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Biomedical subjects

A Rich

Publications and source records attributed to A Rich.

At least 235 records · Page 13Linked to original sources
PubMed1985

Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence.

In left-handed Z-DNA, consecutive nucleotides along the chain alternate in the syn and anti conformations. Purine residues form the syn conformation readily and up to now all Z-DNA crystal structures have sequences of alternating purines and pyrimidines. However, we find that d(C-G-A-T-C-G) with the cytosines brominated or methylated on C-5 crystallizes as Z-DNA. The structure reveals thymines in syn and adenines in anti conformations. This suggests that Z-DNA may occur in sequences other than those with alternating purine-pyrimidine sequence.

Base Sequence↗
PubMed1985

Sequence-dependent energetics of the B-Z transition in supercoiled DNA containing nonalternating purine-pyrimidine sequences.

The likelihood that a given DNA sequence will adopt the Z conformation in negatively supercoiled DNA depends on the energy difference between the B form and the Z form for that sequence relative to other sequences in the same molecule. This energy can be viewed simply as a sum of energies for the nearest-neighbor interactions within the sequence plus the energy required to stabilize the B-Z boundaries. Knowledge of these energetic terms would be of value in predicting when sequences become left-handed in response to negative superhelicity. Here we present an approach that can be used to determine the free-energy changes associated with all the nearest-neighbor interactions that can occur in Z-DNA. Synthetic stretches of d(C-G)n containing one or two transversions were cloned into plasmids, and the extent of the B-Z transition as a function of negative superhelicity was determined for each insert by two-dimensional agarose gel electrophoresis. By subjecting the data to statistical mechanical analysis, it was possible to evaluate the energetic penalty resulting from each base-pair (bp) substitution. Guanine to cytosine transversions cost 2.4 kcal (1 cal = 4.18 J)/(mol X bp), whereas guanine to thymine transversions cost 3.4 kcal/(mol X bp), to stabilize in the Z conformation. We have used these numbers, along with energetic values determined by others for the B-Z transition, to predict that certain strictly nonalternating purine and pyrimidine sequences may adopt the Z form readily.

Base Sequence↗
PubMed1985

Interactions of antitumor drugs and DNA: crystallographic studies.

Several antitumor drugs complexed to DNA double helical fragments have been crystallized and their structures solved by single crystal X-ray diffraction analysis at high resolution. These studies show in great detail the manner in which the planar aromatic components of the drugs intercalate between base pairs from the minor groove side of B-DNA, as well as hydrogen bonding components which anchor the drug to DNA through its interaction with base pairs on either side of the intercalative site. Analysis at this level makes it possible to contemplate the rational design of antitumor drugs that might bind more strongly or interact more specifically with certain nucleic acid sequences.

Antibiotics, Antineoplastic↗
PubMed1984

The molecular structure of a DNA-triostin A complex.

The molecular structure of triostin A, a cyclic octadepsipeptide antibiotic, has been solved complexed to a DNA double helical fragment with the sequence CGTACG (C, cytosine; G, guanine; T, thymine; A, adenine). The two planar quinoxaline rings of triostin A bis intercalate on the minor groove of the DNA double helix surrounding the CG base pairs at either end. The alanine residues form hydrogen bonds to the guanines. Base stacking in the DNA is perturbed, and the major binding interaction involves a large number of van der Waals contacts between the peptides and the nucleic acid. The adenine residues in the center are in the syn conformation and are paired to thymine through Hoogsteen base pairing.

Crystallization↗
PubMed1984

The Raman spectra of left-handed DNA oligomers incorporating adenine-thymine base pairs+.

Raman spectra were obtained from single crystals of [d(CGCATGCG)]2 and [d(m5CGTAm5CG)]2, both of which incorporate A-T pairs into Z-DNA structures and contain C2'-endo/syn conformers of deoxyguanosine at the oligonucleotide ends. Correlation with x-ray results permits the following Raman assignments for nucleoside conformers: C3'-endo/syn G, 623 +/- 1; C2'-endo/syn G, 671 +/- 2; C2'-endo/anti C, 782 +/- 1; C2'endo/anti T, 650 +/- 5 and ca. 750; C3'-endo/syn A, 729 +/- 1 cm-1. These results show that (i) the 670 cm-1 line of syn G is highly sensitive to the change from C3'-endo to C2'-endo pucker, (ii) the 729 cm-1 line of A is affected neither by furanose pucker nor glycosidic bond orientation and (iii) the 1200-1500 cm-1 region of the Raman spectrum of the A-T double helix is greatly altered by the B-to-Z transition. Conformation sensitive Raman frequencies in the 850-1700 cm-1 region are identified for both octamer and hexamer, and the Z-to-B transition of each is monitored by spectral changes which occur upon dissolving the crystal in H2O solution.

Base Sequence↗
PubMed1984

A one- and two-dimensional NMR study of the B to Z transition of (m5dC-dG)3 in methanolic solution.

The deoxyribose hexanucleoside pentaphosphate (m5dC-dG)3 has been studied by 500 MHz 1H NMR in D2O (0.1 M NaCl) and in D2O/deuterated methanol mixtures. Two conformations, in slow equilibrium on the NMR time scale, were detected in methanolic solution. Two-dimensional nuclear Overhauser effect (NOE) experiments were used to assign the base and many of the sugar resonances as well as to determine structural features for both conformations. The results were consistent with the an equilibrium in solution between B-DNA and Z-DNA. The majority of the molecules have a B-DNA structure in low-salt D2O and a Z-DNA structure at high methanol concentrations. A cross-strand NOE between methyl groups on adjacent cytosines is observed for Z-DNA but not B-DNA. The B-DNA conformation predominates at low methanol concentrations and is stabilized by increasing temperature, while the Z-DNA conformation predominates at high methanol concentrations and low temperatures. 31P NMR spectra gave results consistent with those obtained by 1H NMR. Comparison of the 31P spectra with those obtained on poly(dG-m5dC) allow assignment of the lower field resonances to GpC in the Z conformation.

DNA↗
PubMed1984

Bromination stabilizes poly(dG-dC) in the Z-DNA form under low-salt conditions.

Using circular dichroism studies, Pohl & Jovin (1972) [Pohl, F.M., & Jovin, T.M. (1972) J. Mol. Biol. 67, 375-396] demonstrated that poly(dG-dC) undergoes a salt-dependent conformational change characterized by a spectral inversion. The low-salt form corresponds to the right-handed B form of DNA and the high-salt form to the left-handed Z-DNA helix. Modification of poly(dG-dC) by adding bromine atoms to the C8 position of guanine and the C5 position of cytosine residues stabilized this polymer in the Z-DNA form under low-salt conditions. The guanine residues were found to be twice as reactive as the cytosine residues. With a modification of 38% Br8G and 18% Br5C, the polymers formed a stable Z-DNA helix under physiological conditions. The bromination produced spectroscopic features very similar to poly(dG-dC) in 4 M NaCl. However, bromination did not freeze the Z structure as was shown by ethidium bromide intercalation studies. Addition of the dye favored an intercalated B-DNA form. The conversion of B- to Z-DNA leads to profound conformational changes which were also seen by a reduced insensitivity to various exo- and endonucleases. Comparative studies showed that the brominated polymers have a high affinity to nitrocellulose filters. In 1 M NaCl, there was virtually no binding of B-DNA, but a substantial binding of Z-DNA was found even at rather low levels of bromination.(ABSTRACT TRUNCATED AT 250 WORDS)

Bromine↗
PubMed1984

Beta decay and the origin of biological chirality: new experimental results.

The proposed connection between the parity-violating handedness of beta particles in radioactive decay and the sign (L) of biological chirality (the Vester-Ulbricht [V-U] hypothesis) is being investigated by measuring the theoretically predicted asymmetry in the formation of triplet positronium in amino acid enantiomers by low energy positrons under reversal of the helicity of the positrons. We find the asymmetry in leucine to be (0.8 +/- 1.0) X 10(-4), i.e. consistent with the theoretical prediction of 10(-6) to 10(-7). The apparatus is now sensitive enough to test the predicted asymmetry in optically active molecules which have heavy atoms at their chiral centers. The connection between these results and asymmetry in radiolysis by beta-decay electrons is made, and the implications of our limits for the V-U hypothesis discussed. Although the above limits are 10(6) times lower than direct measurements of radiolysis, they are still not small enough to allow us to rule out the V-U hypothesis.

Elementary Particles↗
PubMed1984

AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d(m5CGTAm5CG).

Two hexanucleoside pentaphosphates , 5-methyl and 5-bromo cytosine derivatives of d( CpGpTpApCpG ) have been synthesized, crystallized, and their three-dimensional structure solved. They both form left-handed Z-DNA and the methylated derivative has been refined to 1.2 A resolution. These are the first crystal Z-DNA structures that contain AT base pairs. The overall form of the molecule is very similar to that of the unmethylated or the fully methylated (dC-dG)3 hexamer although there are slight changes in base stacking. However, significant differences are found in the hydration of the helical groove. When GC base pairs are present, the helical groove is systematically filled with two water molecules per base pair hydrogen bonded to the bases. Both of these water molecules are not seen in the electron density map in the segments of the helix containing AT base pairs, probably because of solvent disorder. This could be one of the features that makes AT base pairs form Z-DNA less readily than GC base pairs.

Adenine↗
PubMed1984

Synthesis of pyridine derivatives of L-phenylalanine as antisickling reagents.

Several bicyclic agents composed of L-phenylalanine coupled to various pyridines were synthesized: 2-, 3-, and 4-(L- phenylalanylamino )pyridine. All three compounds at 3 mM gave positive morphological antisickling effects on homozygous SS cells under reduced O2 tension. Studies on two of these compounds, 2- and 3-(L- phenylalanylamino )pyridine, showed that these agents increase the deoxy-HbS solubility ratio, Cs/ Cs0 , by 14% at 20 mM. Observed changes in the mean corpuscular hemoglobin concentration (MCHC) values of treated cells ranged from 4% at 1.3 mM to 15% at 5.6 mM in compound concentration. Very minor lytic activity was found for treated cells, indicating water uptake is responsible for changes in the MCHC. Further, exposure of sickle cells to a 3 mM concentration of these agents also increased by 6- to 7-fold cellular deformability of a treated erythrocyte population as compared to an untreated one at the same total O2 saturation of 47%. These agents demonstrate the potential of bicyclic compounds composed of a common constituent, L-Phe, in the development toward a viable therapeutic agent.

Anemia, Sickle Cell↗
PubMed1984

Potential use of biaromatic L-phenylalanyl derivatives as therapeutic agents in the treatment of sickle cell disease.

N-Phenylacetyl-L-phenylalanine (PAP) and L-phenylalanyl-3-aminopyridine ( PAPA ) are biaromatic agents with properties that make them suitable candidates for the development of a useful therapeutic agent for the treatment of sickle cell disease. PAP and PAPA are taken up by the erythrocyte to give intra-/extracellular concentration ratios of 2.2 and 1.5, respectively, after a 2-hr exposure period. The intracellular buildup of PAP and PAPA produces moderate decreases in the mean corpuscular hemoglobin concentration (MCHC) of 6 and 10%, respectively, at 3 mM and a further decline in MCHC with increased concentration. Both PAP and PAPA increase the deoxy-Hb S solubility, CS. If the solubility in the absence of the agent is COS, PAP and PAPA have CS/COS values of 1.21 and 1.14 at 20 mM, respectively, compared with a value of 1.06 for L-phenylalanine itself. Filterability assays of partially dexygenated homozygous sickle cells shows an increase in cell flexibility of 7 to 16 times more than that of untreated cells when these agents are present at 3-6 mM. These results are largely due to the reduction in the Hb S polymer content of the treated cells. At 3 mM or less, both PAP and PAPA delay the onset of gelation in reversible sickle cells for time periods that are likely to be therapeutically useful.

Anemia, Sickle Cell↗
PubMed1984

In Z-DNA the sequence G-C-G-C is neither methylated by Hha I methyltransferase nor cleaved by Hha I restriction endonuclease.

Plasmids carrying 24- or 32-base-pair inserts of alternating (dG-dC) residues were used to analyze the level of methylation of the G-C-G-C sites by Hha I DNA methyltransferase and their cleavage by Hha I endonuclease in the B-DNA or Z-DNA conformation. In supercoiled plasmids in which the inserts formed Z-DNA, the extent of methylation at the insert G-C-G-C sites was dramatically lower than the level of methylation at the G-C-G-C sites located outside the insert in the same plasmid. Similarly, cleavage by Hha I endonuclease was sharply lowered when the insert was in the Z-DNA form. In the relaxed plasmid, all its G-C-G-C sites were methylated to the same extent and the unmethylated sites were readily cleaved. After treatment with the methylase, the supercoiled plasmid was linearized and then digested with Hha I restriction endonuclease. This exposed unmethylated G-C-G-C sites from the insert that had been protected against cleavage in the Z conformation. A chemical reaction was used to study the distribution of the unmethylated cytosine residues. No accumulation of unmethylated cytosine residues was found anywhere along the entire 32-base-pair insert, which is consistent with a cooperative B-Z transition.

Base Sequence↗
PubMed1984

Secretion of human parathyroid hormone from rat pituitary cells infected with a recombinant retrovirus encoding preproparathyroid hormone.

In order to study the functions of precursors to secreted proteins, we expressed cloned DNA encoding human preproparathyroid hormone (preproPTH) in rat pituitary cells. We first constructed a recombinant plasmid containing human preproPTH cDNA and retroviral control signals. This recombinant plasmid was transfected into psi-2 cells, a packaging cell line that produces Moloney murine leukemia viral particles containing no retroviral RNA. The transfected psi-2 cells generated helper-free recombinant retrovirus encoding preproPTH, and this recombinant retrovirus was used to infect GH4 rat pituitary cells. Clonal lines of the infected GH4 cells contained copies of the recombinant provirus stably integrated via the long terminal repeats, and the expected RNA transcripts of proviral DNA accumulated in the cytoplasm, although no infectious virus was produced. The infected cells synthesized and processed preproPTH appropriately and secreted PTH in response to thyrotropin-releasing hormone, a secretagogue for GH4 cells. Use of recombinant retrovirus permits the introduction of DNA encoding normal and mutant secreted proteins into a number of cell types specialized for secretion. Analysis of the fate of the resultant proteins will help define the specific molecular interactions involved in transmembrane transport and processing of precursor proteins.

Amino Acid Sequence↗
PubMed1984

Restriction endonucleases can be used to study B-Z junctions in supercoiled DNA.

Plasmids containing (C-G)n inserts have been used to study the inhibition of cleavage by restriction endonucleases due to Z-DNA formation in negatively supercoiled plasmids. The enzyme BssHII, which recognizes G-C-G-C-G-C, is strongly inhibited when the insert forms Z-DNA. The BamHI recognition sequence (G-G-A-T-C-C) was placed in four different positions near the B-Z junction and the inhibition of BamHI cleavage was determined as a function of negative superhelical density. Formation of Z-DNA in the (C-G)n insert inhibited cleavage by BamHI when its recognition sequence was located immediately adjacent to the insert or four base pairs away from it. However, no inhibition was found when the BamHI recognition site was eight base pairs away. These experiments help to define the limits of the structural perturbation associated with the B-Z junction.

Cloning, Molecular↗
PubMed1984

Nucleotide sequence of human monocyte interleukin 1 precursor cDNA.

Interleukin 1 (IL-1) is a protein with several biological activities regulating host defense and immune responses. We report here the isolation of human IL-1 cDNA. It encodes a precursor polypeptide of 269 amino acids (30,747 Mr). mRNA isolated by hybridization to this cDNA was translated in a reticulocyte cell-free system, yielding immunoprecipitable IL-1. Furthermore, this hybrid-selected mRNA was injected into Xenopus laevis oocytes, which subsequently secreted biologically active IL-1. The cDNA nucleotide sequence suggests that IL-1 is initially translated as a precursor molecule that is subsequently processed into the 15,000-20,000 Mr protein usually associated with IL-1 activity.

Amino Acid Sequence↗