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J Leszczynski

Publications and source records attributed to J Leszczynski.

At least 37 records · Page 2Linked to original sources
PubMed1997

Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study.

Base-stacking interactions in canonical and crystal B-DNA and in Z-DNA steps are studied using the ab initio quantum-chemical method with inclusion of electron correlation. The stacking energies in canonical B-DNA base-pair steps vary from -9.5 kcal/mol (GG) to -13.2 kcal/mol (GC). The many-body nonadditivity term, although rather small in absolute value, influences the sequence dependence of stacking energy. The base-stacking energies calculated for CGC and a hypothetical TAT sequence in Z-configuration are similar to those in B-DNA. Comparison with older quantum-chemical studies shows that they do not provide even a qualitatively correct description of base stacking. We also evaluate the base-(deoxy)ribose stacking geometry that occurs in Z-DNA and in nucleotides linked by 2',5'-phosphodiester bonds. Although the molecular orbital analysis does not rule out the charge-transfer n-pi* interaction of the sugar 04' with the aromatic base, the base-sugar contact is stabilized by dispersion energy similar to that of stacked bases. The stabilization amounts to almost 4 kcal/mol and is thus comparable to that afforded by normal base-base stacking. This enhancement of the total stacking interaction could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation.

Base Composition↗
PubMed1997

Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: ab initio quantum-chemical and empirical potential study.

Neutral (G.GC, A.AT, G.AT, T.AT, and C(imino).GC) and protonated (CH+.GC and AH+.GC) hydrogen-bonded trimers of nucleic acid bases were characterized by ab initio methods with the inclusion of electron correlation. In addition, the influence of metal cations on the third-strand binding in Purine-Purine-Pyrimidine (Pu.PuPy) reverse-Hoogsteen triplets has been studied. The ab initio calculations were compared with those from recently introduced force fields (AMBER4.1, CHARMM23, and CFF95). The three-body term in neutral trimers is mostly negligible, and the use of empirical potentials is justified. The only exception is the neutral G.GC Hoogsteen trimer with a three-body term of -4 kcal/mol. Protonated trimers are stabilized by molecular ion-molecular dipole attraction and the interaction within the complex is nonadditive, with the three-body term on the order of -3 kcal/mol. There is a significant induction interaction between the third-strand protonated base and guanine. The calculations indicate an enhancement of the third-strand binding in the G.GC reverse-Hoogsteen trimer due to-metal cation coordination to the N7/O6 position of the third-strand guanine. Interactions between metal cations and complexes of DNA bases are in general highly non-additive; the three-body term is above-10 kcal/mol in a complex of a divalent cation (Ca2+) with the GG reverse-Hoogsteen pair. The pairwise additive empirical potentials qualitatively underestimate the binding energy between cation and base.

Adenine↗
PubMed1996

An enzyme immunoassay based micro-neutralization test for titration of antibodies to human cytomegalovirus (CMV) and its correlation with direct ELISA measuring CMV IgG antibodies.

An ELISA-based micro-neutralization (Nt) test in MRC-5 cells for titration of neutralizing antibodies against human cytomegalovirus (CMV) in human plasma and preparations of immune globulins was developed to eliminate microscopic reading of cytopathic effect (CPE), a process that is subjective and time consuming. Un-neutralized CMV from the Nt reaction and grown in MRC-5 cells as per the standard micro-Nt test was coated in the same plates by various methods and CMV antigen was quantified by polyclonal or monoclonal CMV antibodies. Optimal coating of plates with CMV antigen (100 TCID50 of virus grown on MRC-5 cells for 7 days) was obtained by freezing/thawing of virus infected MRC-5 cells in phosphate buffered saline, ph 7.2. The CMV antigen treated sequentially with CMV monoclonal antibody to late nuclear protein antigen, goat anti-mouse IgG3 alkaline phosphatase conjugate and phosphatase substrate gave an absorbance of 1 at 410 nm wavelength whereas uninfected MRC-5 cells treated under similar conditions did not show any absorbance. The optimal Nt reaction occurred at 37 degrees C for 1-2 h and was unaffected by complement. At 4 degrees C, CMV was inactivated in 1-2 h. The antibody titres were affected by the virus dose used in the Nt test over a range of 20 to 798 TCID50. When the titre was determined against a reference serum, the effect of virus dose on the Nt titre was reduced. Complete neutralization virus read microscopically correlated with ELISA absorbance of < 0.1. CPE produced by approximately 1 TCID50 of CMV showed an absorbance of 0.1 or more. The correlation coefficient (r) between Nt titres and CMV IgG antibodies determined by ELISA was 0.69 (P < 0.001) for 257 human plasma samples and 0.85 (P < 0.001) for 50 immune globulin preparations.

Antibodies, Viral↗
PubMed1996

IgG subclass antibodies to human cytomegalovirus (CMV) in normal human plasma samples and immune globulins and their neutralizing activities.

An enzyme-linked immunoabsorbent assay (ELISA) was developed for quantitation of IgG subclass antibodies to human cytomegalovirus (CMV) in human serum or plasma samples and in immune globulin (IG) preparations. The assay was based on the parallel titration of known concentrations of purified IgG subclass myeloma proteins and a specific CMV antiserum. The purified IgG subclass myeloma proteins were captured on an ELISA plate pre-coated with anti-human kappa, anti-human lambda or a mixture of anti-human kappa and lambda antibodies and the specific antiserum was titrated against CMV antigen coated on the plate. IgG subclass antibodies, captured or bound to antigen, were quantitated with IGG subclass heavy chain specific monoclonal antibodies. The method was highly reproducible, specific and sensitive. Using this method, 257 human plasma samples and 50 IG preparations were assayed for CMV specific IgG subclass and IgM antibodies. The major IgG subclass antibody to CMV was IgG1 which represented more than 96% of CMV IgG antibodies, followed by IgG3 (mean CMV IgG3 antibody content was 3% of IgG antibodies in IG preparations and 1.8% in plasma samples). A majority of the samples had low levels of IgG2 antibodies and a few samples exhibited low levels of IgG4 antibodies. IG preparations showed very low levels of CMV IgM antibodies whereas plasma samples had 14.2% of CMV antibodies (IgG and IgM) as IgM antibodies. Virus neutralizing (Nt) activity of these samples showed a significant correlation with CMV IgG1 antibodies. Nine samples of plasma and IGs were further evaluated for Nt activity of IgG1 and IgG3 antibodies by separating IgG3 from the rest of the antibodies with protein A agarose. IgG3 antibodies showed much higher Nt activity than IgG1 antibodies suggesting that enrichment of IgG3 antibodies in IG preparations may be useful in preparing CMV specific IG.

Antibodies, Viral↗
PubMed1996

Stabilization of respiratory syncytial virus (RSV) against thermal inactivation and freeze-thaw cycles for development and control of RSV vaccines and immune globulin.

A high-titered and stable respiratory syncytial virus (RSV) is essential for the development of RSV vaccines and quality control of vaccines and RSV immune globulin. We increased the virus titer of RSV seed stock, and virus preparations made from this seed stock, 100 times by removing defective interfering particles using limiting dilution procedure. RSV preparations made from the new seed stock had infectivity titers ranging from 10(7.6) to 10(8.2) TCID50 per ml for five lots made over a period of 3 years. Unstabilized RSV lost most of its infectivity at -86 degrees C within 2-3 weeks, at 37 degrees C within 24 hr, at 56 degrees C within 3 min and after five freeze-thaw cycles. The high titered virus was stabilized at -86 degrees C for 3 years, at 37 degrees C for 3 days, at 56 degrees C for 6 min and against five freeze-thaw cycles. Most effective stabilizers included 25% sucrose, 10% trehalose and 45% fetal bovine serum (FBS) in Medium 199 whereas 3.5% dimethyl sulfoxide, > or = 45% FBS in phosphate buffered saline, 40% glycerol and 10% sorbitol also stabilized RSV to lesser and variable degrees. A mixture of 0.5% gelatine and 0.3% sodium glutamate stabilized the virus for a short period whereas 0.1 M MgCl2 and 25% FBS did not stabilize the virus. The stabilized high-titered virus is very useful for achieving reproducibility in serologic assays. A broad spectrum of stabilizers, such as those evaluated in this study, would be useful in choosing the most suitable formulation for stabilizing a live RSV vaccine.

Cryopreservation↗
PubMed1996

Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions.

An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are more stable than the neutral base pairs. Two energy contributions not present in the neutral base pairs stabilize the protonated base pairs: the molecular ion - dipole interaction, and the induction interaction. The molecular ion - dipole stabilization dominates in base pairs with highly polar neutral monomers, such as the C...CH+ base pair. The induction interaction is not included in the commonly used empirical potentials, which do not reproduce the changes in intermolecular stabilization due to protonation. We demonstrate that the base stacking of several consecutive C...CH + pairs, as proposed for polycytidylic acid and i-DNA, is strongly repulsive. We also show that the intermolecular interactions strongly prefer protonation of adenine in protonated adenine-cytosine pairs.

Base Composition↗
PubMed1996

Nonplanar DNA base pairs.

Three-dimensional structures of a representative set of more than 30 hydrogen-bonded nucleic acids pairs have been studied by reliable ab initio quantum mechanical methods. We show that many hydrogen-bonded nucleic acid base pairs are intrinsically nonplanar, mainly due to the partial sp3 hybridization of nitrogen atoms of their amino groups and secondary electrostatic interactions. This finding extends the variability of intermolecular interactions of DNA bases in that i) flexibility of the base pairs is larger than has been assumed before, and ii) attractive proton-proton acceptor interactions oriented out of the base pair plane are allowed. For example, all four G-A mismatch base pairs are propeller twisted, and the energy preferences for the nonplanar structures range from less than 0.1 kcal/mol to 1.8 kcal/mol. We predict that nonplanarity of the amino group of guanine in the G(anti)...A(anti) pair of the ApG step of the d(CCAAGATTGG)2 crystal structure is an important stabilizing factor that improves the energy of this structure by almost 3 kcal/mol. Currently used empirical potentials are not accurate enough to properly cover the interactions associated with amino-group and base-pair nonplanarity.

Base Composition↗
PubMed1996

Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies.

Ab initio quantum-chemical calulations with inclusion of electron correlation made since 1994 (such reliable calculations were not feasible before) significantly modified our view on interactions of nucleic acid bases. These calculations allowed to perform the first reliable comparison of the strength of stacked and hydrogen bonded pairs of nucleic acid bases, and to characterize the nature of the base-base interactions. Although hydrogen-bonded complexes of nucleobases are primarily stabilized by the electrostatic interaction, the dispersion attraction is also important. The stacked pairs are stabilized by dispersion attraction, however, the mutual orientation of stacked bases is determined rather by the electrostatic energy. Some popular theories of stacking were ruled out: The theory based on attractive interactions of polar exocyclic groups of bases with delocalized electrons of the aromatic rings (Bugg et al., Biopolymers 10, 175 (1971), and the pi-pi interactions model (C.A. Hunter, J. Mol. Biol. 230, 1025 (1993)). The calculations demonstrated that amino groups of nucleobases are very flexible and intrinsically nonplanar, allowing hydrogen-bond-like interactions which are oriented out of the plane of the nucleobase. Many H-bonded DNA base pairs are intrinsically nonplanar. Higher-level ab initio calculations provide a unique set of reliable and consistent data for parametrization and verification of empirical potentials. In this article, we present a short survey of the recent calculations, and discuss their significance and limitations. This summary is written for readers which are not experts in computational quantum chemistry.

Base Composition↗
PubMed1994

Comparison of antibody concentrations and protective activity of respiratory syncytial virus immune globulin and conventional immune globulin.

Relative to conventional immune globulins (IG, 13 lots), IGs prepared from donors with high activity by microneutralization assay to respiratory syncytial virus (RSVIG, 8 lots) had significantly higher neutralizing antibodies to 6 RSV strains (mean enrichment, 5.2-fold; range, 2.6- to 10.0-fold). In contrast, IgG antibody concentrations to whole RSV, fusion protein, or glycoproteins of A and B strains were similar in RSVIG and IG. Treatment of cotton rats with RSVIG at 0.5 g/kg 24 h before RSV challenge reduced RSV by 99% in the lungs (P < .001). RSVIG at 5.0 g/kg reduced RSV by 99% in the nose. IG at 5.0 g/kg had efficacy similar to that of RSVIG at 0.5 g/kg. Serum plaque-reduction neutralization titers of 1/390 resulted in 99% reduction of lung RSV and titers of 1/3500 resulted in 99% reduction in nose RSV. Relative to IG, RSVIG is enriched selectively in RSV neutralizing antibodies and has approximately 10 times greater protective activity in cotton rats.

Animals↗
PubMed1983

Evaluation of varicella-zoster immune globulin: protection of immunosuppressed children after household exposure to varicella.

Varicella-zoster immune globulin (VZIG), an immunoglobulin prepared from normal donor plasma selected for high titer of antibody to varicella-zoster virus (VZV), and zoster immune globulin (ZIG), prepared from the plasma of donors convalescing from herpes zoster, were compared in a double-blind, randomized clinical trial to determine their relative efficacy in protecting immunosuppressed children from severe varicella. VZV infection occurred in 49 (60.4%) of 81 recipients of VZIG and in 57 (68.6%) of 83 recipients of ZIG. These rates and the clinical severity of varicella were not significantly different; however, the subclinical infection rate was significantly higher in ZIG recipients (31.3% vs. 16.0%). This difference was accounted for by a subgroup of patients receiving immunosuppressive therapy for nonneoplastic diseases. Doubling the dose of VZIG administered reduced the rate of subclinical infection. These data indicate that VZIG can be used to protect immunosuppressed children from severe chicken pox.

Chickenpox↗
PubMed1983

Prevention of cytomegalovirus infection by cytomegalovirus immune globulin after marrow transplantation.

In an effort to prevent cytomegalovirus infection among seronegative patients having marrow transplants, a globulin with high antibody levels against cytomegalovirus was given before and for 11 weeks after transplantation in a randomized trial. Among 36 patients who received no prophylactic granulocyte transfusions, globulin recipients had significantly fewer infections than controls (2 of 17 versus 8 of 19, p = 0.05 by Fisher's exact test and p = 0.03 by Mantel-Cox test). Conversely, infection rates were high and unchanged by globulin use among patients who received granulocytes from seropositive donors (7 of 8 recipients versus 6 of 7 controls). The lack of effect of the globulin among patients receiving transfusions of granulocytes from seropositive donors may suggest that the dose of antibody was insufficient or that antibody is ineffective against virus transmitted in granulocytes. We conclude that cytomegalovirus infection can be prevented by immunoprophylaxis in seronegative patients having marrow transplants who are not given granulocyte transfusions.

Adolescent↗
PubMed1975

Pigmented villonodular synovitis in multiple joints. Occurrence in a child with cavernous haemangioma of lip and pulmonary stenosis.

A case is presented of pigmented villonodular synovitis involving three joints in a 7-year-old girl. The diagnosis was confirmed at surgery and by histology. The patient also exhibited a haemangioma of the upper lip and a congenital pulmonary stenosis of mild degree. Subtotal synovectomy of the right knee and of both ankles was performed. The lesion recurred in both ankles after 6 months. Review of the literature failed to reveal any previous report of multiple joint involvement by pigmented villonodular synovitis in childhood and it appears that simultaneous involvement of three joints has not previously been described. Scintiscanning with 99mTc stannous pyrophosphate showed increased vascularity of the involved joints immediately after injection, but no increased osteoblastic activity was seen on the delayed scan. This radionuclide scanning technique is therefore helpful in distinguishing pigmented villonodular synovitis from other arthropathies.

Ankle↗
PubMedDate not supplied

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases.

This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C [bond] H...O interbase contacts, sugar-base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino-acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation-pi interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed.

Cations↗