ABSTRACT
Conformational flexibility in nucleic acids provides a basis for complex structures, binding, and signaling. One-base bulges directly neighboring single-base mismatches in nucleic acids can be present in a minimum of two distinct conformations, complicating the examination of the thermodynamics by calorimetry or UV-monitored melting techniques. To provide additional information about such structures, we demonstrate how electron paramagnetic resonance (EPR) active spin-labeled base analogues, base-specifically incorporated into the DNA, are monitors of the superposition of different bulge-mismatch conformations. EPR spectra provide information about the dynamic environments of the probe. This information is cast in terms of "dynamic signatures" that have an underlying basis in structural variations. By examining the changes in the equilibrium of the different states across a range of temperatures, the enthalpy and entropy of the interconversion among possible conformations can be determined. The DNA constructs with a single bulge neighboring a single-base mismatch ("bulge-mismatches") may be approximately modeled as an equilibrium between two possible conformations. This structural information provides insight into the local composition of the bulge-mismatch sequences. Experiments on the bulge-mismatches show that basepairing across the helix can be understood in terms of purine and pyrimidine interactions, rather than specific bases. Measurements of the enthalpy and entropy of formation for the bulge-mismatches by differential scanning calorimetry and UV-monitored melting confirm that the formation of bulge-mismatches is in fact more complicated than a simple two-state process, consistent with the base-specific spectral data that bulge-mismatches exist in multiple conformations in the premelting temperature region. We find that the calculations with the nearest-neighbor (NN) model for the two likely conformations do not correlate well with the populations of structures and thermodynamic parameters inferred from the base-specific EPR dynamics probe. We report that the base-specific spin probes are able to identify a bistable, temperature dependent, switching between conformations for a particular complex bulged construct.
Subject(s)
DNA/chemistry , Electron Spin Resonance Spectroscopy/methods , Base Sequence , Calorimetry, Differential Scanning/methods , Hot Temperature , Models, Chemical , Models, Statistical , Molecular Conformation , Molecular Sequence Data , Nucleic Acid Conformation , Spectrophotometry, Ultraviolet/methods , Temperature , ThermodynamicsABSTRACT
We report that the monolayer phase diagram for binary mixtures of dimyristoylphosphatidylethanolamine (DMPE) and dihydrocholesterol (DChol) is largely unchanged when each phospholipid molecule is replaced by two myristic acid (MA) molecules or various mixtures of the lysophospholipid and myristic acid. The corresponding phase diagrams all show the formation of "condensed complexes" of DChol and lipid. The condensed complex stoichiometry is thus largely determined by the C14 fatty acid acyl chains, in this case about 4-4.6 per DChol molecule.
Subject(s)
Cholesterol/chemistry , Fatty Acids/chemistry , Phospholipids/chemistry , Cholestanol/chemistry , In Vitro Techniques , Lipid Bilayers/chemistry , Lysophospholipids/chemistry , Membrane Lipids/chemistry , Molecular Structure , Myristic Acid/chemistry , Phosphatidylethanolamines/chemistryABSTRACT
Electron paramagnetic resonance (EPR) spectroscopy was used to investigate changes in dynamics of spin-labeled nucleotides in the TAR RNA (U23, U25, U38, and U40) upon binding to cations, argininamide, and two peptides derived from the Tat protein. Nearly identical changes in dynamics were obtained for either calcium or sodium ions, indicating the absence of a calcium-specific structural change for the TAR RNA in solution that had previously been suggested by crystallographic data. Similar dynamic signatures were obtained for two Tat-derived peptides that have the same important binding determinant (R52) and similar binding affinities to the TAR RNA. However, U23 and U38 were substantially less mobile for the wild-type peptide (YGRKKRRQRRR) than for the mutant (YKKKKRKKKKA), demonstrating that, flanking R52, amino acids in the wild-type sequence make specific contacts to the RNA.
Subject(s)
Arginine/analogs & derivatives , Cations/metabolism , Gene Products, tat/metabolism , HIV Long Terminal Repeat , HIV-1/chemistry , RNA, Viral/chemistry , RNA-Binding Proteins/chemistry , Arginine/metabolism , Calcium/metabolism , Electron Spin Resonance Spectroscopy , HIV-1/genetics , HIV-1/metabolism , Nucleic Acid Conformation , Peptide Fragments , RNA, Viral/genetics , RNA, Viral/metabolism , RNA-Binding Proteins/metabolism , Sodium/metabolism , Transcriptional Activation , tat Gene Products, Human Immunodeficiency VirusABSTRACT
An important component of protein-DNA recognition is the charge neutralization of DNA backbone phosphates and subsequent protein-induced DNA bending. Replacement of phosphates by neutral methylphosphonates has previously been shown to be a model for protein-induced bending. In addition to bending, the neutralization process may change the inherent flexibility of the DNA--a feature never before tested. We have developed a method to measure the differential flexibility of duplex DNA when methylphosphonate substitutions are made and find that the local flexibility is increased up to 40%. These results imply that backbone-neutralization-dependent DNA flexibility augments DNA-binding motifs in protein-DNA recognition processes.
