Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Fragmentation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,675 records · Page 93Linked to original sources
PubMed2005

Carbon position-specific isotope analysis of alanine and phenylalanine analogues exhibiting nonideal pyrolytic fragmentation.

Recent advances in gas chromatography combustion-isotope ratio mass spectrometry (GCC-IRMS) has made compound-specific isotope analysis routine, but reports on position-specific isotopic analysis are still scarce. On-line GC-pyrolysis (Py) coupled to GCC-IRMS is reported here for isolation and isotopic characterization of alaninol and phenethylamine, analogues of alanine and phenylalanine, respectively. Ideally, pyrolytic fragments will originate from unique sites within the parent molecule, and isotope ratios for each position within the parent can either be measured directly or calculated from fragment isotope ratios without substantially degrading the analytical precision. Alaninol pyrolysis yielded several fragments, of which CO and CH4 were used for isotope ratio calculations. Isotope labeling experiments showed that CO derived entirely from the C(1) position, while all three positions of alaninol contributed to CH4 (29.0 +/- 0.3% from C(1), 3.6 +/- 0.2% from C(2), and 66.9 +/- 1.1% from C(3)). We demonstrate iterative use of mass balance to calculate isotope ratios from all positions despite the nonideal positional fidelity of CH4. Pyrolysis of phenethylamine generated benzene and toluene fragments. Benzene derived entirely from C(ring), and toluene was proportionately formed from C(3) and C(ring). Relative intramolecular isotope ratios (Deltadelta13C) were calculated directly from delta13C of fragments or indirectly by mass balance. Though the C(3) isotope ratio was calculated from the benzene and toluene fragments, propagation of errors showed that the final precision of the determination was degraded due to the small contribution that C(3) makes to toluene. Samples of each amino acid from four different vendors showed natural variability between sources, especially at the C(1) position of alaninol (range of Deltadelta13C approximately 50 per thousand). The average precision was SD(Deltadelta13C) < 0.20 per thousand for directly measured positions of alaninol and phenethylamine. The precision of indirectly measured positions was poorer (SD(Deltadelta13C) = 0.94 per thousand for alaninol, 6.54 per thousand for phenethylamine) due to propagation of errors. These data demonstrate that GC-Py-GCC-IRMS data can be used to extract high-precision isotope ratios from amino acids despite nonideal positional fidelity in fragments and that natural intramolecular variability in delta13C can be used to distinguish different sources of amino acids.

Carbon Isotopes↗
PubMed1991

Preparation of the Fv fragment from a short-chain mouse IgG2a anti-dansyl monoclonal antibody and use of selectively deuterated Fv analogues for two-dimensional 1H NMR analyses of the antigen-antibody interactions.

The Fv fragment, a univalent antigen-binding unit with a molecular weight of 25,000, has successfully been prepared in high yield by limited proteolysis with clostripain of a short-chain mouse IgG2a anti-dansyl monoclonal antibody in which the entire CH1 domain is deleted [Igarashi, T., Sato, M., Takio, K., Tanaka, T., Nakanishi, M., & Arata, Y. (1990) Biochemistry 29, 5727-5733]. The Fv fragment obtained is stable at room temperature and retains its full antigen-binding capability. It has been shown that selective deuterium labeling of the Fv fragment, which is half the size of the Fab fragment, provides 1H NMR spectral data at a sufficient resolution for a detailed structural analysis of the antigen-combining site. NOESY spectra of an Fv analogue, in which all aromatic protons except for His C2'-H and Tyr C3',5'-H had been deuterated, were measured in the presence of varying amounts of dansyl-L-lysine. On the basis of the NOESY data obtained, it was possible to assign all the ring proton resonances for the dansyl group that is bound to the Fv fragment. It was also possible to obtain information about His and Tyr residues of the Fv fragment in the absence and presence of the antigen. On the basis of the NMR data obtained, we have shown that at least two Tyr residues along with one of the amide groups are directly involved in antigen binding. The mode of interaction of the dansyl ring with these residues in the Fv fragment has briefly been discussed.

Animals↗
PubMed1991

Use of fluorescence energy transfer to characterize the compactness of the constant fragment of an immunoglobulin light chain in the early stage of folding.

The CL fragment of a type-kappa immunoglobulin light chain in which the C-terminal cysteine residue was modified with N-(iodoacetyl)-N'-(5-sulfo-1-naphthyl)ethylenediamine (CL-AEDANS fragment) was prepared. This fragment has only one tryptophan residue at position 148. The compactness of the fragment whose intrachain disulfide bond was reduced in order for the tryptophan residue to fluoresce (reduced CL-AEDANS fragment) was studied in the early stages of refolding from 4 M guanidine hydrochloride by fluorescence energy transfer from Trp 148 to the AEDANS group. The AEDANS group attached to the SH group of a cysteine scarcely fluoresced when excited at 295 nm. For the reduced CL-AEDANS fragment, the fluorescence emission band of the Trp residue overlapped with the absorption band of the AEDANS group, and the fluorescence energy transfer was observed between Trp 148 and the AEDANS group in the absence of guanidine hydrochloride. In 4 M guanidine hydrochloride, the distance between the donor and the acceptor was larger, and the efficiency of the energy transfer became lower. The distance between Trp 148 and the AEDANS group for the intact protein estimated by using the energy-transfer data was in good agreement with that obtained by X-ray crystallographic analysis. By the use of fluorescence energy transfer, tryptophyl fluorescence, and circular dichroism at 218 nm, the kinetics of unfolding and refolding of the reduced fragment were studied. These three methods gave the same unfolding kinetic pattern. However, the refolding kinetics measured by fluorescence energy transfer were different from those measured by tryptophyl fluorescence and circular dichroism, the latter two giving the same kinetic pattern.(ABSTRACT TRUNCATED AT 250 WORDS)

Circular Dichroism↗
PubMed1983

Melting order of successively longer yeast phenylalanine-accepting transfer ribonucleic acid fragments with a common 5' end.

Temperature-jump methods were used to study the kinetics of the helix to coil transition in three fragments of yeast tRNAPhe that share a common 5' terminus (the 5' end of the mature tRNA). Correlation of the extrapolated helix dissociation time constants with NMR exchange broadening results allows assignment of the structural basis of the optical melting transition in the fragments. The results confirm nuclear magnetic resonance findings on these fragments: the 5' 1/4 fragment has no helical structure; the 5' 1/2 fragment contains the D stem; and the 5' 3/5 fragment contains the D stem and the anticodon stem. These are the structures expected if sequential folding of the tRNA during biosynthesis were to occur. The D stem is the last helix to melt in the 5' 3/5 fragment. We suggest that structural elements in addition to the four Watson-Crick base pairs of the D-stem helix are responsible for the anomalously high Tm of that hairpin.

Kinetics↗
PubMed1986

Conformation and stability of the constant fragment of the immunoglobulin light chain containing an intramolecular mercury bridge.

The constant fragment of the immunoglobulin light chain in which the intramolecular disulfide bond is reduced (reduced CL fragment) assumes a conformation very similar to that of the intact CL fragment and contains two sulfhydryl groups buried in the interior of the molecule [Goto, Y., & Hamaguchi, K. (1979) J. Biochem. (Tokyo) 86, 1433-1441]. In order to understand the role of the disulfide bond, a derivative in which the disulfide bond is replaced by an S-Hg-S bond was prepared and its conformation and stability were studied. The derivative was prepared by reacting the reduced CL fragment with mercuric chloride. Kinetic studies showed that the reaction is rate-limited by the unfolding process of the reduced CL fragment. The mercury derivative was as compact as the intact CL or reduced CL fragment, and a tryptophyl residue was found to be buried near the S-Hg-S bond in the interior of the protein molecule. Judging from the circular dichroic spectrum, however, the beta-structure characteristic of the immunoglobulin fold was disturbed. The stability of the derivative to guanidine hydrochloride was lower than that of the intact CL fragment, but the unfolding transition was reversible and cooperative. Decreased stability of the mercury derivative is due to its folded conformation being distorted by introduction of the S-Hg-S bond.

Bence Jones Protein↗
PubMed1987

Reactivity of chemically cross-linked fibrinogen and its fragments D toward the staphylococcal clumping receptor.

It has been established that the binding domain for the staphylococcal clumping receptor exists in fragment D of human fibrinogen [Hawiger J., Timmons, S., Strong, D. D., Cottrell, B. A., Riley, M., & Doolittle, R. F. (1982) Biochemistry 21, 1407; Strong, D. D., Laudano, A., Hawiger, J., & Doolittle, R. F. (1982) Biochemistry 21, 1414]. To examine the role of valency in the adhesive function of fibrinogen, its fragments were prepared by digestion with plasmin in the presence of calcium and purified by a two-step chromatographic procedure. Fragments D1 and E did not induce the staphylococcal clumping reaction. After they were prepared in oligomeric form by chemical cross-linking with glutaraldehyde, fragment D1 (Mr 94,000) became functionally reactive toward the staphylococcal clumping receptor, and fragment D3 (Mr 75,000) and fragment E (Mr 50,000) remained inactive. Fragment D dimer derived from enzymatic cross-linking was not reactive. Human fibrinogen cross-linked with glutaraldehyde usually reached a 250 times higher reactivity toward the staphylococcal clumping receptor, depending on the condition of the cross-linking reaction. It is concluded that the valency of fibrinogen in regard to its receptor binding domain and the availability of this domain are essential for the staphylococcal clumping reaction.

Aldehydes↗
PubMed1989

Interaction of two complementary fragments of the bovine spinal cord myelin basic protein with phospholipid bilayers. An ESR spin-label study.

The myelin basic protein (MBP) from bovine spinal cord was cleaved at the single tryptophan residue to produce an N-terminal fragment (F1) of molecular weight 12.6K and a C-terminal fragment (F2) of molecular weight 5.8K. The interactions of the two fragments with bilayers of the acidic lipid dimyristoylphosphatidylglycerol (DMPG) were compared with those of the intact protein, by using both chemical binding assays and spin-label electron spin resonance spectroscopy. The saturation binding stoichiometries of the two fragments were found to sum to that of the MBP, having values of 11, 24, and 36 mol of DMPG/mol of protein for F2, F1, and the MBP, respectively. The strength of binding was found to increase in the order F2 less than F1 less than MBP, which follows that of the net charges on the different fragments. The ionic strength dependence of the protein binding indicated that the interaction is primarily of electrostatic origin. The efficiency of displacement of the proteins by salt was in the order F2 greater than F1 greater than MBP, which correlates with both the strength of binding and the net charge on the different protein fragments. Nitroxide derivatives of phosphatidylglycerol (PG) labeled on the sn-2 chain were used to probe the protein-induced changes in the acyl chain dynamics. Both the fragments and the MBP decreased the lipid chain mobility as recorded by the C-5 atom and C-12 atom position nitroxide-PG spin-labels, in a manner which followed the protein binding curves.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1980

Binding of Escherichia coli ribonucleic acid polymerase holoenzyme to a bacteriophage T7 promoter-containing fragment: selectivity exists over a wide range of solution conditions.

The selectivity of binding of Escherichia coli RNA polymerase holoenzyme to a promoter-containing fragment of T7 DNA has been investigated over a range of solution conditions by using a double-label nitrocellulose filter binding assay. A 32P-labeled HaeIII restriction fragment of T7 D111 DNA containing the A1 and D promoters for the E. coli enzyme and a 3H-labeled nonpromoter HaeIII fragment of comparable size were incubated with sigma-saturated holoenzyme and filtered through a nitrocellulose membrane filter. We find that the extent of binding of polymerase to the promoter-containing fragment decreases dramatically with increasing salt concentrations and with increasing pH and increases moderately with increasing temperature in the range 0-37 degrees C. By contrast, the nonspecific interaction of polymerase with the nonpromoter fragment is known to be relatively insensitive to pH and temperature, though a strong function of salt concentration [deHaseth, O. L., Lohman, T. M., Burgess, R. R., & Record, M. T., Jr. (1978) Biochemistry 17, 1612-1622]. Selectivity of binding of RNA polymerase in our assay is demonstrated by a greater fractional retention of the promoter-containing fragment than of the nonpromoter fragment on the filter. We observe selective binding over the temperature range from 0 to 37 degrees C near neutral pH and over a wide range of Na+ concentrations, in the presence or absence of Mg2+. Because of the different dependences of promoter and nonpromoter binding on pH and temperature, the extent of selectivity increases with increasing temperature and decreases with increasing pH. Quantitative treatment of these binding data [Strauss, H. S., Burgess, R. R., & Record, M. t., Jr. (1980) Biochemistry (second paper of four in this issue)] confirms these conclusions and shows that selectivity is a function of ion concentration as well.

DNA Restriction Enzymes↗
PubMed1977

Transcription and translation of cloned Drosophila DNA fragments in Escherichia coli.

The expression of three unique DNA fragments from Drosophila melanogaster which have been inserted into Escherichia coli (E. coli) via the plasmid, pSC 101, was studied. The hybrid plasmid DNA molecules containing Drosophila DNA were transformed into the minicell producing strain of E. coli, X1411. Drosophila DNA-directed RNA synthesis was studied by hybridizing newly synthesized RNA isolated from the minicells with various DNA fragments which were immobilized on nitrocellulose filters. RNA was synthesized as readily from the inserted Drosophila DNA as from the original bacterial plasmid, pSC 101. In one case, transcription appeared to be initiated preferentially on one of the two strands of a Drosophila DNA fragment regardless of the orientation of that Drosophila DNA fragment with respect to the pSC 101 sequences. Two of the three Drosophila DNA fragments did not induce the synthesis of new polypeptides in minicells as detected by autoradiography of [35S]methionine-labeled polypeptides on polyacrylamide gels. The third Drosophila DNA fragment caused the synthesis of one additional polypeptide of 29 000 daltons. When an 8200 base pair portion of the third inserted Drosophila DNA (63% OF THE TOTAL Drosophila insertion) was removed by digestion with the restriction enzyme, Eco R1, this new polypeptide was no longer synthesized by minicells containing the remaining Drosophila DNA. When the 8200 base pair fragment was placed back into its parent plasmid as an inversion, the new polypeptide did not reappear. In addition, the presence of some, but not all, of the Drosophila DNA insertions affected the relative synthesis of the six polypeptides coded for by the parent plasmid, pSC 101.

Animals↗
PubMed2006

Proteolytic fragments of insulysin (IDE) retain substrate binding but lose allosteric regulation.

Treatment of an N-terminal-containing His6-tagged insulysin (His6-IDE) with proteinase K led to the initial cleavage of the His tag and linker region. This was followed by C-terminal cleavages resulting in intermediate fragments of approximately 95 and approximately 76 kDa and finally a relatively stable approximately 56 kDa fragment. The approximately 76 and approximately 56 kDa fragments exhibited a low level of catalytic activity but retained the ability to bind the substrate with a similar affinity as the native enzyme. The kinetics of the reaction of the IDE approximately 76 and approximately 56 kDa proteolytic fragments with a synthetic fluorogenic substrate produced hyperbolic substrate versus velocity curves, rather than the sigmoidal curve obtained with His6-IDE. The approximately 76 and approximately 56 kDa IDE proteolytic fragments were active toward the physiological peptides beta-endorphin, insulin, and amyloid beta peptide 1-40. Although activity was reduced by a factor of approximately 103-104 with these substrates, the relative activity and the cleavage sites were unchanged. Both the approximately 76 and approximately 56 kDa fragments retained the regulatory cationic binding site that binds ATP. Thus, the two proteinase K cleavage fragments of IDE retain the substrate- and ATP-binding sites but have low catalytic activity and lose the allosteric kinetic behavior of IDE. These data suggest a role of the C-terminal region of IDE in allosteric regulation.

Allosteric Regulation↗
PubMedDate not supplied

Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets.

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.

Algorithms↗
PubMed2006

Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking.

The computer program DAIM (Decomposition and Identification of Molecules) has been developed to automatically break up compounds in small-molecule libraries for fragment-based docking as well as database analysis. Here, DAIM is evaluated on 130 ligands derived from known crystal structures of ligand-protein complexes. The decomposition and a new fingerprint-based identification technique are used to select anchor fragments for docking. The docking results show that the DAIM selection is superior to size-based or random selection of fragments. To evaluate the usefulness for analyzing the fragment composition of a large library, DAIM is applied to a collection of about 1.85 million commercially available compounds. Interestingly, it is found that the set of most frequent cyclic and acyclic fragments originating from the decomposition of the 1.85 million molecules shows a large overlap with the most frequent fragments in a library of 5120 known drugs. DAIM has been successfully used in the in silico screening for inhibitors of beta-secretase and EphB4 kinase by fragment-based high-throughput docking. Possible future applications for de novo ligand design are briefly discussed.

Amyloid Precursor Protein Secretases↗
PubMed2006

Theoretical study of adsorption of sarin and soman on tetrahedral edge clay mineral fragments.

This study provides details of the structure and interactions of Sarin and Soman with edge tetrahedral fragments of clay minerals. The adsorption mechanism of Sarin and Soman on these mineral fragments containing the Si(4+) and Al(3+) central cations was investigated. The calculations were performed using the B3LYP and MP2 levels of theory in conjunction with the 6-31G(d) basis set. The studied systems were fully optimized. Optimized geometries, adsorption energies, and Gibbs free energies of Sarin and Soman adsorption complexes were computed. The number and strength of formed intermolecular interactions have been analyzed using the AIM theory. The charge of the systems and a termination of the mineral fragment are the main contributing factors on the formation of intermolecular interactions in the studied systems. In the neutral complexes, Sarin and Soman is physisorbed on these mineral fragments due to the formation of C-H...O, and O-H...O hydrogen bonds. The chemical bond is formed between a phosphorus atom of Sarin and Soman and an oxygen atom of the -2 charged clusters containing an Al(3+) central cation and -1 charged complex containing a Si(4+) central cation (chemisorption). Sarin and Soman interact mostly in the same way with the same terminated edge mineral fragments containing different central cations. However, the interaction energies of the complexes with an Al(3+) central cation are larger than these values for the Si(4+) complexes. The interaction enthalpies of all studied systems corrected for the basis set superposition error were found to be negative. However, on the basis of the Gibbs free energy values, only strongly interacting complexes containing a charged edge mineral fragment with an Al(3+) central cation are stable at room temperature. We can conclude that Sarin and Soman will be adsorbed preferably on this type of edge mineral surfaces. Moreover, on the basis of the character of these edge surfaces, a tetrahedral edge mineral fragment can provide effective centers for the dissociation.

Journal Article↗
PubMed2006

Electron impact fragmentation of size-selected krypton clusters.

Clusters of krypton are generated in a supersonic expansion and size selected by deflection from a helium target beam. By measuring angular distributions for different fragment masses and time-of-flight distributions for fixed deflection angles and fragment masses, the complete fragmentation patterns for electron impact ionization at 70 eV are obtained from the dimer to the heptamer. For each of the neutral Kr(n) clusters studied, the main fragment is the monomer Kr(+) ion with a probability f(n)(1) > 90%. The probability of observing dimer Kr(2)(+) ions is much smaller than expected for each initial cluster size. The trimer ion Kr(3)(+) appears first from the neutral Kr(5), and its fraction increases with increasing neutral cluster size n, but is always much smaller than that of the monomer or dimer. For neutral Kr(7), all possible ion fragments are observed, but the monomer still represents 90% of the overall probability and fragments with n > 3 contribute less than 1% of the total. Aspects of the Kr(n) cluster ionization process and the experimental measurements are discussed to provide possible reasons for the surprisingly high probability of observing fragmentation to the Kr(+) monomer ion.

Journal Article↗
PubMed2001

Discovery of a novel serine protease inhibitor utilizing a structure-based and experimental selection of fragments technique.

We report a set of strategies to develop novel ligands (Structure Based and Experimental Selection of Fragments: SbE-SF). First, a docking simulation utilizing DOCK3.5 is performed in order to screen the fragment database, which was generated with the in-house program FRAGMENT++ specifically for docking simulation purposes. Although the affinity of these small molecules (fragments) is expected to be low, the affinity of fragments selected by computation is assayed by experiment to determine which ones can be potent inhibitors. After determining such key fragments. additional fragments are attached to the key ones in order to increase the binding affinity,taking into account the binding modes predicted by computation. This method has been applied to a thrombin inhibitor study, resulting in the discovery of a novel inhibitor exhibiting pIC50 = 7.9.

Drug Design↗
PubMed1998

REP-PCR fragments as biomarkers for differentiating gastroduodenal disease-specific Helicobacter pylori strains.

We previously identified four potential putative gastroduodenal disease fragments by using the interspersed repetitive extragenic palindromic DNA sequence based PCR (REP-PCR) technique. We investigated these fragments with regard to their disease specificity. The putative disease-specific REP-PCR fragments were cloned, mapped by restriction enzymes, cross-hybridized, and confirmed by Southern hybridization. The four fragments were also used as probes against REP-PCR amplicons from H. pylori isolates obtained from gastritis (N = 20), duodenal ulcer (N = 30), and gastric cancer patients (N = 30). Three of these fragments (1.4- and 0.76-kb for gastritis; 1.35 kb for duodenal ulcer) were amplified without any discrimination between any disease-specific H. pylori isolates. However, amplification following hybridization with the fourth 0.81-kb fragment was observed only from gastritis (60%) and duodenal ulcer (52%) but with none (0%) of gastric cancer patients. Nucleotide sequence analysis of the 0.81-kb fragment revealed that it was an open reading frame of the hypothetical protein HP0373 matched to the position of 380,966 to 383,068 nucleotides of the H. pylori complete genome sequence. Hence, the REP-PCR sequence was not a extragenic palindromic DNA sequence. The hypothetical protein was also present in all the tested isolates. The REP-PCR fingerprinting technique is useful to differentiate disease-specific H. pylori strains based on the interspersed repetitive extragenic palindromic DNA sequences; however, it may not be useful to identify disease-specific virulence determinant(s) without being confirmed by DNA sequence analysis and functional studies.

Amino Acid Sequence↗
PubMed1978

Studies of visual synthesis: integration of fragments into forms.

On each of a series of trials, subjects indicated whether two sequential visual forms were the same or different. The first form was presented on some trials as a whole within a square frame and on others in fragments--with its perimeter distributed over two or three frames. The subject was instructed to visualize the first form as a whole in any case, and study time (ST) for the form was recorded. The same/different reaction time (RT) for the second, test, form (always presented in one frame) was also recorded. Experiment 1 revealed that variables affecting ST had little effect on RT and indicated that subjects can process fragments of forms in parallel. Experiment 2 demonstrated that the representation encoded from fragments differed from one generated from long-term memory. Whereas the first experiments used wholes as test stimuli, in Experiments 3 and 4 on some trials, fragments were used. In Experiment 3, RT was facilitated when a test fragment coincided with an intact fragment of the first stimulus. This indicated that first stimuli were not encoded as complete wholes. In Experiment 4, irregular forms were used as stimuli, and the RT data departed from predictions of the parallel model. Taken as a whole, the results place constraints on the codes produced by constructive processes acting to synthesize fragments into wholes.

Discrimination, Psychological↗
PubMed2004

LDFF, the large molecular weight DNA fragmentation factor, is responsible for the large molecular weight DNA degradation during apoptosis in Xenopus egg extracts.

DNA degradation is a biochemical hallmark in apoptosis. It has been demonstrated in many cell types that there are two stages of DNA fragmentation during the apoptotic execution. In the early stage, chromatin DNA is cut into large molecular weight DNA fragments, although the responsible nuclease(s) has not been recognized. In the late stage, the chromatin DNA is cleaved further into short oligonucleosomal fragments by a well-characterized nuclease in apoptosis, the caspase-activated DNase (CAD/DFF40). In this study, we demonstrate that large molecular weight DNA fragmentation also occurs in Xenopus egg extracts in apoptosis. We show that the large molecular weight DNA fragmentation factor (LDFF) is not the Xenopus CAD homolog XCAD. LDFF is activated by caspase-3. The large molecular weight DNA fragmentation activity of LDFF is Mg2+-dependent and Ca2+-independent, can occur in both acidic and neutral pH conditions and can tolerate 45 degrees C treatment. These results indicate that LDFF in Xenopus egg extracts might be a new DNase (or DNases) responsible for the large DNA fragmentation.

Animals↗