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Results for “peptide nucleic acid”

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At least 19 recordsLinked to original sources
PubMed2026

Dual recognition drives site-directed G-quadruplex stabilization: Oligonucleotide design in G4 ligand-oligonucleotide conjugates.

G-quadruplex (G4) DNA structures are increasingly recognized for their roles in transcriptional regulation and genome stability, making them attractive therapeutic targets. Selective recognition of individual G4s remains challenging due to the high structural similarity among G4 motifs. G4 Ligand-Oligonucleotides conjugates (GL-Os) address this challenge by combining small-molecule G4 ligands with the sequence specificity of oligonucleotides, targeting sequences flanking the intended G4 target. Here, we systematically investigate how oligonucleotide length, backbone composition, and sequence complementarity govern GL-O binding, selectivity, and G4 stabilization. We show that effective G4 recognition depends on the interdependence between oligonucleotide hybridization and G4 ligand binding, such that both elements cooperatively reinforce complex stability and site specificity. Longer oligonucleotides promote more stable complexes and stronger G4 stabilization, whereas central mismatches disrupt this dual-recognition mechanism. Replacement of DNA with peptide nucleic acids (PNAs) enhances binding strength, thermal stability, and metabolic stability. Importantly, ligand conjugation redirects PNA oligonucleotides from nonspecific polymerase stalling toward selective G4 stabilization. Finally, we demonstrate receptor-mediated cellular uptake of modified GL-Os, supporting the feasibility of cellular delivery while highlighting remaining delivery barriers. Together, these findings show the molecular design principles governing GL-O behavior and provide a foundation for the future development and evaluation of selective G4-targeting therapeutics.

G-quadruplex DNA↗
PubMed2025

DescribePROT Database of Residue-Level Protein Structure and Function Annotations.

DescribePROT is a freely available online database of structural and functional descriptors of proteins at the amino acid level. It provides access to 13 diverse descriptors that include sequence conservation, putative secondary structure, solvent accessibility, intrinsic disorder, and signal peptides, and putative annotations of residues that interact with proteins, peptides and nucleic acids. These data can be used to elucidate protein functions, to support efforts to develop therapeutics, and to develop and evaluate future predictors of protein structure and function. DescribePROT includes 7.8 billion predictions for 1.4 million proteins from 83 complete proteomes of popular model organisms. This information can be downloaded at multiple levels of scope (entire database, specific organisms, and individual proteins) and can be interacted with using a graphical interface that simultaneously displays data on multiple descriptors. We describe the contents of this resource, provide directions on how to use its interface, and offer instructions on how to obtain and interact with the underlying data. Moreover, we briefly discuss plans for a future expansion of this database. DescribePROT is available at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/ .

Databases, Protein↗
PubMed1977

Specific recognition of single-stranded nucleic acids. Interaction of tryptophan-containing peptides with native, denatured, and ultraviolet-irradiated DNA.

The binding of the tripeptide Lys-Trp-Lys to native, denatured, and ultraviolet-irradiated DNAs has been investigated by fluorescence spectroscopy. Two types of complexes are formed which both involve electrostatic interactions. Only one of them involves a stacking of the tryptophyl ring with nucleic acid bases. Quantitative analysis of fluorescence data shows that this stacking interaction is strongly favored in denatured as compared to native DNA. In ultraviolet-irradiated DNA, the peptide Lys-Trp-Lys binds selectively to unpaired regions around thymine dimers. Due to the stacking interaction of the aromatic amino acid with nucleic acid bases, this simple tripeptide is therefore able to discriminate between single-stranded and double-stranded regions in a nucleic acid.

Animals↗
PubMed2026

Initiation of Hybrid Polyketide-Nonribosomal Peptide Biosynthesis via Two Distinct Pathways in C. elegans.

Nemamide A and B are hybrid polyketide-nonribosomal peptides that are produced by the PKS-1-NRPS-1 enzymatic assembly line in the canal-associated neurons (CANs) of the nematode Caenorhabditis elegans. These signaling molecules promote survival during and recovery from starvation-induced larval arrest. Here, using genome editing and targeted metabolomics, we probed the roles of the different domains of PKS-1 in the initiation of nemamide biosynthesis. We showed that the first four domains of PKS-1 are not required for the biosynthesis of the triene-containing nemamide A, but are required for the biosynthesis of the tetraene-containing nemamide B. By targeting genes that are highly expressed in the CANs, we identified two additional enzymes that participate in the biosynthetic pathway: the peroxisomal carnitine O-octanoyl transferase CROT-1, which is required for the biosynthesis of nemamide A, and the enoyl-CoA hydratase ECH-7, which is required for the biosynthesis of nemamide B. We heterologously expressed CROT-1 and showed that it prefers hexanoyl-CoA and octanoyl-CoA as substrates, converting them to the corresponding carnitine esters. According to our model, ECH-7 is needed to supply the starter unit for nemamide B biosynthesis, which is loaded onto the first carrier protein of PKS-1 and extended by the first module, thereby installing the double bond that is unique to nemamide B. Meanwhile, CROT-1 is needed to supply the starter unit for nemamide A biosynthesis, which is loaded onto the second carrier protein of PKS-1. Our data suggest that the biosynthetic pathways of nemamide A and B are under the control of two different initiation mechanisms and, thus, that the production of these two secondary metabolites may be independently regulated.

Animals↗
PubMed2026

Nerpa 2: probabilistic linking of biosynthetic gene clusters to nonribosomal peptides.

MOTIVATION: Nonribosomal peptides (NRPs) are bioactive microbial metabolites with high pharmaceutical potential. Although genome mining enables large-scale detection of biosynthetic gene clusters (BGCs) predicted to encode NRPs, reliably linking these clusters to their chemical products remains challenging due to the flexible and heterogeneous organization of NRP assembly pathways. RESULTS: We present Nerpa 2, a probabilistic framework for accurate and scalable linking of NRP BGCs to candidate chemical structures. The method represents assembly lines as hidden Markov models (HMMs) that capture uncertainty and alternative biosynthetic routes. On curated datasets of experimentally validated BGC-product pairs, our tool outperforms existing methods in linking accuracy and pathway reconstruction. When applied to large genome mining datasets, Nerpa 2 efficiently identifies BGCs likely associated with known compounds and highlights potential producers of novel chemistry. AVAILABILITY AND IMPLEMENTATION: Nerpa 2 is freely available at https://github.com/gurevichlab/nerpa.

Multigene Family↗
PubMed1979

Specific thymic peptides-DNA interaction. Correlation with the possible stereochemical kinking scheme of DNA.

Low molecular weight peptides from calf thymus cause a strong dose-dependent stabilization of the DNA. The strength od DNA-peptide interaction is pH-dependent and decreases repidly above pH 6.5. Moreover the complete kinetics of DNA denaturation and renaturation demonstrates that the peptide fraction increases significantly the DNA renaturation mostly at low temperature, showing that the interaction DNA-thymic effector helps the recombination of complementary DNA segments. The DNA stabilization rate by the peptide fraction is comparable to that obtained by means of high concentration of histones or synthetic polycationic peptides. However, the lack of basic amino acids in the peptide structure is not in favor of strong electrostatic interactions and implies a specific binding of peptide to DNA. The possible correlation of the specific thymic peptides-DNA interaction with the stereochemical kinking scheme of DNA is discussed.

Chemical Phenomena↗
PubMed1979

Regulation of protein synthesis in rat ventral prostate: cell-free translation of mRNA.

Androgenic steroids regulate both a class of abundant poly(A)-containing RNA and four major proteins secreted by the rat ventral prostate. That this class of RNA was mRNA coding for the major proteins was demonstrated by translating total poly(A)-containing RNA in a wheat-germ cell-free system and using the technique of hybrid arrested translation. RNA alone resulted in the synthesis of four major translation products, whereas RNA hybridized with DNA complementary to the class of abundant poly(A)-containing RNA failed to direct their cell-free synthesis. The synthesis of the polypeptides was androgen dependent, but their relative mobilities on denaturing acrylamide gels were not identical to those of the polypeptides synthesized in whole cells. Because these polypeptides are secreted to form part of the prostatic fluid, the possibility that the immediate translation products are precursors to the polypeptides was investigated. Prostatic RNA, translated in an L-cell cell-free system supplemented with microsomal membranes isolated from dog pancreas and rat prostate, caused the appearance of four translation products with relative mobilities similar to those of the androgen-dependent polypeptides synthesized in whole cells. The relationship of one of the polypeptides synthesized in minced tissue with the immediate translation products and processed polypeptides was further investigated by tryptic peptide fingerprint analysis, which revealed identical peptide maps.

Animals↗
PubMed1978

Relationship of San Miguel sea lion virus to other members of the calicivirus group.

San Miguel sea lion virus (SMSV) is indistinguishable from vesicular exanthema virus (VEV) and feline calicivirus (FCV) in its morphology and in possessing a single capsid polypeptide with a molecular weight of approximately 65 X 10(3). Neutralization tests readily differentiate the three viruses, but immunodiffusion tests show that SMSV is closely related serologically to VEV but not to FCV. Although the RNAs of the three caliciviruses have similar base compositions, homology tests show that SMSV is closely related to VEV but is not related to FCV. Tryptic peptide maps of the single major polypeptide comprising the capsid of each virus also show that SMSV and VEV are more closely related to each other than to FCV.

Animals↗
PubMed1978

Bacillus subtilis bacteriophages SP82, SPO1, and phie: a comparison of DNAs and of peptides synthesized during infection.

The genomes of Bacillus subtilis phages phie, SPO1, and SP82 were compared by DNA-DNA hybridization, analysis of DNA fragments produced by digestion with restriction endonucleases, comparison of the arrays of peptides synthesized during infection, and phage neutralization. DNA-DNA hybridization experiments indicated that about 78% of the SP82 DNA was homologous with SPO1 DNA, whereas 40% of the phie DNA was homologous to either SPO1 or SP82 DNA. Agarose gel electrophoresis was used to compare the molecular weights of DNA fragments produced by cleavage of SP82, SPO1, and phie DNAs with the restriction endonucleases Hae III, Sal I, Hpa II, and Hha I. Digestion of the DNAs with Hae III and Sal I produced only a few fragments, whereas digestion with Hpa II and Hha I yielded 29 to 40 fragments, depending on the DNA and the enzyme. Comparing the Hpa II fragments, 51% of the SP82 fragments had mobilities which matched those of SPO1 fragments, 32% of the SP82 fragments matched the phie fragments, and 34% of the SPO1 fragments matched the phie fragments. Comparing the Hha I digestion products, 62% of the SP82 fragments had mobilities matching the SPO1 fragments, 24% of the SP82 fragments matched the phie fragments, and 22% of the SPO1 fragments matched the phie fragments. Analysis of peptides by electrophoresis on one-dimensional sodium dodecyl sulfate-polyacrylamide slab gels showed that approximately 70 phage-specific peptides were synthesized in the first 24 min of each infection. With mobility and the intervals of synthesis as criteria, 66% of the different SP82 peptides matched the SPO1 peptides, 34% of the SP82 peptides matched the phie peptides, and 37% of the SPO1 peptides matched the phie peptides. Phage neutralization assays using antiserum to SP82 yielded K values of 510 for SP82, 240 for SPO1, and 120 for phie.

Bacillus subtilis↗
PubMed1977

Purification of immunoglobulin heavy chain messenger RNA by immunoprecipitation from the mouse myeloma tumor, MOPC-31C.

Immunoglobulin heavy chain mRNA was purified from immunoprecipitated polysomes derived from the mouse myeloma tumor, MOPC-31C. The purified mRNA migrated predominantly as a single band upon polyacrylamide gel electrophoresis in 98% formamide and the molecular weight of this mRNA was calculated to be 700,000. This mRNA was as active as the purified light chain mRNA when it was employed as a template in a cell-free protein synthesizing system from wheat germ. The translation product had a molecular weight of 55,000 daltons, and migrated slightly faster than mature heavy chain upon polyacrylamide gel electrophoresis in sodium dodecylsulfate. The protein synthesized by the direction of this mRNA was shown to yield tryptic peptides corresponding to those derived from the mature heavy chain protein except that one missing peptide was replaced by another additional peptide. DNA complementary to the mRNA was synthesized by RNA-dependent DNA polymerase from avian myeloblastosis virus. Hybridization kinetic analysis between the heavy chain mRNA and its complementary DNA indicated that the RNA was essentially homogenous with rabbit globin mRNA as a standard.

Animals↗
PubMed1976

Relationships between intracisternal type A and extracellular oncornavirus-like particles produced in murine MOPC-460 myeloma cells.

Oncornavirus-like particles of the "A" (both intracisternal and intracytoplasmic) and "B" or "C" (extracellular) types are produced by murine MOPC-460 myeloma cells. This communication describes a comparative study on tracisternal A and extracellular particles. Both types of particles contain an RNA-dependent DNA polymerase activity, traces of 35S and 70 S RNA in addition to larger amounts of degraded RNA, and proteins of approximately 76,000 and 45, 000 daltons. The 76,000-dalton proteins from intracisternal A and extracellular particles have the same cyanogen bromide peptides. Hybridization kinetic analysis indicates that the RNAs in the two particles are identical or very closely related and share partial homology with Moloney leukemia virus RNA. In contrast, the particles appear to have little or no relationship to murine mammary tumor virus as judged by several different criteria. Electron microscope studies indicate that the extracellular particles arise from the budding of core components through the plasma membrane. These results suggest that the intracisternal A and extracellular oncornavirus-like particles produced by MOPC-460 cells are closely related.

Animals↗
PubMed1978

The peptide chain elongation factor genes tufA and fus of Escherichia coli are intimately related physically.

Recent work from several laboratories has established the following points about the synthesis of the polypeptide chain elongation factors Tu and G in Escherichia coli. (i) Elongation factor Tu is the product of duplicate, highly conserved genes, tufA and tufB, which are widely separate parts of the chromosome. (ii) The molar concentration of this factor is considerably higher than that of elongation factor G which is encoded by the fus gene. (iii) Although the tufA and fus genes are close together and can be co-transcribed in the direction from fus to tufA, the tufA gene product is synthesized at several times the rate of the fus gene product. In an attempt to understand what mechanism(s) could account for the differential expression of the tufA and fus genes, we sought to obtain more precise information on the physical relationship of these genes. By examining heteroduplexes between restriction endonuclease-generated fragments of DNA containing the tufA, fus, and tufB genes, we have demonstrated that the fus and tufA genes are intimately related physically in one of two possible arrangements. Either the NH2-terminal region of the tufA gene is contiguous with the COOH-terminal region of the fus gene or the beginning of the tufA gene overlaps part of the fus gene. These results mean that if the tufA gene is always co-transcribed with the fus gene, then some mechanism must allow the tufA portion of the transcript to be translated more often than the fus gene portion of the transcript.

DNA, Bacterial↗