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1.
RNA ; 7(10): 1454-63, 2001 Oct.
Article in English | MEDLINE | ID: mdl-11680850

ABSTRACT

Tertiary structure in globular RNA folds can create local environments that lead to pKa perturbation of specific nucleotide functional groups. To assess the prevalence of functionally relevant adenosine-specific pKa perturbation in RNA structure, we have altered the nucleotide analog interference mapping (NAIM) approach to include a series of a phosphorothioate-tagged adenosine analogs with shifted N1 pKa values. We have used these analogs to analyze the hairpin ribozyme, a small self-cleaving/ligating RNA catalyst that is proposed to employ a general acid-base reaction mechanism. A single adenosine (A10) within the ribozyme active site displayed an interference pattern consistent with a functionally significant base ionization. The exocyclic amino group of a second adenosine (A38) contributes substantially to hairpin catalysis, but ionization of the nucleotide does not appear to be important for activity. Within the hairpin ribozyme crystal structure, A10 and A38 line opposite edges of a solvent-excluded cavity adjacent to the 5'-OH nucleophile. The results are inconsistent with the model of ribozyme chemistry in which A38 acts as a general acid-base catalyst, and suggest that the hairpin ribozyme uses an alternative mechanism to achieve catalytic rate enhancement that utilizes functional groups within a solvent-excluded cleft in the ribozyme active site.


Subject(s)
Adenosine/chemistry , Nucleotides/chemistry , RNA, Catalytic/chemistry , Base Sequence , Catalysis , Nucleic Acid Conformation , Transcription, Genetic
2.
Biochemistry ; 40(37): 11211-8, 2001 Sep 18.
Article in English | MEDLINE | ID: mdl-11551220

ABSTRACT

The hairpin catalytic motif in tobacco ringspot virus satellite RNA consists of two helix-loop-helix elements on two adjacent arms of a four-way helical junction. The bases essential for catalytic activity are located in the loops that are brought into proximity by a conformational change as a prerequisite for catalysis. The two loops interact via a ribose zipper motif involving the 2'-hydroxyls of A10, G11, A24, and C25 [Rupert, P. B., and Ferre d'Amare, A. R. (2001) Nature 401, 780-786]. To quantify the energetic importance of the ribose zipper hydrogen bonds, we have incorporated deoxy modifications at these four positions and determined the resulting destabilization of the docked conformer by means of time-resolved fluorescence resonance energy transfer. In a minimal form of the ribozyme, in which the loops are placed on the arms of a two-way helical junction, all modifications lead to a significant loss in tertiary structure stability and altered Mg2+ binding. Surprisingly, no significant destabilization was seen with the natural four-way junction ribozyme, suggesting that hydrogen bonding interactions involving the 2'-hydroxyls do not contribute to the stability of the docked conformer. These results suggest that the energetic contributions of ribose zipper hydrogen bonds are highly context dependent and differ significantly for the minimal and natural forms of the ribozyme.


Subject(s)
Nepovirus , RNA, Catalytic/chemistry , RNA, Satellite/chemistry , RNA, Viral/chemistry , Energy Transfer , Hydrogen Bonding , Models, Molecular , Models, Theoretical , Nucleic Acid Conformation , RNA Stability , Ribose/chemistry , Thermodynamics
3.
Methods ; 25(1): 62-77, 2001 Sep.
Article in English | MEDLINE | ID: mdl-11558998

ABSTRACT

Prior to undergoing postsynthetic 3'-5' editing (proofreading), a defective DNA primer terminus must be transferred from the 5'-3' polymerase active site to a remote 3'-5' exonuclease site. To elucidate the mechanisms by which this occurs, we have used time-resolved fluorescence spectroscopy to study the interaction of dansyl-labeled DNA primer/templates with the Klenow fragment of Escherichia coli DNA polymerase I. The dansyl probe is positioned such that when the DNA substrate occupies the polymerase active site, the probe is solvent-exposed and possesses a short average fluorescence lifetime (4.7 ns) and extensive angular diffusion (42.5 degrees). Conversely, when the DNA substrate occupies the exonuclease active site, the probe becomes buried within the protein, resulting in an increase in the average lifetime (14.1 ns) and a decrease in the degree of angular diffusion (14.4 degrees ). If both polymerase and exonuclease binding modes are populated (lower limit approximately 5%), their markedly different fluorescence properties cause the anisotropy to decay with a characteristic "dip and rise" shape. Nonlinear least-squares analysis of these data recovers the ground-state mole fractions of exposed (x(e)) and buried (x(b)) probes, which are equivalent to the equilibrium proportions of the DNA substrate bound at the polymerase and exonuclease sites, respectively. The distribution between the polymerase and exonuclease binding modes is given by the equilibrium partitioning constant K(pe) (equal to x(b)/x(e)). The important determinants of the proofreading process can therefore be identified by changes made to either the protein or DNA that perturb the partitioning equilibrium and hence alter the magnitude of K(pe).


Subject(s)
DNA Polymerase I/metabolism , DNA Replication , Spectrometry, Fluorescence/methods , DNA Primers/metabolism , Dansyl Compounds , Escherichia coli/enzymology , Fluorescence Polarization , Protein Binding
4.
Biochemistry ; 40(8): 2580-7, 2001 Feb 27.
Article in English | MEDLINE | ID: mdl-11327881

ABSTRACT

The hairpin ribozyme is a small endonucleolytic RNA motif with potential for targeted RNA inactivation. It optimally cleaves substrates containing the sequence 5'-GU-3' immediately 5' of G. Previously, we have shown that tertiary structure docking of its two domains is an essential step in the reaction pathway of the hairpin ribozyme. Here we show, combining biochemical and fluorescence structure and function probing techniques, that any mutation of the substrate base U leads to a docked RNA fold, yet decreases cleavage activity. The docked mutant complex shares with the wild-type complex a common interdomain distance as measured by time-resolved fluorescence resonance energy transfer (FRET) as well as the same solvent-inaccessible core as detected by hydroxyl-radical protection; hence, the mutant complex appears nativelike. FRET experiments also indicate that mutant docking is kinetically more complex, yet with an equilibrium shifted toward the docked conformation. Using 2-aminopurine as a site-specific fluorescent probe in place of the wild-type U, a local structural rearrangement in the substrate is observed. This substrate straining accompanies global domain docking and involves unstacking of the base and restriction of its conformational dynamics, as detected by time-resolved 2-aminopurine fluorescence spectroscopy. These data appear to invoke a mechanism of functional interference by a single base mutation, in which the ribozyme-substrate complex becomes trapped in a nativelike fold preceding the chemical transition state.


Subject(s)
Catalytic Domain/genetics , Mutation , RNA, Catalytic/chemistry , RNA, Catalytic/genetics , 2-Aminopurine/chemistry , Base Composition/genetics , Catalysis , Energy Transfer , Enzyme Stability/genetics , Guanine/chemistry , Guanine/metabolism , Hydrolysis , Kinetics , Nucleic Acid Conformation , RNA, Catalytic/metabolism , Spectrometry, Fluorescence , Substrate Specificity/genetics , Thermodynamics , Uridine/chemistry , Uridine/metabolism
5.
Methods ; 23(3): 240-54, 2001 Mar.
Article in English | MEDLINE | ID: mdl-11243837

ABSTRACT

Fluorescence resonance energy transfer (FRET) results from nonradiative coupling of two fluorophores and reports on distances in the range 10-100 A. It is therefore a suitable probe to determine distances in RNA molecules and define their global structure, to follow kinetics of RNA conformational changes during folding in real time, to monitor ion binding, or to analyze conformational equilibria and assess the thermodynamic stability of tertiary structure conformers. Along with the basic principles of steady-state and time-resolved fluorescence resonance energy transfer measurements, approaches to investigate RNA conformational transitions and folding are described and illustrated with selected examples. The versatility of FRET-based techniques has recently been demonstrated by implementations of FRET in high-throughput screening of potential drugs as well as studies of energy transfer that monitor RNA conformational changes on the single-molecule level.


Subject(s)
Diagnostic Imaging/methods , Fluorescent Dyes/chemistry , Nucleic Acid Conformation , RNA/chemistry , Ions , Kinetics , Spectrometry, Fluorescence , Thermodynamics , Time Factors
7.
Biopolymers ; 61(3): 159-79, 2001.
Article in English | MEDLINE | ID: mdl-11987179

ABSTRACT

The biological functions of nucleic acids in processes of DNA replication, transcription, homologous recombination, mRNA translation, and ribozyme catalysis are intimately linked to their three-dimensional structures and to conformational changes induced by proteins, metal ions and other ligands. Fluorescence spectroscopy is a powerful technique for probing the structure and conformational dynamics of biological macromolecules under a wide range of solution conditions. Fluorescence resonance energy transfer (FRET) provides long-range distance information from 10 to 100 A, a range that is useful for probing the global structure of nucleic acids. While steady-state measurements of FRET provide the average distance between donor and acceptor, much more information is available from the analysis of the nanosecond emission decay of the donor in time-resolved FRET (trFRET) experiments. Analysis of the decay in terms of donor-acceptor distance distributions can resolve different conformers in a heterogeneous mixture, providing information on the global structure and flexibility of each species as well as their equilibrium populations. In this review, we outline the principles of trFRET and the methods used to incorporate fluorescent probes into DNA and RNA. Examples of specific applications are presented to illustrate the versatility of trFRET as a tool to define global structures, to identify conformational heterogeneity and flexibility, to investigate the energetics of tertiary structure formation and to probe structural rearrangements of nucleic acids.


Subject(s)
DNA/chemistry , Energy Transfer , RNA/chemistry , Spectrometry, Fluorescence/instrumentation , Spectrometry, Fluorescence/methods , Base Sequence , Models, Chemical , Models, Statistical , Molecular Sequence Data , Nucleic Acid Conformation , Protein Conformation , Protein Structure, Tertiary , RNA, Catalytic/chemistry , Time Factors
8.
Biochemistry ; 39(44): 13478-86, 2000 Nov 07.
Article in English | MEDLINE | ID: mdl-11063584

ABSTRACT

To understand in atomic detail how a chromophore and a protein interact to sense light and send a biological signal, we are characterizing photoactive yellow protein (PYP), a water-soluble, 14 kDa blue-light receptor which undergoes a photocycle upon illumination. The active site residues glutamic acid 46, arginine 52, tyrosine 42, and threonine 50 form a hydrogen bond network with the anionic p-hydroxycinnamoyl cysteine 69 chromophore in the PYP ground state, suggesting an essential role for these residues for the maintenance of the chromophore's negative charge, the photocycle kinetics, the signaling mechanism, and the protein stability. Here, we describe the role of T50 and Y42 by use of site-specific mutants. T50 and Y42 are involved in fine-tuning the chromophore's absorption maximum. The high-resolution X-ray structures show that the hydrogen-bonding interactions between the protein and the chromophore are weakened in the mutants, leading to increased electron density on the chromophore's aromatic ring and consequently to a red shift of its absorption maximum from 446 nm to 457 and 458 nm in the mutants T50V and Y42F, respectively. Both mutants have slightly perturbed photocycle kinetics and, similar to the R52A mutant, are bleached more rapidly and recover more slowly than the wild type. The effect of pH on the kinetics is similar to wild-type PYP, suggesting that T50 and Y42 are not directly involved in any protonation or deprotonation events that control the speed of the light cycle. The unfolding energies, 26.8 and 25.1 kJ/mol for T50V and Y42F, respectively, are decreased when compared to that of the wild type (29.7 kJ/mol). In the mutant Y42F, the reduced protein stability gives rise to a second PYP population with an altered chromophore conformation as shown by UV/visible and FT Raman spectroscopy. The second chromophore conformation gives rise to a shoulder at 391 nm in the UV/visible absorption spectrum and indicates that the hydrogen bond between Y42 and the chromophore is crucial for the stabilization of the native chromophore and protein conformation. The two conformations in the Y42F mutant can be interconverted by chaotropic and kosmotropic agents, respectively, according to the Hofmeister series. The FT Raman spectra and the acid titration curves suggest that the 391 nm form of the chromophore is not fully protonated. The fluorescence quantum yield of the mutant Y42F is 1.8% and is increased by an order of magnitude when compared to the wild type.


Subject(s)
Bacterial Proteins/chemistry , Photoreceptors, Microbial , Pigments, Biological/chemistry , Ammonium Chloride/chemistry , Ammonium Sulfate/chemistry , Bacterial Proteins/genetics , Crystallography, X-Ray , Hydrogen Bonding , Hydrogen-Ion Concentration , Mutagenesis, Site-Directed , Phenylalanine/genetics , Photolysis , Protein Conformation , Protein Denaturation , Spectrometry, Fluorescence , Spectrophotometry, Ultraviolet , Spectrum Analysis, Raman , Threonine/genetics , Tyrosine/genetics , Valine/genetics
9.
Biochemistry ; 39(42): 12970-8, 2000 Oct 24.
Article in English | MEDLINE | ID: mdl-11041862

ABSTRACT

Helical junctions are ubiquitous structural elements that govern the folding and tertiary structure of RNAs. The tobacco ringspot virus hairpin ribozyme consists of two helix-loop-helix elements that lie on adjacent arms of a four-way junction. In the active form of the hairpin ribozyme, the loops are in proximity. The nature of the helical junction determines the stability of the hairpin ribozyme tertiary structure [Walter, N. G., Burke, J. M., and Millar, D. P. (1999) Nat. Struct. Biol. 6, 544-549] and thus its catalytic activity. We used two-, three-, and four-way junction hairpin ribozymes as model systems to investigate the thermodynamic basis for the different tertiary structure stabilities. The equilibrium between docked and extended conformers was analyzed as a function of temperature using time-resolved fluorescence resonance energy transfer (trFRET). As the secondary and tertiary structure transitions overlap, information from UV melting curves and trFRET had to be combined to gain insight into the thermodynamics of both structural transitions. It turned out that the higher tertiary structure stability observed in the context of a four-way junction is the result of a lower entropic cost for the docking process. In the two- and three-way junction ribozymes, a high entropic cost counteracts the favorable enthalpic term, rendering the docked conformer only marginally stable. Thus, two- and three-way junction tertiary structures are more sensitive toward regulation by ligands, whereas four-way junctions provide a stable scaffold. Altogether, RNA folding and stability appear to be governed by principles similar to those for the folding of proteins.


Subject(s)
Nucleic Acid Conformation , RNA, Catalytic/chemistry , RNA, Viral/chemistry , Energy Transfer , Enzyme Stability , Hot Temperature , Magnesium/chemistry , Nepovirus/enzymology , Reproducibility of Results , Spectrometry, Fluorescence/methods , Spectrophotometry, Ultraviolet , Thermodynamics
10.
Science ; 290(5490): 307-13, 2000 Oct 13.
Article in English | MEDLINE | ID: mdl-11030644

ABSTRACT

The forte of catalytic antibodies has resided in the control of the ground-state reaction coordinate. A principle and method are now described in which antibodies can direct the outcome of photophysical and photochemical events that take place on excited-state potential energy surfaces. The key component is a chemically reactive optical sensor that provides a direct report of the dynamic interplay between protein and ligand at the active site. To illustrate the concept, we used a trans-stilbene hapten to elicit a panel of monoclonal antibodies that displayed a range of fluorescent spectral behavior when bound to a trans-stilbene substrate. Several antibodies yielded a blue fluorescence indicative of an excited-state complex or "exciplex" between trans-stilbene and the antibody. The antibodies controlled the isomerization coordinate of trans-stilbene and dynamically coupled this manifold with an active-site residue. A step was taken toward the use of antibody-based photochemical sensors for diagnostic and clinical applications.


Subject(s)
Antibodies, Catalytic/chemistry , Antibodies, Monoclonal/chemistry , Fluorescence , Stilbenes/chemistry , Stilbenes/immunology , Binding Sites , Binding Sites, Antibody , Chemical Phenomena , Chemistry, Physical , Crystallography, X-Ray , Haptens , Ligands , Microscopy, Fluorescence , Models, Chemical , Models, Molecular , Photochemistry , Spectrometry, Fluorescence , Stereoisomerism , Temperature , Ultraviolet Rays
11.
Chem Biol ; 7(9): 743-51, 2000 Sep.
Article in English | MEDLINE | ID: mdl-10980454

ABSTRACT

BACKGROUND: The four arms of the Holliday junction are known to stack in pairs forming two helical domains whose orientations are antiparallel, but twisted positively by about 60 degrees, based on electrophoretic, FRET and AFM measurements. Recent gel retardation studies suggest that a bowtie junction (containing 5',5' and 3',3' linkages in its crossover strands) may adopt a parallel conformation. RESULTS: An AFM study of two-dimensional arrays produced by parallelograms of bowtie junctions shows that the angle between helical domains is in the range of -68+/-2 degrees. We demonstrate by AFM that the domains are parallel by constructing V-shaped structures whose arms are separated by approximately 68 degrees and approximately 112 degrees. CONCLUSIONS: The arms of the bowtie junction are parallel rather than antiparallel. The parallel or antiparallel nature of the junction apparently is determined by the local structure of the junction, but the sign of the angle appears to be a consequence of interarm electrostatic interactions.


Subject(s)
DNA/chemistry , DNA/ultrastructure , Nucleic Acid Conformation , Hydrogen Bonding , Microscopy, Atomic Force/methods , Models, Molecular , Software
13.
Nat Struct Biol ; 6(6): 544-9, 1999 Jun.
Article in English | MEDLINE | ID: mdl-10360357

ABSTRACT

The equilibrium distributions of hairpin ribozyme conformational isomers have been examined by time-resolved fluorescence resonance energy transfer. Ribozymes partition between active (docked) and inactive (extended) conformers, characterized by unique interdomain distance distributions, which define differences in folding free energy. The active tertiary structure is stabilized both by specific interactions between the catalytic and the substrate-binding domains and by the structure of the intervening helical junction. Under physiological conditions, the docking equilibrium of the natural four-way junction dramatically favors the active conformer, while those of a three-way and the two-way junction used in gene therapy applications favor the inactive conformer.


Subject(s)
Nucleic Acid Conformation , RNA, Catalytic/chemistry , Binding Sites/drug effects , Catalysis/drug effects , Catalytic Domain , Cations/metabolism , Cations/pharmacology , Drug Design , Energy Transfer , Enzyme Stability , Fluorescence , Genetic Therapy , Magnesium/metabolism , Magnesium/pharmacology , Mutation , Nucleic Acid Conformation/drug effects , RNA, Catalytic/genetics , RNA, Catalytic/metabolism , RNA, Catalytic/therapeutic use , Sodium/metabolism , Sodium/pharmacology , Stereoisomerism , Temperature , Thermodynamics
14.
Biochemistry ; 38(16): 5138-46, 1999 Apr 20.
Article in English | MEDLINE | ID: mdl-10213619

ABSTRACT

The basic helix-loop-helix domain of the Drosophila transcription factor Deadpan (Dpn) was prepared by total chemical protein synthesis in order to characterize its DNA binding properties. Circular dichroism spectroscopy was used to correlate structural changes in Dpn with physiologically relevant monovalent (KCl) and divalent (MgCl2) cation concentrations. In addition, we have used electrophoretic mobility shift assay (EMSA) and fluorescence anisotropy methods to determine equilibrium dissociation constants for the interaction of Dpn with two biologically relevant promoters involved in neural development and sex determination pathways. In this study, we have optimized DNA binding conditions for Dpn, and we have found a markedly higher DNA binding affinity for Dpn than reported for other bHLH domain transcription factors. Dpn binds as a homodimer (Kd = 2.6 nM) to double-stranded oligonucleotides containing the binding site CACGCG. In addition, we found that Dpn bound with the same affinity to a single or tandem binding site, indicating no cooperativity between adjacent DNA-bound Dpn dimers. DNA binding was also monitored as a function of physiologically relevant KCl and MgCl2 concentrations, and we found that this activity was significantly different in the presence and absence of the nonspecific competitor poly(dI-dC). Moreover, Dpn displayed moderate sequence selectivity, exhibiting a 100-fold higher binding affinity for specific DNA than for poly(dI-dC). This study constitutes the first detailed biophysical characterization of the DNA binding properties of a bHLH protein.


Subject(s)
DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , DNA/metabolism , Drosophila Proteins , Helix-Loop-Helix Motifs , Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Peptide Fragments/chemistry , Peptide Fragments/metabolism , Amino Acid Sequence , Animals , Basic Helix-Loop-Helix Transcription Factors , Binding Sites , Circular Dichroism , DNA-Binding Proteins/chemical synthesis , Drosophila , Fluorescence Polarization , Kinetics , Magnesium Chloride/chemistry , Molecular Sequence Data , Nuclear Proteins/chemical synthesis , Peptide Fragments/chemical synthesis , Potassium Chloride/chemistry , Protein Binding , Repetitive Sequences, Amino Acid , Spectrometry, Fluorescence , Ultracentrifugation
15.
Biochemistry ; 38(9): 2661-8, 1999 Mar 02.
Article in English | MEDLINE | ID: mdl-10052936

ABSTRACT

Frameshift mutagenesis occurs through the misalignment of primer and template strands during DNA synthesis and involves DNA intermediates that contain one or more extrahelical bases in either strand of the DNA substrate. To investigate whether these DNA structures are recognized by the proofreading apparatus of DNA polymerases, time-resolved fluorescence spectroscopy was used to examine the interaction between the Klenow fragment of DNA polymerase I and synthetic DNA primer-templates containing extrahelical bases at defined positions within the template strand. A dansyl probe attached to the DNA was used to measure the fractional occupancies of the polymerase and 3'-5' exonuclease sites of the enzyme for DNA substrates with and without the extrahelical bases. The presence of an extrahelical base at the first position from the primer 3' terminus increased the level of partitioning of the DNA substrates into the 3'-5' exonuclease site by 3-7-fold, relative to the perfectly base-paired primer-template, depending on the identity of the extrahelical base. The ability of different extrahelical bases to promote partitioning of DNA into the 3'-5' exonuclease site decreased in the following order: G > A approximately T > C. The results of partitioning measurements for DNA substrates containing a bulged adenine base at different positions within the template showed that an extrahelical base is recognized up to five bases from the primer 3' terminus. The largest effects were observed for the extrahelical base at the third or fourth positions from the primer terminus, which increased the level of partitioning of DNA into the 3'-5' exonuclease site by 8- and 18-fold, respectively, relative to that of the perfectly base-paired substrate. Steady-state fluorescence measurements of analogous primer-templates containing 2-aminopurine (AP) at the primer 3' terminus indicate that extrahelical bases increase the degree of terminus unwinding, especially when close to the terminus. In addition, steady-state kinetic measurements of removal of AP from the primer-templates indicate that the exonucleolytic cleavage activity of Klenow fragment is correlated with the increased level of partitioning of bulged DNA substrates to the 3'-5' exonuclease site relative to that of properly base-paired DNA. The results of this study indicate that misalignment of primer and template strands to generate an extrahelical base strongly promotes transfer of a DNA substrate to the 3'-5' exonuclease site, suggesting that the premutational intermediates in frameshift mutagenesis are subject to proofreading by the polymerase.


Subject(s)
DNA Polymerase I/chemistry , DNA/biosynthesis , DNA/chemistry , Frameshift Mutation , Nucleic Acid Heteroduplexes/chemistry , 2-Aminopurine/chemistry , Base Pairing , DNA/genetics , DNA Polymerase I/genetics , DNA Primers/chemistry , Exodeoxyribonuclease V , Exodeoxyribonucleases/chemistry , Hydrolysis , Kinetics , Nucleic Acid Heteroduplexes/genetics , Substrate Specificity , Templates, Genetic
16.
Biochemistry ; 37(6): 1513-22, 1998 Feb 10.
Article in English | MEDLINE | ID: mdl-9484221

ABSTRACT

Site-directed mutagenesis and time-resolved fluorescence spectroscopy were used to evaluate the contributions of individual amino acid side chains to the binding of DNA primer-templates to the 3'-5' exonuclease site of the large proteolytic fragment (Klenow fragment) of DNA polymerase I. Mutations were introduced into side chains that have been shown crystallographically to be in close proximity to a DNA 3' terminus bound at the 3'-5' exonuclease site. The wild-type residues were replaced by alanine in each case. To assess the effects of the mutations on DNA binding, time-resolved fluorescence anisotropy measurements were performed on dansyl-labeled primer-templates bound to the mutant enzymes. In contrast to techniques that simply monitor the overall binding of proteins to DNA, the time-resolved fluorescence anisotropy technique was used to determine the fractional occupancies of the polymerase and 3'-5' exonuclease active sites of Klenow fragment. Equilibrium constants describing the partitioning of DNA between the two active sites were obtained for nine different mutant enzymes bound to both matched and mismatched DNA sequences. Mutations of Leu361 and Phe473 caused the largest effects, significantly destabilizing the binding of mismatched DNA substrates to the 3'-5' exonuclease site relative to DNA bound at the polymerase site, consistent with structural data showing that the side chains of these residues are involved in intimate hydrophobic interactions with the 3' terminal and penultimate bases of the primer strand [Beese, L., and Steitz, T. A. (1991) EMBO J. 10, 25-33]. Mutations of the His660 and Glu357 side chains also resulted in significant effects on the binding of mismatched DNA to the 3'-5' exonuclease site. Surprisingly, mutation of Tyr497 increased the partitioning of mismatched DNA into the 3'-5' exonuclease site, suggesting that the tyrosine side chain in the wildtype enzyme destabilizes substrate binding, despite crystallographic data showing that Tyr497 is H-bonded to the DNA substrate. The effects of mutating the amino acid side chains that serve as ligands to two divalent metal ions bound at the 3'-5' exonuclease site, designated A and B, indicated that metal A also helps to bind DNA to the 3'-5' exonuclease site. These results demonstrate that the time-resolved fluorescence anisotropy technique can be used to quantify the energetic contributions associated with each of the crystallographically defined DNA-protein contacts at the 3'-5' exonuclease site.


Subject(s)
DNA Polymerase I/genetics , DNA Polymerase I/metabolism , DNA/metabolism , Exodeoxyribonucleases/genetics , Mutagenesis, Site-Directed , Amino Acid Substitution/genetics , Amino Acids/genetics , Amino Acids/metabolism , Binding Sites/genetics , Carboxylic Acids/metabolism , Cations, Divalent , Dansyl Compounds , Fluorescence Polarization , Ligands , Metals/metabolism , Substrate Specificity/genetics
17.
Biochemistry ; 37(7): 1800-9, 1998 Feb 17.
Article in English | MEDLINE | ID: mdl-9485305

ABSTRACT

The Rev protein of the human immunodeficiency virus type 1 (HIV-1) has been studied by time-resolved fluorescence spectroscopy. The single tryptophan residue of Rev, Trp45, located within the arginine-rich RNA-binding domain of the protein, was utilized as an intrinsic spectroscopic probe. In addition, five peptides spanning different lengths of the arginine-rich domain, each containing the tryptophan residue, and two C-terminal deletion mutants of Rev, Rev M9 delta 14 and Rev M11 delta 14, were examined. Rev M9 delta 14 lacks residues 68-112 whereas Rev M11 delta 14 is missing residues 92-112 of the C-terminus of Rev. The fluorescence decay of Trp45 in wild-type Rev was resolved into four discrete lifetime components, and decay-associated spectra (DAS) were obtained for each component. The fluorescence decays of all five peptides and Rev M9 delta 14 were resolved into three lifetime components. The fluorescence decay of Rev M11 delta 14 was resolved into four components similar to those found for wild-type Rev. These results indicate that the activation domain (residues 78-93), present in wild-type Rev and Rev M11 delta 14, induced a unique tryptophan environment, characterized by a short-lived, blue-shifted emission, attributed to higher order assembly of Rev. In addition, fluorescence anisotropy decay data obtained for wild-type Rev and the two C-terminal deletion mutants also indicate that the activation domain mediates self-association of Rev. Based on the anisotropy decay results for wild-type Rev, the distribution of oligomers is independent of salt concentration. The average fluorescence lifetime of Trp45 was reduced upon complexation of Rev with a 40-mer fragment of the Rev response element containing the minimal element for Rev binding (F8-RRE), and the emission was blue-shifted. In addition, the local rotation of the tryptophan side chain was blocked in the protein-RRE complex. These results indicate that Trp45 directly interacts with the RRE. Rev is also shown to bind to 5S RNA, resulting in very similar changes in the time-resolved tryptophan fluorescence to those observed upon complexation of Rev with F8-RRE.


Subject(s)
Gene Products, rev/chemistry , HIV-1/chemistry , Nuclear Proteins/chemistry , RNA, Ribosomal, 5S/chemistry , Amino Acid Sequence , Base Sequence , Binding Sites , Fluorescence Polarization , Gene Products, rev/genetics , Gene Products, rev/metabolism , Macromolecular Substances , Molecular Sequence Data , Nuclear Proteins/metabolism , Peptides/chemistry , Peptides/genetics , RNA, Ribosomal, 5S/metabolism , Sequence Deletion , Spectrometry, Fluorescence , Tryptophan , rev Gene Products, Human Immunodeficiency Virus
18.
Biochemistry ; 37(7): 1898-904, 1998 Feb 17.
Article in English | MEDLINE | ID: mdl-9485315

ABSTRACT

Time-resolved fluorescence spectroscopy was used to investigate the influence of sequence-directed DNA structure upon the interaction between the Klenow fragment of DNA polymerase I and a series of defined oligonucleotide primer/templates. 17/27-mer (primer/template) oligonucleotides containing a dansyl fluorophore conjugated to a modified deoxyuridine residue within the primer strand were used as substrates for binding to Klenow fragment. The time-resolved fluorescence anisotropy decay of the dansyl probe was analyzed in terms of two local environments, either solvent-exposed or buried, corresponding to primer/templates positioned with the primer 3' terminus in the polymerase site or the 3'-5' exonuclease site of the enzyme, respectively. Equilibrium constants for partitioning of DNA between the two sites were evaluated from the anisotropy decay data for primer/templates having different (A + T)-rich sequences flanking the primer 3' terminus. Primer/templates with AAAATG/TTTTAC and CGATAT/GCTATA terminal sequences (the nucleotides on the left refer to the last six bases at the 3' end of the primer, and the nucleotides on the right are the corresponding bases in the template) were bound mostly at the polymerase site. The introduction of single mismatches opposite the primer 3' terminus of these DNA substrates increased their partitioning into the 3'-5' exonuclease site, in accord with the results of an earlier study [Carver, T.E., Hochstrasser, R.A., and Millar, D.P. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 10670-10674]. In contrast, a primer/template with the terminal sequence CAATTT/GTTAAA, containing an A-tract element AATTT, exhibited a surprising preference for binding at the 3'-5' exonuclease site, despite the absence of mismatched bases in the DNA substrate. Interruption of the A-tract with a single AG step, to give the terminal sequence CAGTTT/GTCAAA, reversed the effect of the A-tract, causing the DNA to partition in favor of the polymerase site. Moreover, the presence of a single mismatch opposite the primer 3' terminus was also sufficient to reverse the effect of the A-tract, resulting in a distribution of DNA between polymerase and 3'-5' exonuclease sites that was similar to that observed for the other mismatched DNA substrates. Taken together, these results suggest that the A-tract adopts an unusual conformation that is disruptive to binding at the polymerase site. The effect of the A-tract on binding of DNA to the polymerase site is discussed in terms of the unusual helix structural parameters associated with these sequence elements and the difference between the local geometry of the A-tract and the conformation adopted by duplex DNA within the polymerase cleft. The results of this study show that in addition to base mismatches, Klenow fragment can also recognize irregularities in the helix geometry of perfectly base-paired DNA.


Subject(s)
DNA Polymerase I/chemistry , DNA/chemistry , Base Composition , Base Sequence , Binding Sites/genetics , DNA Polymerase I/genetics , DNA Primers/chemistry , Exodeoxyribonuclease V , Exodeoxyribonucleases/chemistry , Exodeoxyribonucleases/genetics , Fluorescence Polarization , Substrate Specificity/genetics , Templates, Genetic
19.
Proc Natl Acad Sci U S A ; 94(17): 9080-4, 1997 Aug 19.
Article in English | MEDLINE | ID: mdl-9256438

ABSTRACT

Recombination of genes is essential to the evolution of genetic diversity, the segregation of chromosomes during cell division, and certain DNA repair processes. The Holliday junction, a four-arm, four-strand branched DNA crossover structure, is formed as a transient intermediate during genetic recombination and repair processes in the cell. The recognition and subsequent resolution of Holliday junctions into parental or recombined products appear to be critically dependent on their three-dimensional structure. Complementary NMR and time-resolved fluorescence resonance energy transfer experiments on immobilized four-arm DNA junctions reported here indicate that the Holliday junction cannot be viewed as a static structure but rather as an equilibrium mixture of two conformational isomers. Furthermore, the distribution between the two possible crossover isomers was found to depend on the sequence in a manner that was not anticipated on the basis of previous low-resolution experiments.


Subject(s)
DNA/chemistry , Recombination, Genetic , Base Sequence , DNA/genetics , Isomerism , Molecular Sequence Data
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