Expansion of a Synthesized Library of N-Benzyl Sulfonamides Derived from an Indole Core to Target Pancreatic Cancer

In an effort to further investigate previously observed activity of indolyl sulfonamides towards pancreatic cancer cell lines, a library of 44 compounds has been synthesized. The biological activity of the compounds has been determined using two different screening assay techniques against 7 pancreatic cancer cell lines and 9 non-pancreatic cancer cell lines. In the first assay, the cytotoxicity of the compounds was evaluated using a traditional (48 hour compound exposure) method. An in silico investigation was conducted to determine if the compounds might be inducing cell death by inhibiting the S100A2-p53 protein-protein interaction. In the second assay, the potential role of the compounds as metabolic inhibitors of ATP production was evaluated using a rapid screening (1-2 hour compound exposure) method. IC50 values of the hit compounds were obtained and four compounds displayed sub-micromolar potency against PANC-1 cells. The investigation has provided several compounds that display selective in vitro activity toward pancreatic cancer that warrant further development.

Synthesis and Biological Evaluation of a Library of Sulfonamide Analogs of Memantine to Target Glioblastoma

A library of 34 lipophilic sulfonamides based upon the memantine core has been synthesized to identify potential drug candidates to cross the blood-brain barrier and target glioblastoma. The library was screened for in vitro activity against 4 mammalian cell lines, including U-87 (glioblastoma). Additional synthetic variation of the active compounds has validated the importance of specific regions of the pharmacophore, with the sulfonamide functionality and S-aryl unit displaying the most significant impact. In silico investigations suggest the active compounds might target DDR1 or RET proteins. The investigation has resulted in several compounds that warrant further development for lead optimization.

Synthesis and biological evaluation of N-alkyl sulfonamides derived from polycyclic hydrocarbon scaffolds using a nitrogen-centered radical approach

Polycyclic hydrocarbons (PH) provide intriguing potential as lipophilic scaffolds within medicinal chemistry, but are currently limited by the availability of synthetic tools for predictable modification of the PH unit. Herein we report the development of new methods for installation of a sulfonamide unit to PH cores. In the first method, a xanthate ester serves as reagent for aminosulfonation using pre-formed imidoiodinane as N-source. An investigation of the reaction mechanism was performed to implicate a process involving a N-centered radical. An additional method for sulfonamide installation is described that involves the use of commercially available reagents and operationally convenient conditions. Using the new synthetic methods, 22 compounds were prepared and screened for biological activity against 6 mammalian cell lines along with Gram-positive and Gram-negative bacterial strains. Results of the viability assays have identified compounds that exhibit higher potency than other known anticancer agents such as indisulam and ABT-751. Additionally, the physicochemical and drug-likeness properties of the synthesized compounds have been determined experimentally and using in silico predictive tools. The initial exploration into sulfonamide insertion into PH cores has resulted in a number of compounds that warrant further development to produce molecules with therapeutic value.

Development of a Rapid In Vitro Screening Assay Using Metabolic Inhibitors to Detect Highly Selective Anticancer Agents

Traditional long exposure (24-72 h) cell viability assays for identification of potential drug compounds can fail to identify compounds that are: (a) biologically active but not toxic and (b) inactive without the addition of a synergistic additive. Herein, we report the development of a rapid (1-2 h) compound screening technique using a commercially available cell viability kit (CellTiter-Glo) that has led to the detection of compounds that were not identified as active agents using traditional cytotoxicity screening methods. These compounds, in combination with metabolic inhibitor 2-deoxyglucose, display selectivity toward a pancreatic cancer cell line. An evaluation of 11 mammalian cell lines against 30 novel compounds and two metabolic inhibitors is reported. The inclusion of metabolic inhibitors during an initial screening process, and not simply during mechanistic investigations of a previously identified hit compound, provides a rapid and sensitive tool for identifying drug candidates potentially overlooked by other methods.

PhI(OAc)2 and iodine-mediated synthesis of N-alkyl sulfonamides derived from polycyclic aromatic hydrocarbon scaffolds and determination of their antibacterial and cytotoxic activities

The development of new approaches toward chemo- and regioselective functionalization of polycyclic aromatic hydrocarbon (PAH) scaffolds will provide opportunities for the synthesis of novel biologically active small molecules that exploit the high degree of lipophilicity imparted by the PAH unit. Herein, we report a new synthetic method for C-X bond substitution that is speculated to operate via a N-centered radical (NCR) mechanism according to experimental observations. A series of PAH sulfonamides have been synthesized and their biological activity has been evaluated against Gram-negative and Gram-positive bacterial strains (using a BacTiter-Glo assay) along with a series of mammalian cell lines (using CellTiter-Blue and CellTiter-Glo assays). The viability assays have resulted in the discovery of a number of bactericidal compounds that exhibit potency similar to other well-known antibacterials such as kanamycin and tetracycline, along with the discovery of a luciferase inhibitor. Additionally, the physicochemical and drug-likeness properties of the compounds were determined experimentally and using in silico approaches and the results are presented and discussed within.

Staphylococcus aureus enhances biofilm formation, aerotolerance, and survival of Campylobacter strains isolated from retail meats

In retail meat products, Campylobacter jejuni, C. coli, and Staphylococcus aureus have been reported in high prevalence. The polymicrobial interaction between Campylobacter and other bacteria could enhance Campylobacter survival during the adverse conditions encountered during retail meat processing and storage. This study was designed to investigate the potential role of S. aureus from retail meats in enhancing the survival of Campylobacter exposed to low temperature, aerobic conditions, and biofilm formation. Results indicated that viable S. aureus cells and filter-sterilized cell-free media obtained from S. aureus prolonged the survival of Campylobacter at low temperature and during aerobic conditions. Biofilm formation of Campylobacter strains was significantly enhanced in the presence of viable S. aureus cells, but the results were inconclusive when extracts from cell-free media were used. In conclusion, the presence of S. aureus cells enhances survivability of Campylobacter strains in adverse conditions such as low temperature and aerobic conditions. Further investigations are warranted to understand the interaction between Campylobacter and S. aureus, and effective intervention strategies are needed to reduce the incidence of both foodborne pathogens in retail meat products.

Molecular characterization of megaplasmids encoding the type VI secretion system in Campylobacter jejuni isolated from chicken livers and gizzards

Megaplasmids in Campylobacter spp. likely play important roles in antibiotic resistance, virulence, and horizontal gene transfer. In this study, megaplasmids pCJDM202 (119 kb) and pCJDM67L (116 kb) from C. jejuni strains WP2-202 and OD2-67, respectively, were sequenced and characterized. These megaplasmids contained genes for tetracycline resistance [tet(O)], the Type IV secretion system, conjugative transfer and the Type VI secretion system (T6SS). The T6SS genes in Campylobacter plasmids encoded genes and proteins that were similar to those identified in Campylobacter chromosomal DNA. When the megaplasmid pCJDM202 from C. jejuni WP2-202 was transferred via conjugation to C. jejuni NCTC11168 Nal⁺, transconconjugants acquired tetracycline resistance and enhanced cytotoxicity towards red blood cells. A T6SS mutant of strain WP2-202 was generated and designated Δhcp3; the mutant was significantly impaired in its ability to lyse red blood cells and survive in defibrinated blood. The cytotoxicity of Campylobacter strains towards the human embryonic kidney cell line HEK 293 was not impacted by the T6SS. In summary, the T6SS encoded by Campylobacter megaplasmids mediates lysis of RBCs and likely contributes to survival on retail meats where blood cells are abundant.

Synthesis and identification of heteroaromatic N-benzyl sulfonamides as potential anticancer agents

Sulfonamides are a crucial class of bioisosteres that are prevalent in a wide range of pharmaceuticals, however, the available methods for their production directly from heteroaryl aldehyde reagents remains surprisingly limited. A new approach for regioselective incorporation of a sulfonamide unit to heteroarene scaffolds has been developed and is reported within. As a result, a variety of primary benzylic N-alkylsulfonamides have been prepared via a two-step (one pot) formation from the in situ reduction of an intermediate N-sulfonyl imine under mild, practical conditions. The compounds have been screened against a variety of cell lines for cytotoxicity effects using a Cell Titer Blue assay. The cell viability investigation identifies a subset of N-benzylic sulfonamides derived from the indole scaffold to be targeted for further development into novel molecules with potential therapeutic value. The most cytotoxic of the compounds prepared, AAL-030, exhibited higher potency than other well-known anticancer agents Indisulam and ABT-751.

Topoisomerase I inactivation by a novel thiol reactive naphthoquinone

The naphthoquinone adduct 12,13-dihydro-N-methyl-6,11,13-trioxo-5H-benzo[4,5]cyclohepta[1,2-b]naphthalen-5,12-imine (hereafter called TU100) contains structural features of both the anthracycline and isoquinone chemotherapeutics. An initial characterization showed TU100 is cytotoxic to mammalian cells and can inhibit topoisomerase I and II. Analysis using topoisomerase I now reveals TU100 is a slow acting inhibitor targeting the enzyme in the absence of DNA. Diluting pre-incubated TU100 and topoisomerase I failed to alleviate inhibition, suggesting the enzyme is being covalently modified. Critical cysteine thiols were identified as the possible target based on the ability of reducing agents to reverse TU100 inhibition. Consistent with this idea, TU100 protected topoisomerase I from inactivation by the sulfhydryl modifying agent N-ethylmaleimide (NEM). Unlike agents nonspecifically reacting with thiols, however, TU100 is specific for topoisomerase because it failed to inhibit a cysteine dependent protease. These results indicate TU100 is a novel naphthoquinone that inactivates free topoisomerase I via alkylation of cysteine residues.

Deregulation of cell cycle machinery in pancreatic cancer

Disrupted cell cycle machinery is commonly thought to result in loss of proliferative control. Standard therapies target these rapidly dividing cells, yet they are ineffective against pancreatic cancer, suggesting that its development and/or progression might deviate from standard paradigms. Supposedly essential cell cycle components are actually dispensable in mice, and accumulating evidence indicates that they play more diverse roles during apoptosis, signal transduction, and cell migration. A better understanding of how pancreatic cancer cells proliferate and the contribution of disrupted cell cycle machinery would provide much needed opportunities for developing new diagnostic and therapeutic options to improve patient outcome.

Akt1 sequentially phosphorylates p27kip1 within a conserved but non-canonical region

BACKGROUND

p27kip1 (p27) is a multifunctional protein implicated in regulation of cell cycling, signal transduction, and adhesion. Its activity is controlled in part by Phosphatylinositol-3-Kinase (PI3K)/Akt1 signaling, and disruption of this regulatory connection has been identified in human breast cancers. The serine/threonine protein kinase Akt1 directly phosphorylates p27, so identifying the modified residue(s) is essential for understanding how it regulates p27 function. Various amino acids have been suggested as potential targets, but recent attention has focused on threonine 157 (T157) because it is located in a putative Akt1 consensus site. However, T157 is not evolutionarily conserved between mouse and human. We therefore re-evaluated Akt1 phosphorylation of p27 using purified proteins and in cells.

RESULTS

Here we show purified Akt1 phosphorylates human and mouse p27 equally well. Phospho-peptide mapping indicates Akt1 targets multiple sites conserved in both species, while phospho-amino acid analysis identifies the targeted residues as serine rather than threonine. P27 deletion mutants localized these sites to the N-terminus, which contains the major p27 phosphorylation site in cells (serine 10). P27 phosphorylated by Akt1 was detected by a phospho-S10 specific antibody, confirming this serine was targeted. Akt1 failed to phosphorylate p27S10A despite evidence of a second site from mapping experiments. This surprising result suggested S10 phosphorylation might be required for targeting the second site. We tested this idea by replacing S10 with threonine, which as expected led to the appearance of phospho-threonine. Phospho-serine was still present, however, confirming Akt1 sequentially targets multiple serines in this region. We took two approaches in an attempt to explain why different residues were previously implicated. A kinetic analysis revealed a putative Akt1 binding site in the C-terminus, which may explain why mutations in this region affect p27 phosphorylation. Furthermore, commercially available recombinant Akt1 preparations exhibit striking differences in substrate specificity and site selectivity. To confirm S10 is a relevant site, we first showed that full-length wild type Akt1 purified from mammalian cells phosphorylates both human and mouse p27 on S10. Finally, we found that in cultured cells under physiologically relevant conditions such as oxidative stress or growth factor deprivation, endogenous Akt1 causes p27 accumulation by phosphorylating S10.

CONCLUSION

Identifying where Akt1 phosphorylates p27 is essential for understanding its functional implications. We found that full-length wild type Akt1--whether purified, transiently overexpressed in cells, or activated in response to cellular stress--phosphorylates p27 at S10, a noncanonical but evolutionarily conserved site known to regulate p27 activity and stability. Using recombinant Akt1 recapitulating this specificity, we showed modification of p27S10 also leads to phosphorylation of an adjacent serine. These results integrate PI3K/Akt1 signaling in response to stress with p27 regulation through its major phosphorylation site in cells, and thus identify new avenues for understanding p27 deregulation in human cancers.

Ubiquitination of p21Cip1/WAF1 by SCFSkp2: substrate requirement and ubiquitination site selection

Multiple proteolytic pathways are involved in the degradation of the cyclin-dependent kinase inhibitor p21(Cip1/WAF1). Timed destruction of p21(Cip1/WAF1) plays a critical role in cell-cycle progression and cellular response to DNA damage. The SCF(Skp2) complex (consisting of Rbx1, Cul1, Skp1, and Skp2) is one of the E3 ubiquitin ligases involved in ubiquitination of p21(Cip1/WAF1). Little is known about how SCF(Skp2) recruits its substrates and selects particular acceptor lysine residues for ubiquitination. In this study, we investigated the requirements for SCF(Skp2) recognition of p21(Cip1/WAF1) and lysine residues that are ubiquitinated in vitro and inside cells. We demonstrate that ubiquitination of p21(Cip1/WAF1) requires a functional interaction between p21(Cip1/WAF1) and the cyclin E-Cdk2 complex. Mutation of both the cyclin E recruitment motif (RXL) and the Cdk2-binding motif (FNF) at the N terminus of p21(Cip1/WAF1) abolishes its ubiquitination by SCF(Skp2), while mutation of either motif alone has minimal effects, suggesting either contact is sufficient for substrate recruitment. Thus, SCF(Skp2) appears to recognize a trimeric complex consisting of cyclin E-Cdk2-p21(Cip1/WAF1). Furthermore, we show that p21(Cip1/WAF1) can be ubiquitinated at four distinct lysine residues located in the carboxyl-terminal region but not two other lysine residues in the N-terminal region. Any one of these four lysine residues can be targeted for ubiquitination in the absence of the others in vitro, and three of these four lysine residues are also ubiquitinated in vivo, suggesting that there is limited specificity in the selection of ubiquitination sites. Interestingly, mutation of the carboxyl-terminal proline to lysine enables ubiquitin conjugation at the carboxyl terminus of the substrate both in vitro and in vivo. Thus, our results highlight a unique property of the ubiquitination enzymatic reaction in that substrate ubiquitination site selection can be remarkably diverse and occur in distinct spatial areas.

G1 phase: components, conundrums, context

A eukaryotic cell must coordinate DNA synthesis and chromosomal segregation to generate a faithful replica of itself. These events are confined to discrete periods designated synthesis (S) and mitosis (M), and are separated by two gap periods (Gl and G2). A complete proliferative cycle entails sequential and regulated progression through G1, S, G2, and M phases. During G1, cells receive information from the extracellular environment and determine whether to proliferate or to adopt an alternate fate. Work in yeast and cultured mammalian cells has implicated cyclin dependent kinases (Cdks) and their cyclin regulatory partners as key components controlling G1. Unique cyclin/Cdk complexes are temporally expressed in response to extracellular signaling, whereupon they phosphorylate specific targets to promote ordered G1 progression and S phase entry. Cyclins and Cdks are thought to be required and rate-limiting for cell proliferation because manipulating their activity in yeast and cultured mammalian cells alters G1 progression. However, recent evidence suggests that these same components are not necessarily required in developing mouse embryos or cells derived from them. The implications of these intriguing observations for understanding G1 progression and its regulation are discussed.

p27Kip1 inhibition of GRB2-SOS formation can regulate Ras activation

p27(Kip1) (p27) is often inappropriately downregulated in aggressive human cancers. Although p27 can inhibit cyclin-dependent kinases (CDKs), low p27 does not always correlate with increased CDK activity. Furthermore, cells derived from p27(-/-) mice respond to antimitogens, maintain restriction point control, and do not deregulate CDKs. Thus, disruption of a p27 function other than CDK inhibition may contribute to the disease state. A yeast two-hybrid screen identified growth factor receptor-bound protein 2 (GRB2) as a p27 binding partner. We now demonstrate that p27 can inhibit GRB2 function by blocking its association with the guanine nucleotide exchange factor SOS. Endogenous p27 is rapidly exported from the nucleus to the cytoplasm in response to mitogen stimulation, where it binds GRB2 concomitant with a decrease in GRB2-associated SOS. As predicted, mitogen-stimulated p27(-/-) cells maintained their GRB2-SOS complexes for significantly longer. The Ras/mitogen-activated protein kinase pathway does not appear to be deregulated in cells lacking p27 despite excess GRB2-SOS, suggesting that additional control mechanisms are present. A transient-transfection approach was employed to show that p27 can inhibit Ras activation by targeting GRB2 and further revealed that the CDK and GRB2 inhibitory functions of p27 are separable and distinct. Thus, p27 downregulation may compromise control of Ras, one of the most common oncogenic events in human cancer.

p27kip1 contributions to cancer

Deregulation of the tumor suppressor p27kip1 (p27) has been implicated in a variety of human cancers, suggesting it might be a viable therapeutic target. Developing p27-specific intervention strategies requires understanding its role and regulation in normal and pathologic states. Although p27 has been extensively characterized as an inhibitor of cyclin-dependent kinases, disruption of this function is inadequate to explain its role in tumorigenesis. A more comprehensive understanding of p27 biology would facilitate development of therapeutic responses to p27 disruption in human cancers.

Proteasomal turnover of p21Cip1 does not require p21Cip1 ubiquitination

The Cdk inhibitor p21Cip1 is an unstable protein. Pharmacologic inhibition of the proteasome increases the half-life of p21 from less than 30 min to more than 2 hr and results in the accumulation of p21-ubiquitin conjugates. To determine whether ubiquitination was required for proteasomal degradation of p21, we constructed mutant versions of p21 that were not ubiquitinated in vivo. Remarkably, these mutants remained unstable and increased in abundance upon proteasome inhibition, indicating that direct ubiquitination of p21 is not necessary for its turnover by the proteasome. The frequently observed correlation between protein ubiquitination and proteasomal degradation is insufficient to conclude that ubiquitination is a prerequisite for degradation.

Cyclin E-CDK2 is a regulator of p27Kip1

CDK inhibitors are thought to prevent cell proliferation by negatively regulating cyclin-CDK complexes. We propose that the opposite is also true, that cyclin-CDK complexes in mammmalian cells can promote cell cycle progression by directly down-regulating CDK inhibitors. We show that expression of cyclin E-CDK2 in murine fibroblasts causes phosphorylation of the CDK inhibitor p27Kip1 on T187, and that cyclin E-CDK2 can directly phosphorylate p27 T187 in vitro. We further show that cyclin E-CDK2-dependent phosphorylation of p27 results in elimination of p27 from the cell, allowing cells to transit from G1 to S phase. Moreover, mutation of T187 in p27 to alanine creates a p27 protein that causes a G1 block resistant to cyclin E and whose level of expression is not modulated by cyclin E. A kinetic analysis of the interaction between p27 and cyclin E-CDK2 explains how p27 can be regulated by the same enzyme it targets for inhibition. We show that p27 interacts with cyclin E-CDK2 in at least two distinct ways: one resulting in p27 phosphorylation and release, the other in tight binding and cyclin E-CDK2 inhibition. The binding of ATP to the CDK governs which state predominates. At low ATP (< 50 microM) p27 is primarily a CDK inhibitor, but at ATP concentrations approaching physiological levels (> 1 mM) p27 is more likely to be a substrate. Thus, we have identified p27 as a biologically relevant cyclin E-CDK2 substrate, demonstrated the physiological consequences of p27 phosphorylation, and developed a kinetic model to explain how p27 can be both an inhibitor and a substrate of cyclin E-CDK2.

End of the line: proteolytic degradation of cyclin-dependent kinase inhibitors

Cyclin-dependent kinase inhibitors (CKIs) are crucial regulators of cell-cycle progression. The CKI Sic1 controls the timing of DNA replication by inhibiting Clb-Cdc28 kinase. Phosphorylation of Sic1 by CIn-Cdc28 kinase alleviates this inhibition by targeting Sic1 for degradation through the ubiquitin-mediated proteolytic pathway.

Turnover of cyclin E by the ubiquitin-proteasome pathway is regulated by cdk2 binding and cyclin phosphorylation

Cyclin E is a mammalian G1 cyclin that is both required and rate limiting for entry into S phase. The expression of cyclin E is periodic, peaking at the G1-S transition and then decaying as S phase progresses. To understand the mechanisms underlying cyclin E periodicity, we have investigated the regulation of cyclin E degradation. We find that cyclin E is degraded by the ubiquitin-proteasome system, and that this degradation is regulated by both cdk2 binding and cdk2 catalytic activity. Free cyclin E is readily ubiquitinated and degraded by the proteasome. Binding to cdk2 protects cyclin E from ubiquitination, and this protection is reversed by cdk2 activity in a process that involves phosphorylation of cyclin E itself. The data are most consistent with a model in which cdk2 activity initiates cyclin E degradation by promoting the disassembly of cyclin E-cdk2 complexes, followed by the ubiquitination and degradation of free cyclin E.

Interactions of calf thymus DNA polymerase alpha with primer/templates

The interactions of calf thymus DNA polymerase alpha (pol alpha) with primer/templates were examined. Simply changing the primer from DNA to RNA had little effect on primer/template binding or dNTP polymerization (Km, Vmax and processivity). Surprisingly, however, adding a 5'-triphosphate to the primer greatly changed its interactions with pol alpha (binding, Vmax and Km and processivity). While changing the primer from DNA to RNA greatly altered the abilit of pol alpha to discriminate against nucleotide analogs, it did not compromise the ability of pol alpha to discriminate against non-cognate dNTPs. Thus the nature of the primer appears to affect 'sugar fidelity', without altering 'base fidelity'. DNase protection assays showed that pol alpha strongly protected 9 nt of the primer strand, 13 nt of the duplex template strand and 14 nt of the single-stranded template from hydrolysis by DNase I and weakly protected several bases outside this core region. This large DNA binding domain may account for the ability of a 5'-triphosphate on RNA primers to alter the catalytic properties of pol alpha.

Tumor suppression. Lessons in p16 from phylum Falconium

Increasingly, biochemical and genetic evidence indicates that mutations in the gene encoding p16, an inhibitor of cyclin-dependent kinases, may play a role in some forms of hereditary and sporadic tumors.

Misincorporation of nucleotides by calf thymus DNA primase and elongation of primers containing multiple noncognate nucleotides by DNA polymerase alpha

Misincorporation of nucleotides by calf thymus DNA primase was examined using synthetic DNA templates of defined sequence. Primase seldom misincorporated NTPs during initiation of a new primer (i.e. polymerization of two NTPs to generate the dinucleotide). Following dinucleotide formation, however, primase readily misincorporated NTPs. Although the rate of misincorporation varied according to both the identity of the mismatch and the template sequence, primase is by far the least accurate nucleotide-polymerizing enzyme known. In some cases primase discriminated against incorrect NTPs by less than a factor of 100. After primase incorporated a noncognate nucleotide into the primer, the next correct NTP was readily added. Remarkably, primase could also polymerize consecutive noncognate nucleotides and generate primers containing multiple mismatches. Generation of a correctly base-paired primer-template negatively regulated further primer synthesis; however, generation of a primer-template containing multiple mismatches did not. After primase synthesized a primer containing multiple mismatches, the primer was transferred to the polymerase alpha active site via an intramolecular mechanism. Importantly, polymerase alpha readily elongated this primer if dNTPs were present. These data are discussed with respect to the question of why primase is required for DNA replication.

Calf thymus DNA polymerase alpha-primase: "communication" and primer-template movement between the two active sites

The DNA polymerase alpha-primase complex replicates single-stranded DNA by first synthesizing a short RNA primer (primase) which is then further elongated by the incorporation of dNTPs (DNA polymerase alpha). While primase and pol alpha function independently prior to synthesis of an RNA primer, the two activities become coordinated after primer synthesis. After primase generates a primer-template, it moves from the primase active site to the pol alpha active site for further elongation without dissociating into solution. Intramolecular transfer occurs immediately after primer synthesis and is employed on both long templates such as poly(dT) and short synthetic templates (< or = 60 nucleotides). Primer-template transfer and elongation by pol alpha are rapid compared to primer synthesis. After pol alpha elongates the primer, primase reinitiates primer synthesis, and the cycle is repeated. However, if dNTPs are absent such that primer elongation cannot occur, further primase activity is inhibited after a single round of primer synthesis. This "negative regulation" of primase activity is mediated by the newly generated primer-template provided the following conditions are met: (1) Primase synthesizes the primer; (2) the primer is 7-10 nucleotides long and remains bound to the template; (3) the template is of sufficient length; (4) the primer-template dissociates slowly from the enzyme complex; and (5) the primer-template interacts with the pol alpha active site. Polymerization of multiple dNTPs by pol alpha rapidly reactivates primase; hence, negative regulation of primase activity likely ensures a new primer is not synthesized until the previous one has been elongated by pol alpha.

Mechanism of calf thymus DNA primase: slow initiation, rapid polymerization, and intelligent termination

The mechanism by which calf thymus DNA primase synthesizes RNA primers was examined. Primase first binds a single-stranded DNA template (KD << 100 nM) and can then slide along the DNA in order to find a start for initiating primer synthesis. NTP binding appears ordered, such that the NTP which eventually becomes the second nucleotide of the primer binds the E.DNA complex first. The NTP that becomes the second nucleotide of the primer thereby influences where primase initiates. Primer synthesis is remarkably slow (0.0027 s-1 at 20 microM NTP). The rate-limiting step is after formation of the E.DNA.NTP.NTP complex and before or during dinucleotide synthesis. After synthesis of the dinucleotide, additional NTPs are rapidly polymerized. Primase products are 2-10 nucleotides long. If the enzyme fails to synthesize a primer at least 7 nucleotides long, it reinitiates rather than dissociating from the template. Once a primer at least 7 nucleotides long has been generated, however, subsequent primase activity is inhibited. This inhibition is due to the generation of a stable primer-template complex, which likely remains associated with pol alpha.primase. The role of primase is to synthesize primers that pol alpha can elongate. The ability of primase to distinguish between primers at least 7 nucleotides long and shorter products therefore likely reflects the fact that pol alpha only utilizes primers at least 7 nucleotides long.