a bacteriophage T4 replication fork in vivo.
National Institute of Environmental Health Sciences: Selected Publications
Nucleic acids research, 35(17):e112, 2007.]. *McKenna, C.E., Kashemirov B.A., Upton T.G., Batra V.K., Goodman M.F., Pedersen L. ... Abstract Batra, V.K., Beard, W.A., Hou, E.W., Pedersen, L.C., Prasad, R., and Wilson, S.H. Mutagenic conformation of 8-oxo-7,8- ... Nucleic Acids Research 40: 2974-2983, 2012.. ]. *Batra, V.K., Shock, D.D., Beard,W.A., McKenna, Charles E. and Wilson, S.H. ... Nucleic acids research, 37(19):e128, 2009.]. *Yoshizawa, K., Jelezcova E., Brown A.R., Foley J.F., Nyska A., Cui X., Hofseth L ...
NIOSHTIC-2 Search Results - Full View
This reaction is sterically prohibited for the B form DNA conformation. If, however, the nucleic acid structure is deformed, ... It was not possible to uniquely identify the preferred transition-state complex with respect to nucleic acid structure or ... In one, I was located "outside" the nucleic acid structure; in the other geometry, I was intercalated between adjacent base ... Terms: DNA or Deoxyribonucleic acid OR DNA or Deoxyribonucleic acid 578 - 578 of 587 Bibliographic entries ...
Biophysics and Physicobiology
The VUVCD spectra of nucleic acids confirm the contributions of the base composition and sequence to the conformation in ... In the CG-MD-SAXS method, the scattering factors of CG particles for proteins and nucleic acids are evaluated using high- ... A variation of a single amino acid in the amino acid sequence of ABC transporter has been known to be linked with certain ... Therefore, we confirmed the hydration of amino acid residues in the protein unfolding of Cyt c by estimating ΔVu, which allows ...
Scientists Emeriti | NICHD - Eunice Kennedy Shriver National Institute of Child Health and Human Development
Hatter's Library
NMR spectroscopic analysis of the DNA conformation induced by the human testis determining factor SRY - PubMed
The conformation of an eight base pair DNA oligonucleotide duplex bound to the human testis determining factor SRY and the ... Nucleic Acid Conformation Actions. * Search in PubMed * Search in MeSH * Add to Search ... NMR spectroscopic analysis of the DNA conformation induced by the human testis determining factor SRY M H Werner 1 , M E ... NMR spectroscopic analysis of the DNA conformation induced by the human testis determining factor SRY M H Werner et al. ...
U Deva Priyakumar
The ability of the DNA strand in the hybrid duplex to sample conformations corresponding to typical A- and B-type nucleic acids ... Details of key interactions found at the interface of enzyme-nucleic acid complex that are responsible for its stability are ... catalysis to cleave nucleic acids. Long timescale molecular dynamics simulations have been performed on the 𝐵ℎRNase H-DNA-RNA ...
IUCr) Overview of refinement procedures within REFMAC5: utilizing data from different sources
Chemical restraints encapsulate chemical information about the constituent blocks (e.g. amino acids, nucleic acids, ligands) of ... These restraints help to maintain structural integrity of the main-chain conformation at low resolution (3-5 Å). ProSMART can ... Xin, Y. & Olson, W. K. (2009). Nucleic Acids Res. 37, D83-D88. Web of Science CrossRef PubMed CAS Google Scholar. Zweckstetter ... Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Nucleic Acids Res. 25 ...
ENGINEERING OF AN EXTRACELLULAR RIBONUCLEASE BY GENE MODIFICATION | | Project | Fact sheet | FP1 | CORDIS | European Commission
Molecular modelling was used to help interpret data on protein nucleic acid interactions and catalysis, and contributions of ... Mutations were also used as reporter groups in kinetic studies of protein folding to provide information on the conformation of ... Parameters of the enzyme catalyzed reaction were determined for short nucleotides and ribonucleic acid (RNA) substrates, and ...
Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein<...
Nucleic Acid Conformation Medicine & Life Sciences 39% * Oligonucleotide Chemical Compounds 35% View full fingerprint ... Fluorescence lifetime-based analyses of the DNA conformations suggest that free NPOM-DNA retains B-DNA-like conformations ... Fluorescence lifetime-based analyses of the DNA conformations suggest that free NPOM-DNA retains B-DNA-like conformations ... Fluorescence lifetime-based analyses of the DNA conformations suggest that free NPOM-DNA retains B-DNA-like conformations ...
Huddersfield Repository - University of Huddersfield
In addition the nucleic acid hybridisation properties of a thymidyl-pentamer, T5-POM, with an N-terminal phthalimide group were ... Molecular modelling reveals that the lowest energy conformation of a thymidyl-POM monomer is similar to the conformation ... Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide ... Design, synthesis, conformational analysis and nucleic acid hybridisation properties of thymidyl pyrrolidine-amide ...
DeCS
Conformation, Nucleic Acid Conformations, Nucleic Acid Nucleic Acid Conformations RNA Conformation - Narrower Concept UI. ... Conformation, Nucleic Acid. Conformation, RNA. Conformations, DNA. Conformations, Nucleic Acid. Conformations, RNA. DNA ... DNA Conformations. Nucleic Acid Conformations. RNA Conformation. RNA Conformations. Tree number(s):. G02.111.570.820.486. ... Nucleic Acid Conformation - Preferred Concept UI. M0015048. Scope note. The spatial arrangement of the atoms of a nucleic acid ...
Refs2200-2299
Proteins Nucleic Acids 1(1995):235-242.. 2254. P.S. Eder, R.J. DeVine, J.M. Dagle, J.A. Walder, "Substrate specificity and ... T.J. Thomas, N.L. Meryhew, R.P. Messner, "DNA sequence and conformation specificity of lupus autoantibodies. Preferential ... Nadrian C. Seeman, "Nucleic acid junctions and lattices," J. Theor. Biol. 99(1982):237-247; Nadrian C. Seeman et al, "New ... J.S. Hanas, C.G. Gunn, "Inhibition of transcription factor IIIA-DNA interactions by xenobiotic metal ions," Nucleic Acids Res. ...
Code System Concept
MeSH Browser
Nucleic Acid Conformation Preferred Concept UI. M0015048. Scope Note. The spatial arrangement of the atoms of a nucleic acid or ... Carbohydrate Conformation [G02.111.570.820.235] * Nucleic Acid Conformation [G02.111.570.820.486] * Base Pairing [G02.111. ... DNA Conformation RNA Conformation NLM Classification #. QU 58. Previous Indexing. Nucleic Acids (1966-1971). See Also. ... Nucleic Acid Conformation Preferred Term Term UI T028818. Date01/01/1999. LexicalTag NON. ThesaurusID NLM (1972). ...
MeSH Browser
Nucleic Acid Conformation Preferred Concept UI. M0015048. Scope Note. The spatial arrangement of the atoms of a nucleic acid or ... Carbohydrate Conformation [G02.111.570.820.235] * Nucleic Acid Conformation [G02.111.570.820.486] * Base Pairing [G02.111. ... DNA Conformation RNA Conformation NLM Classification #. QU 58. Previous Indexing. Nucleic Acids (1966-1971). See Also. ... Nucleic Acid Conformation Preferred Term Term UI T028818. Date01/01/1999. LexicalTag NON. ThesaurusID NLM (1972). ...
Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase | eLife
... during which a key metastable conformation is predicted and verified by single-molecule measurements. ... how these enzymes change conformations and how transitions between different conformational states regulate nucleic acid ... 2007) Structure and mechanism of helicases and nucleic acid translocases Annual Review of Biochemistry 76:23-50. ... All the structures belonging to the apo state are without nucleic acids bound. The structure in the tilted cluster only has ...
Inhibition of HCV translation by disrupting the structure and interactions of the viral CRE and 3' X-tail - White Rose...
Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the ... We demonstrate that LNAs which block formation of the closed conformation inhibit genome translation. Inhibition was at least ... Using a combination of site-directed mutagenesis and locked nucleic acids (LNA) complementary to defined domains of SL9266 and ... Previous studies demonstrated that SL9266/PK is dynamic, with open and closed conformations predicted to have distinct ...