Novel methods of generating specific oligonucleotide inhibitors of viral polymerases.
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Base Sequence↗
Biomedical subjects
L Gold
Publications and source records attributed to L Gold.
Fibrillary glomerulonephritis related to serum fibrillar immunoglobulin-fibronectin complexes.
Fibrillary glomerulonephritis is a disease of uncertain origin and pathogenesis characterized by nonamyloidotic fibrils in glomeruli. We report immunohistological, immunochemical, and biochemical studies of a serum fibrillar cryoprecipitate obtained from a patient with fibrillary glomerulonephritis, that formed on prolonged storage at 4 degrees C. By Western blot and amino acid sequence analysis, the cryoprecipitated fibril components consisted of immunoglobulins, heavy chains gamma and mu, light chains kappa and lambda, and fibronectin, similar to the proteins identified by immunofluorescence and immunoelectron microscopy in the glomerular fibrils. These findings support the hypothesis that serum precursors may be the source of the fibrillar deposits and suggest a role for immunoglobulin-fibronectin complexes in the pathogenesis of fibrillary glomerulonephritis.
Antigen-Antibody Complex↗
Transforming growth factor-beta protein and messenger RNA expression is increased in the closing ductus arteriosus.
In full-term newborns, permanent closure of the ductus arteriosus is associated with the formation of a neointima that is characterized by extracellular matrix deposition and smooth muscle cell migration. Transforming growth factor-beta (TGF-beta), a potent modulator of extracellular matrix deposition and smooth muscle cell migration, has been found to play a role in the remodeling associated with several forms of vascular disease. We examined the protein and mRNA expression of the three mammalian isoforms of TGF-beta (TGF-beta1, TGF-beta2, and TGF-beta3) during ductus arteriosus closure in full-term lambs. We found that the temporal changes and cellular localization of the proteins and mRNAs of all three TGF-beta isoforms were similar. TGF-beta proteins and mRNAs were present in very low levels in the late-gestation fetal ductus. Within 24 h of delivery, there was enhanced expression of TGF-beta in the newly forming neointima and outer muscle media; this continued to increase over the next 10 d. Increased expression of TGF-beta in the inner muscle media and adventitia lagged behind that of the neointima and outer muscle media. TGF-beta was not found in the luminal endothelial cells at any time. In contrast to the pattern described above, the appearance of TGF-beta protein differed from that of mRNA in the vasa vasorum of the ductus wall. After delivery, there was an increase in TGF-beta immunoreactivity in the smooth muscle cell layers of the vasa vasorum without any concurrent mRNA expression. The appearance of TGF-beta at the time of ductus closure suggests an important role for this growth factor in the reorganization of the ductus wall after birth.
Animals↗
New concepts in tissue repair: skin as an example.
Several heparin-binding growth factors (HBGFs) are thought to play a key role in natural processes of tissue regeneration or repair after release from inflammatory or circulating cells and extracellular matrix-associated heparan sulfate proteoglycosaminoglycans. To clarify how the bioavailability of these HBGFs can help regulate wound-healing processes, we studied the healing effect of various chemically substituted dextrans (RGTA) selected for their affinity for HBGFs. One member of the RGTA family, RGTA11, obtained by substitution of carboxymethyl (CM), benzylamide (B) and benzylamide sulfonate (S) groups in a proportion of 110% (CM), 2.6% (B) and 36.5% (S) respectively was used in these studies. RGTA11 may potentiate the biological activity of fibroblast growth factors 1 and 2 and protect them against heat or pH inactivation and proteolytic degradation. RGTA11 was tested in a rat punch-biopsy skin-healing model for its ability to enhance wound repair. Wounds were filled with collagen plaster alone or soaked with RGTA, and skin regeneration was studied by histological analysis. In collagen plaster, RGTA11 affected both the kinetics and quality of restored skin. It seems likely that endogenous growth factors naturally released during the regeneration process are trapped and protected against natural proteases, thereby preserving their ability to stimulate tissue repair. Since most known growth factors have a nearly ubiquitous distribution and blind to heparin, our hypothesis was verified by studying the ability of RGTA to induce repair in damaged tissue. We demonstrated the RGTA could stimulate wound repair in various models, including bone, muscle, nerve, cornea and colonic anastomosis. The data presented here concern wound-healing in a deep skin model and suggest that heparan-like biopolymers constitute a new family of tissue-repair agents with a wide variety of potential uses. The efficiency of this approach in cases in which impaired healing is associated with a pathology, as in diabetes, remains to be determined.
Animals↗
In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptide.
An in vitro RNA selection for catalytic activity was used to co-select for binding activity to a small peptide. 5'-phosphorothioate-modified RNA (GMPS-RNA) sequences were selected from a randomized pool of oligoribonucleotides for their ability to accelerate a halide substitution reaction with N-bromoacetyl-bradykinin (BrBK). One RNA selected shows a 2,420-fold increase in rate of reaction with BrBK relative to the starting pool. This reaction is specifically inhibited by free bradykinin (Ki 230 microM), indicating that interactions with bradykinin contribute to the rate enhancement. Inhibition of the reaction by the peptide requires both the amino- and carboxy-terminal arginine residues of the peptide for optimal inhibition activity. Reaction with N-bromoacetamide is not enhanced, indicating that the intrinsic reactivity of the 5' phosphorothioate is not increased in the selected RNA. Through 3'-end boundary analysis, much of the catalytic activity of the selected GMPS-RNA is shown to reside in a hairpin structure in the selected region of the molecule. This hairpin structure is also implicated in the recognition of the peptide substrate.
Aldehydes↗
Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands.
We have used an in vitro selection procedure called crosslinking SELEX (SELEX = systematic evolution of ligands by exponential enrichment) to identify RNA sequences that bind with high affinity and crosslink to the Rev protein from human immunodeficiency virus type 1 (HIV-1). A randomized RNA library substituted with the photoreactive chromophore 5-iodouracil was irradiated with monochromatic UV light in the presence of Rev. Those sequences with the ability to photocrosslink to Rev were partitioned from the rest of the RNA pool, amplified, and used for the next round of selection. Rounds of photocrosslinking selection were alternated with rounds of selection for RNA sequences with high affinity to Rev. This iterative, dual-selection method yielded RNA molecules with subnanomolar dissociation constants and high efficiency photocrosslinking to Rev. Some of the RNA molecules isolated by this procedure form a stable complex with Rev that is resistant to denaturing gel electrophoresis in the absence of UV irradiation. In vitro selection of nucleic acids by using modified nucleotides allows the isolation of nucleic acid molecules with potentially limitless chemical capacities to covalently attack a target molecule.
Base Sequence↗
Template recognition by an RNA-dependent RNA polymerase: identification and characterization of two RNA binding sites on Q beta replicase.
Two different SELEX protocols were used to generate two classes of RNA ligands that bound Q beta replicase with nanomolar equilibrium dissociation constants. One set of RNAs appeared to exist as pseudoknots with conserved loop sequences. These ligands bound Q beta replicase and ribosomal protein S1 with equal affinities, indicating that the RNAs bind the replicase through its S1 subunit. The second class of ligands bound the replicase via a pyrimidine rich region. The two sets of ligands did not compete for binding to Q beta replicase, demonstrating that the two RNA families bind unique sites on the phage polymerase. Because the second class of ligands bound ribosomal protein S1 very poorly, it is likely that the second RNA binding site is located on one of the three remaining replicase subunits. Published sequences of RNAs replicated by Q beta replicase possess similarities to the two classes of RNA ligands, providing a possible solution to the question of template recognition by the phage polymerase.
Base Composition↗
Selection and characterization of RNAs replicated by Q beta replicase.
RNAs replicated by Q beta replicase were isolated from two random sequence RNA populations (one 56 nucleotides in length, the second 83) using a replication/dilution protocol. The selected molecules were cloned and sequenced, generating data set of 54 replicatable RNAs bound with higher affinity to Q beta replicase than did the random populations from which they were selected. Deletion analyses on two of the molecules indicated that internal regions of the RNAs were responsible for the specific binding of Q beta replicase. Truncated molecules representing the minimized RNA binding sites could inhibit replication of the full-length molecules, apparently by obstructing their binding to the replicase. The binding regions of the two RNAs were dominated by extended runs of pyrimidines. Similar C/U-rich regions existed in 85% of the sequences in the data set as well as in all of the previously published replicatable sequences. Mutation of the polypyrimidine domain of one of the replicatable sequences reduced the affinity of the molecule for Q beta replicase by 10-fold and completely abolished its ability to be replicated.
Base Sequence↗
RNA ligands to human nerve growth factor.
High affinity RNA ligands to human nerve growth factor (NGF) were selected from pools of random RNA using SELEX [Tuerk, C. and Gold, L. (1990) Science, 249, 505-510]. Nerve growth factor, which is a protein required for the development of neurons, is not known to bind nucleic acids as part of its natural function. We describe two of the selected RNA molecules in detail. One of them is highly structured, folding into a pseudoknot with an additional hairpin-loop; this structure provides salt-resistant binding to NGF. The other is unstructured and elevated salt concentrations inhibit its binding. These molecules compete with each other for NGF binding. Our RNAs may furnish useful diagnostic tools for the study of an important neurotrophic protein; additionally, they illustrate another example of the potential for nucleic acids to take part in novel binding interactions.
Base Sequence↗
High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus.
The reverse transcriptase (RT) of HIV-1 is a plausible target for therapeutic agents aimed at inhibiting propagation of the virus. We have used "irrational drug design", that is, combinatorial chemistry with oligonucleotide libraries, to identify high-affinity ligands aimed at HIV-1 RT. The methodology, termed SELEX (systematic evolution of ligands by exponential enrichment), was employed with a single-stranded DNA library. The selected ssDNA ligands bind HIV-1 RT with Kd values as low as 1 nM and inhibit the RNA-dependent DNA-polymerase activity of the enzyme with Ki values as low as 0.3 nM. We also demonstrate the high specificity of one ligand able to selectively discriminate between the reverse transcriptases of HIV-1, AMV, and MMLV. These ssDNA molecules may be useful as inhibitors or as models for the design of small molecule inhibitors of HIV-1 RT in vivo.
Antiviral Agents↗
Oligonucleotides as research, diagnostic, and therapeutic agents.
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Animals↗
Isolation of high-affinity RNA ligands to HIV-1 integrase from a random pool.
We were able to isolate high-affinity RNAs from a random pool that binds to integrase protein from the human immunodeficiency virus-type 1 using the procedure now known as SELEX. Generally, the RNAs fell into three different classes in binding buffer containing 250 mM NaCl: group I class of molecules binds integrase with a dissociation constant (Kd) on the order of 10 nM, group II molecules had a Kd of about 80 nM, and group III about 800 nM. The RNA with the highest affinity from the group I class of molecules, designated P5, was characterized using computer modeling, chemical and enzymatic probing, and deletion analysis. Our secondary structure model for this RNA suggests interactions between looped-out fixed nucleotides and nucleotides from the randomized region; a GNRA tetraloop is also in the structure. We showed that our integrase was able to process a U5 mimic in vitro. P5 competes effectively for binding with the double-stranded DNA mimic of U5 at 180 mM NaCl concentration.
Base Sequence↗
Crystal structure of the T4 regA translational regulator protein at 1.9 A resolution.
The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs. The crystal structure of regA was determined at 1.9 A resolution; the protein was shown to have an alpha-helical core and two regions with antiparallel beta sheets. One of these beta sheets has four antiparallel strands and has some sequence homology to RNP-1 and RNP-2, which are believed to be RNA-binding motifs and are found in a number of known RNA-binding proteins. Structurally guided mutants may help to uncover the basis for this variety of RNA interaction.
Amino Acid Sequence↗
In vitro selection of RNA ligands to substance P.
RNA ligands to the tachykinin substance P have been selected from a large pool of random sequence RNA molecules. Substance P is an undecapeptide that plays a variety of roles as a neurotransmitter and neuromodulator in the central and peripheral nervous system of mammals. A systematic evolution of ligands by exponential enrichment (SELEX) procedure was used to isolate RNAs that bind substance P immobilized on a solid support. RNAs that also bind substance P in solution were identified, and the tightest binder was subjected to mutagenesis in a second SELEX procedure to evolve ligands with a higher affinity for the peptide. A comparative analysis of 36 ligands isolated from the second SELEX experiment revealed two main sequence classes with highly conserved secondary structures within each class. Dissociation constants for the interaction of these ligands with substance P in solution were determined by equilibrium dialysis. The amino acid residues involved in the interaction with the highest affinity ligand (190 nM Kd) were mapped by determining which of a set of overlapping fragments of substance P can compete with the intact peptide for binding. A binding competition experiment also demonstrated the ability of the same ligand to discriminate between substance P and the reverse orientation of the same amino acid sequence. The results from this study demonstrate that SELEX can yield high affinity RNA ligands to small nonconstrained peptides.
Amino Acid Sequence↗
High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites.
High-affinity RNA ligands were generated against intact 30S ribosomes, S1-depleted 30S ribosomes, and purified ribosomal protein S1. Sequence analysis indicated two classes of ligand: unstructured RNAs containing a Shine-Dalgarno sequence and structured RNAs containing a pseudoknot. The Shine-Dalgarno-containing ligands were generated against S1-depleted 30S ribosomes but, surprisingly, not against intact 30S ribosomes or ribosomal protein S1. In contrast, pseudoknot-containing ligands were generated against intact ribosomes as well as purified S1 protein. The two classes of ligand exhibited specificity for their respective targets, as well as conserved sequence and secondary structure reminiscent of naturally occurring, cis-acting mRNA elements.
Base Sequence↗
Changes in CNS neuropeptide FF-like material, pain sensitivity, and opiate dependence following chronic morphine treatment.
Tolerance and dependence to opiates may be an adaptive process that limits excessive effects of morphine on the CNS. Because no consistent opiate receptor reduction in chronically treated rats seems to underlie the hyposensitivity to morphine, an alternative hypothesis has postulated a role of "antiopioid" peptides. It is possible to speculate that the administration of morphine stimulates antiopioid systems such as neuropeptide FF (NPFF), as part of an homeostatic mechanism contributing to the development of tolerance. To test this hypothesis, pain sensitivity, opiate dependence, and CNS NPFF-IR levels were estimated at different times after implantation of morphine pellets (2 x 75 mg; NIDA). Three hours after morphine pellet treatment the analgesic effect was maximum and it decreased rapidly during the following 12 h. Naloxone-precipitated withdrawal syndrome was detected as soon as 3 h after morphine pellet implantation and was maximal after 24 h. NPFF-IR levels were measured in the spinal cord, brain stem, and hypothalamus. A significant decrease of NPFF-IR was observed 1 h after morphine pellet implantation (-25% to -45% depending on the structures) followed by a drastic increase of NPFF-IR levels (+60 to +140%) between 3 and 6 h. NPFF-IR levels rapidly returned to baseline after 24-36 h. It is suggested that the activity of these NPFF-IR neurones may increase gradually as a consequence of the continuous stimulation of opiate receptors and be part of an adaptive process that is able to counteract morphine effects and to induce dependence and tolerance to the analgesic effects of opiates.
Adaptation, Biological↗
Reorganization of the annual meeting.
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Congresses as Topic↗