SEARCH · PubMed Health

Results for “SSB”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 271 records · Page 15Linked to original sources

PubMed1981

Single-strand and double-strand deoxyribonucleic acid breaks produced by several bleomycin analogues.

Production of single-strand breaks (ssb) and double-strand breaks (dsb) of PM2 phage DNA by several structurally related bleomycin (BLM) analogues was studied by gel electrophoresis. BLM A2 and BLM B2 produced a comparable extent of dsb. In various experiments, BLM A2 and BLM B2, at 22-41 ng/mL, degraded 50% of the form I DNA into 33-38% form II and 12-17% form III DNA. BLM B1' produced ssb and dsb at a ratio similar to that of BLM A2, but both at a rate less than half that of BLM A2. Phleomycin (PLM) D1 induced an equivalent amount of ssb but only one-eighth of dsb induced by BLM B2. The relatively lower extent dsb production for PLM D1 was observed either in borate buffer (pH 9.5) or in Tris-HCl buffer (pH 7.5) and in the presence or absence of exogenous Fe(II). Deamido-BLM A2 produced ssb to an extent approximately half that of BLM A2 and dsb to less than one-eighth that of BLM A2. The following conclusions were drawn. (1) BLM analogues produced ssb and dsb to different extents and ratios. (2) The ratio of dsb to ssb varied depending on the analogue, indicating a lack of a direct correlation between ssb and dsb. (3) The extent of ssb and dsb was affected by modifications on both the C- and N-terminal half-molecules of BLM: modification of either the N-terminal amide or the bithiazole greatly reduced dsb, whereas changes in structure or charge in the C-terminal amine affected ssb and dsb to a similar extent.

Bleomycin↗

PubMedDate not supplied

A common regulatory region shared by divergently transcribed genes of the Escherichia coli SOS system.

The Escherichia coli single-stranded DNA binding protein (SSB) is implicated in DNA replication, recombination and repair. On the chromosome, the ssb gene is located adjacent to the excision repair gene uvrA, but the two genes are transcribed in opposite directions. uvrA has been shown to be part of the E. coli SOS system by introducing Mud(Ap, lac) insertions distal to the regulatory region of the gene in the chromosome. Recent investigations suggest that SSB is also involved in the SOS response. However, because the SSB protein is essential to the cell, the inducibility of the ssb gene cannot be investigated by the insertion method. Therefore, we used plasmids harbouring the regulatory region of ssb fused to the galK structural gene, while leaving an intact ssb gene in the chromosome. We show here that expression of the ssb gene is dependent on two promoters of which one is damage inducible. Evidence is presented that the divergently transcribed ssb and uvrA genes are controlled by a common LexA binding site.

Bacterial Proteins↗

PubMed2003

Three-strand exchange by the Escherichia coli RecA protein using ITP as a nucleotide cofactor: mechanistic parallels with the ATP-dependent reaction of the RecA protein from Streptococcus pneumoniae.

The RecA protein from Escherichia coli promotes an ATP-dependent three-strand exchange reaction between a circular single-stranded DNA (ssDNA) and a homologous linear double-stranded (dsDNA). We have now found that under certain conditions, the RecA protein is also able to promote the three-strand exchange reaction using the structurally related nucleoside triphosphate, ITP, as the nucleotide cofactor. However, although both reactions are stimulated by single-stranded DNA-binding (SSB) protein, the ITP-dependent reaction differs from the ATP-dependent reaction in that it is observed only at low SSB protein concentrations, whereas the ATP-dependent reaction proceeds efficiently even at high SSB protein concentrations. Moreover, the circular ssDNA-dependent ITP hydrolysis activity of the RecA protein is strongly inhibited by SSB protein (suggesting that SSB protein displaces RecA protein from ssDNA when ITP is present), whereas the ATP hydrolysis activity is uninhibited even at high SSB protein concentrations (because RecA protein is resistant to displacement by SSB protein when ATP is present). These results suggest that SSB protein does not stimulate the ITP-dependent strand exchange reaction presynaptically (by facilitating the binding of RecA protein to the circular ssDNA substrate) but may act postsynaptically (by binding to the displaced strand that is generated when the circular ssDNA invades the linear dsDNA substrate). Interestingly, the mechanistic characteristics of the ITP-dependent strand exchange reaction of the E. coli RecA protein are similar to those of the ATP-dependent strand exchange reaction of the RecA protein from Streptococcus pneumoniae. These findings are discussed in terms of the relationship between the dynamic state of the RecA-ssDNA filament and the mechanism of the SSB protein-stimulated three-strand exchange reaction.

Adenosine Triphosphate↗

PubMed1992

Detection of single-strand breaks and base damage in DNA of blood cells from leukaemia patients receiving chemo- and radiotherapy.

Chemotherapy combined with total-body irradiation (TBI), a conditioning regimen for bone-marrow transplantation (BMT), causes lesions in the cellular DNA of the patients treated. To understand possible consequences of the DNA damage induced during such treatment, information is required about the nature of the damage, the level of induction and its persistence, and about the importance of the various lesions for cell-lethality and/or mutation induction. Recently, we developed a sensitive immunochemical method to quantify single-strand breaks (SSB) in the DNA of mammalian cells. In addition, a modification of the so-called alkaline elution technique was introduced which allows quantification of SSB together with base damage (SSB+BD). These methods have now been applied successfully to study the in vivo induction and repair of DNA damage in WBC of leukaemia patients who prior to BMT were treated with cyclophosphamide (CY) and received TBI. SSB and SSB+BD were determined after two treatments with CY (60 mg kg-1) followed by TBI (4.5-8.6Gy). The CY treatments gave rise to rather persistent SSB. In addition to these, radiation-induced SSB and SSB+BD could be detected shortly after TBI. However, 105 min after TBI, these SSB could be observed no longer, as a result of rapid repair.

Acute Disease↗

PubMed1994

Influence of nucleic acid base composition on radiation-induced strand breakage in single stranded DNA: a time resolved study.

The following study investigates the pathways involved in the induction of single strand breaks (ssb) in various samples of single stranded (ss) DNA (calf thymus, Micrococcus lysodeikticus, Clostridium perfringens) with differing nucleic acid base composition. The time scale for the induction of ssb was determined from changes in the light scattering intensity following pulse irradiation of aqueous solutions containing these ssDNA samples at pH7.8 under either aerated or deaerated conditions. The induction of ssb under these conditions is predominantly by the hydroxyl radical and shows various kinetically distinct components. The immediate ssb (t < 0.02 s) account for approximately 40-60% of the total yield of ssb. The majority of these ssb are suggested to arise from the 'common' initial attack of the hydroxyl radicals at the sugar phosphate backbone for each of the three DNA samples. Furthermore, slower components for ssb formation (t > 0.02 s) were observed and are suggested to occur through base radical mediated H-atom abstraction from the sugar moiety. The half lives for formation of the majority of ssb, formed through this base radical-mediated H-atom abstraction(s), are in the range of 20-43 ms. The yields of these 'base-mediated' ssb vary markedly (under both aerobic and anaerobic conditions) and reflect the base composition of the DNA sample. It is suggested from these studies that the OH-induced base radicals of guanine/cytosine are more effective precursors for strand breakage than those from adenine/thymine in ssDNA.

Base Composition↗

PubMed1997

Increase in DNA single-strand break rejoining by continuous exposure of human mononuclear blood cells to radioiodine ((131)I) in vitro.

Radioiodine ((131)I) induced a dose- and time-dependent increase in DNA single-strand breaks (DNA-ssb) in human (G0) mononuclear blood cells (MNC) in vitro. Incubation of MNC with 22MBq (131)I/ml at 4 degrees C caused a linear, time-dependent induction of DNA-ssb (increase in elution rate: 24.7 x 10(-3) h(-1) per 100 min incubation with (131)I). However, if MNC were incubated at 37 degrees C a decrease in the slope of the time effect curve was observed after about 300 min incubation with 22 or 30 MBq (131)I/ml. The goodness of fit of different regression models was assessed by Akaike's Information Criterion (AIC). The best fit was obtained for a non-linear model (y=a+bx+cx(0.5); AIC=53.5; where x is incubation time and y is elution rate), whereas other models including the linear regression model y=a+bx; AIC=38.6) were worse. As the total induction of DNA-ssb at 4 degrees C was constant with time, the decrease in the slope of the time effect curve (DNA-ssb versus time) at 37 degrees C can be interpreted as an increase in rejoining of DNA-ssb. Inhibition of both RNA and protein synthesis clearly increased the extent of DNA-ssb observable after incubation with (131)I. Thus, during continuous exposure of MNC to (131)I, proteins were synthesized which rejoined DNA-ssb. However, incubation of MNC with (131)I (44 MBq/ml) at 37 degrees C under conditions expected to lead to inhibition of RNA and/or protein synthesis still resulted in a decrease of the slope of the time effect curve, indicating a stimulation of DNA-ssb rejoining. Thus, we favour the hypothesis that the increase in the activity of DNA-ssb rejoining, besides de novo synthesis of repair enzymes, is also caused by a post-translational stimulation of DNA-repair enzymes and that this stimulation possibly is mediated by DNA-fragments.

DNA Repair↗

PubMed1991

Comparison of DNA alkali-labile sites induced by 4-(methylnitrosamino)-1(3-pyridyl)-1-butanone and 4-oxo-4-(3-pyridyl)butanal in rat hepatocytes.

4-Oxo-4-(3-pyridyl)butanal (OPB) is an aldehyde formed during the activation of the tobacco-specific N-nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Using the DNA alkaline elution technique, the properties of DNA alkali-labile sites induced in the isolated rat hepatocytes by NNK and OPB were compared. The DNA single-strand break (SSB) frequencies in vitro, as measured by the elution rate (ER), ranged from 0.015 to 0.479 and were proportional (r2 = 0.991) to the dose (0-2 mM) of OPB. These concentrations, however, were slightly cytotoxic. For example, the LC50 after 4 h of exposure was 2.8 mM. This suggests that OPB-induced DNA SSB result from additive effects of OPB-DNA interaction and the indirect DNA damage associated with OPB cytotoxicity. NNK induced a significant and dose-dependent increase of DNA fragmentation at concentrations ranging from 0.5 to 5.0 mM with ER values ranging from 0.012 to 0.274 (r2 = 0.951). Genotoxicity as measured by the DNA-damaging potency coefficient (DDP) was 810, 345, 131 and 75 for N-methyl-N-nitrosourea (MNU), N-nitrosodimethylamine (NDMA), OPB and NNK respectively. Both MNU- and NNK-induced DNA lesions showed increased lability with increased pH (from 12.1 to 12.5) of the eluting buffer (r2 = 0.979 and 0.967 respectively). In contrast, the number of OPB-induced labile sites were not affected by increases in the pH. These results indicate that OPB is not the metabolite contributing the majority of alkali-labile sites generated by NNK. The filter elution procedure was used to study the in vitro rejoining of SSB in DNA induced by NNK. The extent of DNA SSB rejoining after 18 h of culture of hepatocytes in NNK-free medium were dependent on the concentration of NNK (0.5, 2.0 and 5.0 mM) and ranged from 50 to 90%. Rats were injected s.c. with NNK (0.39 mmol/kg). SSB frequency in liver DNA increased rapidly and reached a maximum 12 h after injection. DNA SSB frequency declined during the next 2 weeks with biphasic kinetics. The fast phase (75% rejoining of DNA SSB between 12 h and 2 days) was followed by a slow one (25% of DNA SSB maintained during the next 5 days but not present after 2 weeks). The results of this study better define the role of OPB-induced DNA damage. The persistence of DNA SSB in the liver of NNK-treated rats reflects the inability of this tissue to repair all DNA lesions.

Analysis of Variance↗

PubMed1985

Indirect induction of a clastogenic effect in epidermal cells by a tumor promoter.

The mechanisms by which tumor promoters exert their effects on target tissues are not clearly understood. Recent studies have demonstrated that phorbol ester tumor promoters induce an oxidative burst in phagocytes and DNA single-strand breaks (SSB) in leukocytes. The purpose of the research presented here was to investigate the clastogenic effects of tumor promoters in the target cell population, primary mouse epidermal cells co-incubated with leukocytes. Using the alkaline elution assay to detect DNA SSB, it was demonstrated that tumor promoters induce DNA SSB in primary mouse epidermal cells incubated in the presence of leukocytes. By increasing the ratio of leukocytes to epidermal cells from 1:2 to 10:1, in the presence of 1.6 X 10(-6) M 12-O-tetradecanoylphorbol-13-acetate (TPA), a ratio dependent increase in DNA SSB was observed (from 9 X 10(-2) to 121 DNA SSB per 10(6) nucleotides). A dose response in DNA SSB was seen with TPA over a concentration range of 4 X 10(-9)-1.6 X 10(-6) M. Mezerein, a second stage tumor promoter, induced similar levels of DNA SSB to that of TPA. 4-O-Methyl TPA, a first stage tumor promoter, induced significantly fewer DNA SSB than either TAP or mezerein at similar concentrations. The induction of DNA SSB in epidermal cells treated with TPA and co-incubated with leukocytes was inhibited by catalase but not superoxide dismutase. These data indicate that tumor promoters can act indirectly on target epidermal cells by stimulating the release of a clastogenic factor from leukocytes through a mechanism involving H2O2.

Animals↗

PubMed1986

Analysis of the effect of DNA alkylation on alkaline elution.

Recently, it has been reported that changes in DNA higher-order structure and DNA-associated protein structure in methylmethane sulfonate (MMS)-treated cells can affect the rate of alkaline elution independent of the DNA single-strand break (SSB) frequency. This conclusion was based on the observation that the rate of elution of alkylated DNA increased when the cell lysates were held at pH 10 for extended periods of time prior to alkaline elution; this increase in elution rate was attributed to changes in nucleoprotein structure rather than additional DNA SSB. We have examined this phenomenon in more detail and find evidence that both DNA SSB and alkaline-labile sites are produced spontaneously in alkylated DNA at pH 10. Alkaline elution of DNA from MMS-treated cells was carried out after incubation of the cell lysates at pH 10 for 48 h; the rate of elution was markedly greater at pH 12.8 compared with pH 12.2 elution. Since this pH effect was not seen in control cell DNA, it was attributed to the production of alkaline-labile sites during the pH 10 incubation. When DNA SSB were measured by alkaline unwinding assay, more SSB were detected in alkylated DNA held at pH 10 for 48 h than for 0.25 h. Double-stranded DNA was treated with MMS in vitro and analyzed by neutral or alkaline gel electrophoresis immediately or after 48 h incubation at pH 10; substantially higher levels of DNA SSB were detected with the pH 10 incubation by either neutral or alkaline gel electrophoresis. In order to determine if changes in DNA structure affect the rate of elution independent of the SSB frequency, we attempted to design an experiment which would severely disrupt DNA higher-order structure but not produce DNA SSB in one of the two complementary DNA strands. V79 cells were grown in bromodeoxyurine (BUdR) under conditions such that all unsubstituted strands were base paired with BUdR-substituted DNA. When this DNA was analyzed by alkaline elution, the unifilar substituted BUdR strand hydrolyzed in alkali and eluted from the filter; this had no effect on the elution rate of the unsubstituted strand. These results indicate that the only known cause for an increase in alkaline elution rate is DNA SSB; severe changes in DNA higher order structure including hydrolysis of one strand by unifilar substitution with an alkaline-labile base analog have no effect on the elution rate of the unsubstituted strand.

Alkalies↗

PubMed1991

Repair of near-visible- and blue-light-induced DNA single-strand breaks by the CHO cell lines AA8 and EM9.

The induction of single-strand breaks (SSB) and the kinetics of SSB repair were measured in two Chinese hamster ovary cell lines irradiated with monochromatic photons of near-visible radiation (405 nm) and blue light (434 nm). The radiosensitive and UV-A-sensitive mutant line EM9 is known to repair SSB induced by ionizing radiation or 365-nm UV-A more slowly than the parent line AA8. At the 10% survival level, EM9 cells were 1.7- and 1.6-fold more sensitive than AA8 cells to 405 and 434 nm radiation, respectively. This sensitivity was not due to differences in induction of SSB because AA8 and EM9 cells accumulated the same number of initial breaks when irradiated at 0.5 degrees C with either 405 nm (5.9 SSB per MJ/m2) or 434 nm (5.1 SSB per MJ/m2), as measured by alkaline elution. When the cells repaired these SSB at 37 degrees C in full culture medium, biphasic repair kinetics were observed for both cell lines. In both phases of repair, EM9 cells repaired breaks induced by both wavelengths more slowly than did AA8 cells. The t1/2 values for the repair phases for 405-nm-induced SSB were 3.8 and 150 min for EM9, and 1.5 and 52 min for AA8; the corresponding values for repair of 434 nm breaks were 3.7 and 39 min for EM9, and 2.0 and 30 min for AA8. Because of this slower repair, EM9 cells left more SSB unrepaired after 90 min than did AA8 cells for both wavelengths.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2002

Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein.

Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit and does not represent a recent acquisition of the phage. The P1 and E. coli SSB proteins are fully functionally interchangeable. SSB-P1 is nonessential for phage growth in an exponentially growing E. coli host, and it is sufficient to promote bacterial growth in the absence of the E. coli SSB protein. Expression studies showed that the P1 ssb gene is transcribed only, in an rpoS-independent fashion, during stationary-phase growth in E. coli. Mixed infection experiments demonstrated that a wild-type phage has a selective advantage over an ssb-null mutant when exposed to a bacterial host in the stationary phase. These results reconciled the observed evolutionary conservation with the seemingly redundant presence of ssb genes in many bacteriophages and conjugative plasmids.

Bacteriophage P1↗

PubMed2003

Spatial and temporal cellular responses to single-strand breaks in human cells.

DNA single-strand breaks (SSB) are one of the most frequent DNA lesions produced by reactive oxygen species and during DNA metabolism, but the analysis of cellular responses to SSB remains difficult due to the lack of an experimental method to produce SSB alone in cells. By using human cells expressing a foreign UV damage endonuclease (UVDE) and irradiating the cells with UV through tiny pores in membrane filters, we created SSB in restricted areas in the nucleus by the immediate action of UVDE on UV-induced DNA lesions. Cellular responses to the SSB were characterized by using antibodies and fluorescence microscopy. Upon UV irradiation, poly(ADP-ribose) synthesis occurred immediately in the irradiated area. Simultaneously, but dependent on poly(ADP-ribosyl)ation, XRCC1 was translocated from throughout the nucleus, including nucleoli, to the SSB. The BRCT1 domain of XRCC1 protein was indispensable for its poly(ADP-ribose)-dependent recruitment to the SSB. Proliferating cell nuclear antigen and the p150 subunit of chromatin assembly factor 1 also accumulated at the SSB in a detergent-resistant form, which was significantly reduced by inhibition of poly(ADP-ribose) synthesis. Our results show the importance of poly(ADP-ribosyl)ation in sequential cellular responses to SSB.

Cell Nucleus↗

PubMed1990

The role of human single-stranded DNA binding protein and its individual subunits in simian virus 40 DNA replication.

Human single-stranded DNA binding protein (human SSB) is a multisubunit protein containing polypeptides of 70, 34, and 11 kDa that is required for SV40 DNA replication in vitro. In this report we identify the functions of the SSB and its individual subunits in SV40 DNA replication. The 70 kDa subunit was found to bind to single-stranded DNA, whereas the other subunits did not. Four monoclonal antibodies against human SSB were isolated which inhibited SV40 DNA replication in vitro. The antibodies have been designated alpha SSB70A, alpha SSB70B, alpha SSB70C, and alpha SSB34A to indicate which subunits are recognized. Immunolocalization experiments indicated that human SSB is a nuclear protein. Human SSB is required for the SV40 large tumor antigen-catalyzed unwinding of SV40 DNA and stimulates DNA polymerases (pol) alpha and delta. The DNA unwinding reaction and stimulation of pol delta were blocked by alpha SSB70C, whereas the stimulation of pol alpha by human SSB was unaffected by this antibody. Conversely, alpha SSB70A, -70B, and -34A inhibited the stimulation of pol alpha, but they had no effect on DNA unwinding and pol delta stimulation. None of the antibodies inhibited the binding of SSB to single-stranded DNA. These results suggest that DNA unwinding and stimulation of pol alpha and pol delta are required functions of human SSB in SV40 DNA replication. The human SSB 70-kDa subunit appears to be required for DNA unwinding and pol delta stimulation, whereas both the 70- and 34-kDa subunits may be involved in the stimulation of pol alpha.

Antibodies, Monoclonal↗

PubMed1989

Protein-linked DNA strand breaks induced in mammalian cells by camptothecin, an inhibitor of topoisomerase I.

Camptothecin was recently identified as an inhibitor of mammalian topoisomerase I. Similar to inhibitors of topoisomerase II, camptothecin produces DNA single-strand breaks (SSB) and DNA-protein cross-links (DPC) in mammalian cells. However, their one-to-one association, expected for trapped topoisomerase complexes, has not previously been demonstrated. We have studied camptothecin-induced SSB and DPC in Chinese hamster DC3F cells and their isolated nuclei, using the DNA alkaline elution technique. It was found that the SSB and DPC frequencies detected following camptothecin treatment depend upon the conditions used for lysis. When lysis was with sodium dodecyl sulfate, the observed frequencies of SSB and DPC were 2- to 3-fold greater than when sodium dodecyl sarkosinate (Sarkosyl) was used. In either case, the SSB:DPC ratio was close to 1. All of the camptothecin-induced SSB were protein linked, as indicated by the absence of DNA elution under nondeproteinizing conditions. DNA cleavage assays with purified topoisomerase I also indicated that the weaker Sarkosyl detergent fails to trap all of the enzyme-DNA complexes. In contrast, lysis conditions had little effect on levels of SSB or DPC produced by 4'-(9-acridinylamino)-methanesulfon-m-anisidide, suggesting that trapping of topoisomerase II complexes occurs equally well with either detergent. In experiments using isolated nuclei, it was found that the camptothecin-induced SSB, in contrast to trapped topoisomerase II complexes, can form and reverse within minutes at 4 degrees C. The activity of camptothecin at low temperature was also seen with purified topoisomerase I. These results support the hypothesis that the SSB and DPC induced by camptothecin in mammalian cells are due to an action on topoisomerase I.

Animals↗

PubMedDate not supplied

[Possibility of participation of proteins binding single-stranded DNA in eukaryotic DNA replication].

Main properties of the single-stranded DNA-binding proteins (SSB-proteins) (type of the protein UP 1 from the calf thymus) have been analyzed. The combination of some properties allows one to say about the strong specificity of the term "SSB-proteins type UP 1" and their differences from the HMG-proteins and other DNA-binding proteins and enzymes. Basing on the data from literature and the author's data the hypothesis was made that eukaryotic SSB-proteins may be involved in DNA replication, though they have tight relationship with the proteins of heterogeneous nuclear ribonucleoprotein particles. The following fact evidence for the involvement of SSB-proteins in DNA replication: 1) preferential affinity to the single-strand DNA in comparison with the single-strand RNA; 2) the contact between DNA SSB-proteins in chromatin; 3) strong proportional dependence between the content of SSB-proteins in chromatin and the intensity of DNA synthesis; 4) the dependence between the content of SSB-proteins in the cells and genomic size in different organisms; 5) the capacity of SSB-proteins to specific stimulation of DNA replicative synthesis. Apparently SSB-proteins in chromatin modulate the replication with the aid of the unwinding of DNA, stabilizing of the single-strand region in this molecule and the activation of the DNA synthesis carried out by DNA polymerase.

Animals↗

PubMed1993

Binding and phasing of Escherichia coli single-stranded DNA-binding protein by the secondary structure of phage G4 origin of complementary DNA strand synthesis (G4oric).

The origin of phage G4 DNA complementary strand synthesis (G4oric) consists of three stem-loop structures (stem loops I, II, and III) that have been proposed as a recognition site for primase during primer RNA (pRNA) synthesis (Godson, G. N., Barrell, B. G., Staden, R., and Fiddes, J. C. (1978) Nat. New Biol. 276, 236-247; Fiddes, J. C., Barrell, B. G., and Godson, G. N. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 1081-1085; Sims, J., Capon, D., and Dressler, D. (1979) J. Biol. Chem. 254, 12615-12628). It is generally considered that the double-stranded DNA stem-loop structure is not coated with Escherichia coli single-stranded DNA-binding protein (SSB), but is recognized by primase as naked DNA (Kornberg, A., and Baker, J. (1992) DNA Replication, 2nd Ed., p. 280, W. H. Freeman & Co., New York). Using small G4oric single-stranded DNA fragments of various sizes (302, 278, 149, and 100 nucleotides) consisting of the core 100-nucleotide stem-loop region plus differing lengths of 3'- and 5'-flanking sequence as substrates for gel retardation and DNase I and micrococcal nuclease digestion, we show that under conditions of pRNA synthesis, two SSB tetramers bind to the stem-loop structure. With increasing lengths of 5'- and 3'-flanking sequence, more SSB tetramers are added. Regardless of the number of SSB tetramers bound, however, the region of DNA containing the pRNA initiation site is always left accessible to nuclease digestion. In situ copper-phenanthroline footprinting of individual gel shift assembly intermediates shows that on the 302-nucleotide G4oric, the first two SSB tetramers assemble at random, but the addition of more SSB tetramers results in formation of a unique structure. In this structure, SSB tetramers protect both sides of stem loop III plus the intervening region between stem loops III and I, but leave most of stem loop I and the CTG pRNA initiation site accessible to copper-phenanthroline. Primase can only synthesize pRNA when the stem-loop structure is saturated with SSB and presumably in the unique configuration. The G4oric stem-loop structure therefore appears to dictate the phasing of SSB to leave a primase recognition site as free DNA.

Base Sequence↗

PubMed1998

The role of the 6 lysines and the terminal amine of Escherichia coli single-strand binding protein in its binding of single-stranded DNA.

Differential chemical modification of the lysines and amino-terminus of Escherichia coli single-strand binding (SSB) protein was used to determine their roles in the binding of SSB to single-stranded DNA (ssDNA). A combination of isotope labeling and mass spectrometry was used to determine the rates at which SSB was acetylated by acetic anhydride. First, SSB was labeled by deuterated acetic anhydride for given lengths of time in the presence or absence of single-stranded ssDNA. Then, the protein was denatured and completely acetylated by nondeuterated acetic anhydride. Enzymatic digests of the completely acetylated, isotopically labeled SSB were analyzed by electrospray ionization mass spectrometry. The intensities of the deuterated and nondeuterated forms of acetylated peptides provided accurate quantification of the reactivity of the amines in native SSB, either free or bound to ssDNA. Acetylation rate constants were determined from time course measurements. In the absence of ssDNA, the terminal alpha-amine of SSB was 10-fold more reactive than Lys residues at positions 43, 62, 73, and 87. The reactivities of Lys 7 and 49 were much lower yet, suggesting that they have very limited access to solution under any condition. In the presence of ssDNA, the reactivities of the amino-terminus and Lys residues 43, 62, 73, and 87 were reduced by factors of 3.7-25, indicating that the environments around all of these amines is substantially altered by binding of SSB to ssDNA. Three of these residues are located near putative ssDNA binding sites, whereas Lys 87 is located at the monomer-monomer interface.

Acetylation↗

PubMed1994

Complex formation between phage phi 29 single-stranded DNA binding protein and DNA.

Bacteriophage phi 29 gene 5 encodes a single-stranded DNA (ssDNA) binding protein (SSB) which stimulates viral DNA replication. In the present study, a structural characterization of the complex between ssDNA and the phi 29 SSB was carried out using electron microscopy, band-shift assays and nuclease digestion as well as by monitoring changes in the intrinsic fluorescence of phi 29 SSB upon binding. Phage phi 29 SSB behaves as a monomer in solution and forms complexes with ssDNA which have a homogeneous structure, as if they consist of a continuous array of protein bound to DNA. Interaction of phi 29 SSB with ssDNA leads to a quenching of its tyrosine-dependent intrinsic fluorescence. This fluorescence quenching was directly proportional to the amount of phi 29 SSB bound to the ssDNA and the maximal quenching upon binding was very high (Qmax = 94.6 +/- 3.5%). Direct titration experiments have allowed us to estimate that the stoichiometry (n) of binding to ssDNA was 3.4(+/- 0.3) nucleotides per phi 29 SSB monomer. Both Qmax and n are independent of the salt concentration, suggesting the existence of only one major binding mode. At low salt concentrations, the effective binding constant (Keff = K omega) to poly(dT) was 2.2 x 10(5) M-1, the intrinsic binding constant (K) and the cooperativity parameter (omega) being 4.3 x 10(3) M-1 and 51, respectively. At increasing salt concentrations, the Keff exhibited a small, but significant, decrease. The possible functional significance of the binding parameters of phi 29 SSB during viral DNA replication is discussed.

Bacillus Phages↗