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1.
BMJ Open ; 9(2): e022352, 2019 02 19.
Article in English | MEDLINE | ID: mdl-30782867

ABSTRACT

OBJECTIVES: To evaluate the cost-effectiveness of routine use of cell salvage during caesarean section in mothers at risk of haemorrhage compared with current standard of care. DESIGN: Model-based cost-effectiveness evaluation alongside a multicentre randomised controlled trial. Three main analyses were carried out on the trial data: (1) based on the intention-to-treat principle; (2) based on the per-protocol principle; (3) only participants who underwent an emergency caesarean section. SETTING: 26 obstetric units in the UK. PARTICIPANTS: 3028 women at risk of haemorrhage recruited between June 2013 and April 2016. INTERVENTIONS: Cell salvage (intervention) versus routine care without salvage (control). PRIMARY OUTCOME MEASURES: Cost-effectiveness based on incremental cost per donor blood transfusion avoided. RESULTS: In the intention-to-treat analysis, the mean difference in total costs between cell salvage and standard care was £83. The estimated incremental cost-effectiveness ratio (ICER) was £8110 per donor blood transfusion avoided. For the per-protocol analysis, the mean difference in total costs was £92 and the ICER was £8252. In the emergency caesarean section analysis, the mean difference in total costs was £55 and the ICER was £13 713 per donor blood transfusion avoided. This ICER is driven by the increased probability that these patients would require a higher level of postoperative care and additional surgeries. The results of these analyses were shown to be robust for the majority of deterministic sensitivity analyses. CONCLUSIONS: The results of the economic evaluation suggest that while routine cell salvage is a marginally more effective strategy than standard care in avoiding a donor blood transfusion, there is uncertainty in relation to whether it is a less or more costly strategy. The lack of long-term data on the health and quality of life of patients in both arms of the trial means that further research is needed to fully understand the cost implications of both strategies. TRIAL REGISTRATION NUMBER: ISRCTN66118656.


Subject(s)
Blood Transfusion/statistics & numerical data , Cesarean Section/methods , Hemorrhage/therapy , Operative Blood Salvage/statistics & numerical data , Blood Transfusion/methods , Cesarean Section/adverse effects , Cost-Benefit Analysis , Female , Hemorrhage/etiology , Humans , Operative Blood Salvage/adverse effects , Operative Blood Salvage/methods , Pregnancy , Quality of Life , Quality-Adjusted Life Years , United Kingdom
2.
Health Technol Assess ; 22(2): 1-88, 2018 01.
Article in English | MEDLINE | ID: mdl-29318985

ABSTRACT

BACKGROUND: Caesarean section is associated with blood loss and maternal morbidity. Excessive blood loss requires transfusion of donor (allogeneic) blood, which is a finite resource. Cell salvage returns blood lost during surgery to the mother. It may avoid the need for donor blood transfusion, but reliable evidence of its effects is lacking. OBJECTIVES: To determine if routine use of cell salvage during caesarean section in mothers at risk of haemorrhage reduces the rates of blood transfusion and postpartum maternal morbidity, and is cost-effective, in comparison with standard practice without routine salvage use. DESIGN: Individually randomised controlled, multicentre trial with cost-effectiveness analysis. Treatment was not blinded. SETTING: A total of 26 UK obstetric units. PARTICIPANTS: Out of 3054 women recruited between June 2013 and April 2016, we randomly assigned 3028 women at risk of haemorrhage to cell salvage or routine care. Randomisation was stratified using random permuted blocks of variable sizes. Of these, 1672 had emergency and 1356 had elective caesareans. We excluded women for whom cell salvage or donor blood transfusion was contraindicated. INTERVENTIONS: Cell salvage (intervention) versus routine care without salvage (control). In the intervention group, salvage was set up in 95.6% of the women and, of these, 50.8% had salvaged blood returned. In the control group, 3.9% had salvage deployed. MAIN OUTCOME MEASURES: Primary - donor blood transfusion. Secondary - units of donor blood transfused, time to mobilisation, length of hospitalisation, mean fall in haemoglobin, fetomaternal haemorrhage (FMH) measured by Kleihauer-Betke test, and maternal fatigue. Analyses were adjusted for stratification factors and other factors that were believed to be prognostic a priori. Cost-effectiveness outcomes - costs of resources and service provision taking the UK NHS perspective. RESULTS: We analysed 1498 and 1492 participants in the intervention and control groups, respectively. Overall, the transfusion rate was 2.5% in the intervention group and 3.5% in the control group [adjusted odds ratio (OR) 0.65, 95% confidence interval (CI) 0.42 to 1.01; p = 0.056]. In a planned subgroup analysis, the transfusion rate was 3.0% in the intervention group and 4.6% in the control group among emergency caesareans (adjusted OR 0.58, 95% CI 0.34 to 0.99), whereas it was 1.8% in the intervention group and 2.2% in the control group among elective caesareans (adjusted OR 0.83, 95% CI 0.38 to 1.83) (interaction p = 0.46, suggesting that the difference in effect between subgroups was not statistically significant). Secondary outcomes did not differ between groups, except for FMH, which was higher under salvage in rhesus D (RhD)-negative women with RhD-positive babies (25.6% vs. 10.5%, adjusted OR 5.63, 95% CI 1.43 to 22.14; p = 0.013). No case of amniotic fluid embolism was observed. The additional cost of routine cell salvage during caesarean was estimated, on average, at £8110 per donor blood transfusion avoided. CONCLUSIONS: The modest evidence for an effect of routine use of cell salvage during caesarean section on rates of donor blood transfusion was associated with increased FMH, which emphasises the need for adherence to guidance on anti-D prophylaxis. We are unable to comment on long-term antibody sensitisation effects. Based on the findings of this trial, cell salvage is unlikely to be considered cost-effective. FUTURE WORK: Research into risk of alloimmunisation among women exposed to cell salvage is needed. TRIAL REGISTRATION: Current Controlled Trials ISRCTN66118656. FUNDING: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 22, No. 2. See the NIHR Journals Library website for further project information.


Subject(s)
Blood Transfusion/statistics & numerical data , Cesarean Section/methods , Hemorrhage/therapy , Operative Blood Salvage/statistics & numerical data , Adult , Blood Transfusion/methods , Cesarean Section/adverse effects , Cost-Benefit Analysis , Female , Health Resources/economics , Health Resources/statistics & numerical data , Hemoglobins/analysis , Hemorrhage/etiology , Humans , Length of Stay , Operative Blood Salvage/adverse effects , Operative Blood Salvage/methods , Quality of Life , Quality-Adjusted Life Years , Technology Assessment, Biomedical , United Kingdom
3.
PLoS Med ; 14(12): e1002471, 2017 Dec.
Article in English | MEDLINE | ID: mdl-29261655

ABSTRACT

BACKGROUND: Excessive haemorrhage at cesarean section requires donor (allogeneic) blood transfusion. Cell salvage may reduce this requirement. METHODS AND FINDINGS: We conducted a pragmatic randomised controlled trial (at 26 obstetric units; participants recruited from 4 June 2013 to 17 April 2016) of routine cell salvage use (intervention) versus current standard of care without routine salvage use (control) in cesarean section among women at risk of haemorrhage. Randomisation was stratified, using random permuted blocks of variable sizes. In an intention-to-treat analysis, we used multivariable models, adjusting for stratification variables and prognostic factors identified a priori, to compare rates of donor blood transfusion (primary outcome) and fetomaternal haemorrhage ≥2 ml in RhD-negative women with RhD-positive babies (a secondary outcome) between groups. Among 3,028 women randomised (2,990 analysed), 95.6% of 1,498 assigned to intervention had cell salvage deployed (50.8% had salvaged blood returned; mean 259.9 ml) versus 3.9% of 1,492 assigned to control. Donor blood transfusion rate was 3.5% in the control group versus 2.5% in the intervention group (adjusted odds ratio [OR] 0.65, 95% confidence interval [CI] 0.42 to 1.01, p = 0.056; adjusted risk difference -1.03, 95% CI -2.13 to 0.06). In a planned subgroup analysis, the transfusion rate was 4.6% in women assigned to control versus 3.0% in the intervention group among emergency cesareans (adjusted OR 0.58, 95% CI 0.34 to 0.99), whereas it was 2.2% versus 1.8% among elective cesareans (adjusted OR 0.83, 95% CI 0.38 to 1.83) (interaction p = 0.46). No case of amniotic fluid embolism was observed. The rate of fetomaternal haemorrhage was higher with the intervention (10.5% in the control group versus 25.6% in the intervention group, adjusted OR 5.63, 95% CI 1.43 to 22.14, p = 0.013). We are unable to comment on long-term antibody sensitisation effects. CONCLUSIONS: The overall reduction observed in donor blood transfusion associated with the routine use of cell salvage during cesarean section was not statistically significant. TRIAL REGISTRATION: This trial was prospectively registered on ISRCTN as trial number 66118656 and can be viewed on http://www.isrctn.com/ISRCTN66118656.


Subject(s)
Blood Loss, Surgical/prevention & control , Blood Transfusion, Autologous/methods , Cesarean Section , Operative Blood Salvage/methods , Adult , Blood Donors , Cesarean Section/adverse effects , Cesarean Section/methods , Female , Humans , Patient Care Planning , Pregnancy , Prognosis , Treatment Outcome
4.
Curr Opin Obstet Gynecol ; 28(6): 492-498, 2016 12.
Article in English | MEDLINE | ID: mdl-27787286

ABSTRACT

PURPOSE OF REVIEW: Caesarean section rates are increasing across the world. Postpartum haemorrhage is a major cause of morbidity and mortality; major haemorrhage is more common after caesarean delivery. There is a wide range of practice in the prevention and treatment of postpartum haemorrhage at caesarean section. The aim of this review is to summarize current opinion in the management of postpartum haemorrhage at caesarean section. RECENT FINDINGS: Recent large randomized controlled trials have shown a possible effect from the routine use of tranexamic acid and ergometrine. Small randomized controlled trials have shown a possible benefit from using carbetocin. SUMMARY: The impact of postpartum haemorrhage can be reduced by antenatal correction of anaemia. Intraoperative medical management consists of oxytocinon, additional oxytocics +/- tranexamic acid, with at present limited evidence as to the order in which these should be considered. Trials of routine use of cell salvage and tranexamic acid are currently underway.


Subject(s)
Cesarean Section/adverse effects , Postpartum Hemorrhage/etiology , Postpartum Hemorrhage/prevention & control , Ergonovine/therapeutic use , Female , Humans , Oxytocics , Oxytocin/analogs & derivatives , Oxytocin/therapeutic use , Pregnancy , Randomized Controlled Trials as Topic , Risk Assessment , Treatment Outcome
5.
Nat Struct Mol Biol ; 21(1): 49-55, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24292646

ABSTRACT

DNA polymerase ɛ (Pol ɛ) is a high-fidelity polymerase that has been shown to participate in leading-strand synthesis during DNA replication in eukaryotic cells. We present here a ternary structure of the catalytic core of Pol ɛ (142 kDa) from Saccharomyces cerevisiae in complex with DNA and an incoming nucleotide. This structure provides information about the selection of the correct nucleotide and the positions of amino acids that might be critical for proofreading activity. Pol ɛ has the highest fidelity among B-family polymerases despite the absence of an extended ß-hairpin loop that is required for high-fidelity replication by other B-family polymerases. Moreover, the catalytic core has a new domain that allows Pol ɛ to encircle the nascent double-stranded DNA. Altogether, the structure provides an explanation for the high processivity and high fidelity of leading-strand DNA synthesis in eukaryotes.


Subject(s)
DNA Polymerase II/metabolism , DNA Replication , Saccharomyces cerevisiae/enzymology , Catalytic Domain , DNA Polymerase II/chemistry , Models, Molecular
6.
Subcell Biochem ; 62: 237-57, 2012.
Article in English | MEDLINE | ID: mdl-22918589

ABSTRACT

DNA polymerase ε (Pol ε) is one of three replicative DNA polymerases in eukaryotic cells. Pol ε is a multi-subunit DNA polymerase with many functions. For example, recent studies in yeast have suggested that Pol ε is essential during the initiation of DNA replication and also participates during leading strand synthesis. In this chapter, we will discuss the structure of Pol ε, the individual subunits and their function.


Subject(s)
DNA Polymerase II/metabolism , DNA Replication/physiology , DNA, Fungal/biosynthesis , Fungal Proteins/metabolism , Yeasts/enzymology , Animals , DNA Polymerase II/genetics , DNA, Fungal/genetics , Eukaryotic Cells/enzymology , Fungal Proteins/genetics , Humans , Yeasts/genetics
7.
Nucleic Acids Res ; 40(6): 2611-22, 2012 Mar.
Article in English | MEDLINE | ID: mdl-22135286

ABSTRACT

The biological role of human DNA polymerase θ (POLQ) is not yet clearly defined, but it has been proposed to participate in several cellular processes based on its translesion synthesis capabilities. POLQ is a low-fidelity polymerase capable of efficient bypass of blocking lesions such as abasic sites and thymine glycols as well as extension of mismatched primer termini. Here, we show that POLQ possesses a DNA polymerase activity that appears to be template independent and allows efficient extension of single-stranded DNA as well as duplex DNA with either protruding or multiply mismatched 3'-OH termini. We hypothesize that this DNA synthesis activity is related to the proposed role for POLQ in the repair or tolerance of double-strand breaks.


Subject(s)
DNA-Directed DNA Polymerase/metabolism , DNA/biosynthesis , Base Pair Mismatch , DNA Breaks, Double-Stranded , Humans , Oligonucleotides/biosynthesis , DNA Polymerase theta
8.
J Mol Biol ; 405(3): 642-52, 2011 Jan 21.
Article in English | MEDLINE | ID: mdl-21050863

ABSTRACT

DNA polymerase θ (POLQ, polθ) is a large, multidomain DNA polymerase encoded in higher eukaryotic genomes. It is important for maintaining genetic stability in cells and helping protect cells from DNA damage caused by ionizing radiation. POLQ contains an N-terminal helicase-like domain, a large central domain of indeterminate function, and a C-terminal polymerase domain with sequence similarity to the A-family of DNA polymerases. The enzyme has several unique properties, including low fidelity and the ability to insert and extend past abasic sites and thymine glycol lesions. It is not known whether the abasic site bypass activity is an intrinsic property of the polymerase domain or whether helicase activity is also required. Three "insertion" sequence elements present in POLQ are not found in any other A-family DNA polymerase, and it has been proposed that they may lend some unique properties to POLQ. Here, we analyzed the activity of the DNA polymerase in the absence of each sequence insertion. We found that the pol domain is capable of highly efficient bypass of abasic sites in the absence of the helicase-like or central domains. Insertion 1 increases the processivity of the polymerase but has little, if any, bearing on the translesion synthesis properties of the enzyme. However, removal of insertions 2 and 3 reduces activity on undamaged DNA and completely abrogates the ability of the enzyme to bypass abasic sites or thymine glycol lesions.


Subject(s)
DNA-Directed DNA Polymerase/chemistry , Amino Acid Sequence , Animals , Base Sequence , DNA Damage , DNA Repair , DNA Replication , DNA-Directed DNA Polymerase/genetics , Genes, pol , Humans , Mice , Molecular Sequence Data , Protein Structure, Tertiary , Thymine/analogs & derivatives , Thymine/chemistry , DNA Polymerase theta
9.
J Mol Biol ; 400(3): 295-308, 2010 Jul 16.
Article in English | MEDLINE | ID: mdl-20493878

ABSTRACT

Structure-based protein sequence alignments of family B DNA polymerases revealed a conserved motif that is formed from interacting residues between loops from the N-terminal and palm domains and between the N-terminal loop and a conserved proline residue. The importance of the motif for function of the bacteriophage T4 DNA polymerase was revealed by suppressor analysis. T4 DNA polymerases that form weak replicating complexes cannot replicate DNA when the dGTP pool is reduced. The conditional lethality provides the means to identify amino acid substitutions that restore replication activity under low-dGTP conditions either by correcting the defect produced by the first amino acid substitution or by generally increasing the stability of polymerase complexes; the second type are global suppressors that can effectively counter the reduced stability caused by a variety of amino acid substitutions. Some amino acid substitutions that increase the stability of polymerase complexes produce a new phenotype-sensitivity to the antiviral drug phosphonoacetic acid. Amino acid substitutions that confer decreased ability to replicate DNA under low-dGTP conditions or drug sensitivity were identified in the new motif, which suggests that the motif functions in regulating the stability of polymerase complexes. Additional suppressor analyses revealed an apparent network of interactions that link the new motif to the fingers domain and to two patches of conserved residues that bind DNA. The collection of mutant T4 DNA polymerases provides a foundation for future biochemical studies to determine how DNA polymerases remain stably associated with DNA while waiting for the next available dNTP, how DNA polymerases translocate, and the biochemical basis for sensitivity to antiviral drugs.


Subject(s)
Bacteriophage T4/enzymology , Bacteriophage T4/genetics , DNA-Directed DNA Polymerase/genetics , DNA-Directed DNA Polymerase/metabolism , Viral Proteins/genetics , Viral Proteins/metabolism , Amino Acid Motifs , Amino Acid Sequence , Amino Acid Substitution , Antiviral Agents/pharmacology , DNA Mutational Analysis , Models, Molecular , Molecular Sequence Data , Phosphonoacetic Acid/pharmacology , Protein Stability , Protein Structure, Tertiary , Sequence Alignment , Suppression, Genetic , Viral Plaque Assay
10.
Biochemistry ; 49(11): 2317-25, 2010 Mar 23.
Article in English | MEDLINE | ID: mdl-20166748

ABSTRACT

The fidelity of DNA replication is under constant threat from the formation of lesions within the genome. Oxidation of DNA bases leads to the formation of altered DNA bases such as 8-oxo-7,8-dihydroguanine, commonly called 8-oxoG, and 2-hydroxyadenine, or 2-OHA. In this work we have examined the incorporation kinetics opposite these two oxidatively derived lesions as well as an abasic site analogue by the replicative DNA polymerase from bacteriophage RB69. We compared the kinetic parameters for both wild type and the low fidelity L561A variant. While nucleotide incorporation rates (k(pol)) were generally higher for the variant, the presence of a lesion in the templating position reduced the ability of both the wild-type and variant DNA polymerases to form ternary enzyme-DNA-dNTP complexes. Thus, the L561A substitution does not significantly affect the ability of the RB69 DNA polymerase to recognize damaged DNA; instead, the mutation increases the probability that nucleotide incorporation will occur. We have also solved the crystal structure of the L561A variant forming an 8-oxoG.dATP mispair and show that the propensity for forming this mispair depends on an enlarged polymerase active site.


Subject(s)
Bacteriophages/enzymology , Base Pair Mismatch , DNA Replication , DNA, Viral/biosynthesis , DNA, Viral/genetics , DNA-Directed DNA Polymerase/metabolism , Viral Proteins/metabolism , Adenosine Triphosphate/metabolism , Amino Acid Substitution , Biocatalysis , Catalytic Domain , Crystallography, X-Ray , DNA, Viral/chemistry , DNA-Directed DNA Polymerase/chemistry , DNA-Directed DNA Polymerase/genetics , Kinetics , Models, Molecular , Viral Proteins/chemistry , Viral Proteins/genetics
11.
Biochemistry ; 47(23): 6130-7, 2008 Jun 10.
Article in English | MEDLINE | ID: mdl-18481871

ABSTRACT

For DNA polymerases to proofread a misincorporated nucleotide, the terminal 3-4 nucleotides of the primer strand must be separated from the template strand before being bound in the exonuclease active center. Genetic and biochemical studies of the bacteriophage T4 DNA polymerase revealed that a prominent beta-hairpin structure in the exonuclease domain is needed to efficiently form the strand-separated exonuclease complexes. We present here further mutational analysis of the loop region of the T4 DNA polymerase beta-hairpin structure, which provides additional evidence that residues in the loop, namely, Y254 and G255, are important for DNA replication fidelity. The mechanism of strand separation was probed in in vitro reactions using the fluorescence of the base analogue 2-aminopurine (2AP) and mutant RB69 DNA polymerases that have modifications to the beta hairpin, to the exonuclease active site, or to both. We propose from these studies that the beta hairpin in the exonuclease domain of the T4 and RB69 DNA polymerases functions to facilitate strand separation, but residues in the exonuclease active center are required to capture the 3' end of the primer strand following strand separation.


Subject(s)
2-Aminopurine , Bacteriophage T4/enzymology , Bacteriophage T4/genetics , DNA Polymerase beta/chemistry , DNA Polymerase beta/metabolism , DNA Replication , Binding Sites , Catalysis , DNA Polymerase beta/genetics , Models, Molecular , Mutagenesis, Site-Directed , Protein Conformation , Spectrometry, Fluorescence , Viral Proteins/chemistry
12.
Proc Natl Acad Sci U S A ; 104(3): 814-8, 2007 Jan 16.
Article in English | MEDLINE | ID: mdl-17210917

ABSTRACT

Thymine glycol (Tg) is a common product of oxidation and ionizing radiation, including that used for cancer treatment. Although Tg is a poor mutagenic lesion, it has been shown to present a strong block to both repair and replicative DNA polymerases. The 2.65-A crystal structure of a binary complex of the replicative RB69 DNA polymerase with DNA shows that the templating Tg is intrahelical and forms a regular Watson-Crick base pair with the incorporated A. The C5 methyl group protrudes axially from the ring of the damaged pyrimidine and hinders stacking of the adjacent 5' template guanine. The position of the displaced 5' template guanine is such that the next incoming nucleotide cannot be incorporated into the growing primer strand, and it explains why primer extension past the lesion is prohibited even though DNA polymerases can readily incorporate an A across from the Tg lesion.


Subject(s)
DNA Replication , DNA-Directed DNA Polymerase/chemistry , DNA-Directed DNA Polymerase/metabolism , DNA/chemistry , DNA/metabolism , Thymine/chemistry , Thymine/metabolism , Crystallography, X-Ray , DNA-Directed DNA Polymerase/genetics , Models, Molecular , Nucleic Acid Conformation , Oxidation-Reduction , Protein Structure, Tertiary , Thymine/analogs & derivatives
13.
J Biol Chem ; 282(2): 1432-44, 2007 Jan 12.
Article in English | MEDLINE | ID: mdl-17098747

ABSTRACT

Replicative DNA polymerases, as exemplified by the B family polymerases from bacteriophages T4 and RB69, not only replicate DNA but also have the ability to proofread misincorporated nucleotides. Because the two activities reside in separate protein domains, polymerases must employ a mechanism that allows for efficient switching of the primer strand between the two active sites to achieve fast and accurate replication. Prior mutational and structural studies suggested that a beta hairpin structure located in the exonuclease domain of family B polymerases might play an important role in active site switching in the event of a nucleotide misincorporation. We show that deleting the beta hairpin loop in RB69 gp43 affects neither polymerase nor exonuclease activities. Single binding event studies with mismatched primer termini, however, show that the beta hairpin plays a role in maintaining the stability of the polymerase/DNA interactions during the binding of the primer DNA in the exonuclease active site but not on the return of the corrected primer to the polymerase active site. In addition, the deletion variant showed a more stable incorporation of a nucleotide opposite an abasic site. Moreover, in the 2.4 A crystal structure of the beta hairpin deletion variant incorporating an A opposite a templating furan, all four molecules in the crystal asymmetric unit have DNA in the polymerase active site, despite the presence of DNA distortions because of the misincorporation, confirming that the primer strand is not stably bound within the exonuclease active site in the absence of the beta hairpin loop.


Subject(s)
Bacteriophage T4/enzymology , DNA Replication , DNA-Directed DNA Polymerase/chemistry , Exodeoxyribonucleases/chemistry , Viral Proteins/chemistry , Bacteriophage T4/genetics , Binding Sites/genetics , Crystallography , DNA, Single-Stranded/genetics , DNA, Single-Stranded/metabolism , DNA-Directed DNA Polymerase/metabolism , Enzyme Activation , Exodeoxyribonucleases/metabolism , Gene Deletion , Protein Structure, Quaternary , Protein Structure, Tertiary , Viral Proteins/metabolism
14.
Nucleic Acids Res ; 34(9): 2528-35, 2006.
Article in English | MEDLINE | ID: mdl-16687658

ABSTRACT

The kinetics of forming a proper Watson-Crick base pair as well incorporating bases opposite furan, an abasic site analog, have been well characterized for the B Family replicative DNA polymerase from bacteriophage T4. Structural studies of these reactions, however, have only been performed with the homologous enzyme from bacteriophage RB69. In this work, the homologous enzymes from RB69 and T4 were compared in parallel reactions to determine the relative abilities of the two polymerases to incorporate correct nucleotides as well as to form improper pairings. The kinetic rates for three different exonuclease mutants for each enzyme were measured for incorporation of an A opposite T and an A opposite furan as well as for the formation of A:C and T:T mismatches. The T4 exonuclease mutants were all approximately 2- to 7-fold more efficient than the corresponding RB69 exonuclease mutants depending on whether a T or furan was in the templating position and which exonuclease mutant was used. The rates for mismatch formation by T4 were significantly reduced compared with incorporation opposite furan, much more so than the corresponding RB69 mutant. These results show that there are kinetic differences between the two enzymes but they are not large enough to preclude structural assumptions for T4 DNA polymerase based on the known structure of the RB69 DNA polymerase.


Subject(s)
DNA-Directed DNA Polymerase/metabolism , DNA/biosynthesis , Viral Proteins/metabolism , Base Pair Mismatch , Base Pairing , Binding Sites , DNA/chemistry , DNA-Directed DNA Polymerase/chemistry , DNA-Directed DNA Polymerase/genetics , Deoxyadenine Nucleotides/chemistry , Furans/chemistry , Kinetics , Mutation , Thymine/chemistry , Viral Proteins/chemistry , Viral Proteins/genetics
15.
Curr Opin Struct Biol ; 15(1): 86-93, 2005 Feb.
Article in English | MEDLINE | ID: mdl-15718138

ABSTRACT

Significant advances have been made recently in the study of polymerases. First came the realization that there are many more DNA polymerases than originally thought; indeed, no fewer than 14 template-dependent DNA polymerases are found in mammals. Concurrent structural studies of DNA polymerases bound to DNA and incoming nucleotide have revealed how these remarkable copying machines select the correct deoxynucleoside triphosphate among a sea of nucleotides. A whole new level of insight into DNA replication fidelity has been reached as a result of recently determined crystal structures of DNA lesions in the context of the active sites of repair, replicative and specialized DNA polymerases. These structures illustrate why some lesions can be bypassed readily, whereas others are strong blocks to DNA replication.


Subject(s)
DNA Damage , DNA Repair , DNA Replication , DNA-Directed DNA Polymerase/chemistry , DNA/chemistry , Models, Chemical , Models, Genetic , Models, Molecular , Binding Sites , Protein Binding , Structure-Activity Relationship
17.
EMBO J ; 23(7): 1483-93, 2004 Apr 07.
Article in English | MEDLINE | ID: mdl-15057283

ABSTRACT

Abasic sites are common DNA lesions, which are strong blocks to replicative polymerases and are potentially mutagenic when bypassed. We report here the 2.8 A structure of the bacteriophage RB69 replicative DNA polymerase attempting to process an abasic site analog. Four different complexes were captured in the crystal asymmetric unit: two have DNA in the polymerase active site whereas the other two molecules are in the exonuclease mode. When compared to complexes with undamaged DNA, the DNA surrounding the abasic site reveals distinct changes suggesting why the lesion is so poorly bypassed: the DNA in the polymerase active site has not translocated and is therefore stalled, precluding extension. All four molecules exhibit conformations that differ from the previously published structures. The polymerase incorporates dAMP across the lesion under crystallization conditions, indicating that the different conformations observed in the crystal may be part of the active site switching reaction pathway.


Subject(s)
DNA Damage , DNA Replication , DNA-Directed DNA Polymerase/chemistry , DNA-Directed DNA Polymerase/metabolism , DNA/chemistry , Nucleic Acid Conformation , Protein Structure, Tertiary , Viral Proteins/chemistry , Viral Proteins/metabolism , Binding Sites , Crystallography, X-Ray , Humans , Macromolecular Substances , Models, Molecular , Molecular Sequence Data
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