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C Mao

Publications and source records attributed to C Mao.

At least 73 records · Page 4Linked to original sources

The dihydrosphingosine-1-phosphate phosphatases of Saccharomyces cerevisiae are important regulators of cell proliferation and heat stress responses.

We have identified YSR2 and YSR3 of Saccharomyces cerevisiae as genes encoding dihydrosphingosine-1-phosphate phophatases which are involved in regulation of sphingolipid metabolism [Mao, Wadleigh, Jenkins, Hannun and Obeid (1997) J. Biol. Chem. 272, 28690-28694]. In this study, we explored the physiological roles that these enzymes may have in S. cerevisiae. Deletion of either YSR2, YSR3 or both did not affect viability or growth rate of yeast cells. However, overexpression of YSR2 significantly prolonged the doubling time of cell growth, whereas overexpression of YSR3 affected cell growth only slightly. Cell cycle analysis suggested that overexpression of either YSR2 or, to a lesser extent, YSR3 caused cell cycle arrest at the G1 phase. Disruption of YSR2, but not YSR3, conferred increased thermotolerance. On the other hand, overexpression of either YSR2 or YSR3 diminished thermotolerance. Using labelled dihydrosphingosine and dihydrosphingosine-1-P (DHS-1-P), we found that overexpression of YSR2 significantly increased ceramide formation, whereas deletion of YSR2, YSR3, or both, accumulated DHS-1-P, and deletion of YSR2 decreased ceramide formation. Together, these results show that the phenotypes of YSR2 are associated with changes in endogenous levels of the different sphingolipids. Green fluorescent protein tagging showed that in the exponentially growing cells, YSR2 and YSR3 had the same cellular localization to endoplasmic reticulum. However, YSR2 and YSR3 differ in mRNA levels: YSR2 had significantly higher mRNA levels than YSR3. This discrepancy might result in the functional differences that these proteins exhibited. In addition, this study implicates sphingolipids and their metabolism in the regulation of growth and heat stress responses of the yeast S. cerevisiae.

Cell Division↗

X-Ray structure of glycerol kinase complexed with an ATP analog implies a novel mechanism for the ATP-dependent glycerol phosphorylation by glycerol kinase.

Glycerol kinase (GK) catalyzes the Mg-ATP-dependent phosphorylation of glycerol which yields glycerol 3-phosphate. The 2.8 A new crystal structure of GK complexed with an ATP analog revealed an unexpected position of the gamma-phosphoryl group, which was 7.2 A distant from the 3-hydroxyl group of glycerol, 5.5 A away from the 3-phosphate of the product (glycerol 3-phosphate) and is stabilized by a beta-hairpin structure. Based on the presented crystal structure and the previously determined structures of GK product complexes, we propose a 3-D model of a nucleophilic in-line transfer mechanism for the ATP-dependent phosphorylation of glycerol by GK.

Adenosine Triphosphate↗

Rational design of N-[2-(2,5-dimethoxyphenylethyl)]-N'-[2-(5-bromopyridyl)]-thiourea (HI-236) as a potent non-nucleoside inhibitor of drug-resistant human immunodeficiency virus.

The novel thiourea compound N-[2-(2,5-dimethoxyphenylethyl)]-N'-[2-(5-bromopyridyl)]-thi ourea (HI-236) targeting the non-nucleoside inhibitor (NNI) binding pocket of HIV-1 reverse transcriptase (RT) was rationally designed using a computer model of the NNI binding pocket. The NNI binding pocket model takes into consideration changes in binding pocket size, shape, and changes in residue character that result from clinically-observed NNI resistance-associated mutations of HIV RT. RT assays revealed that HI-236 was not only more potent than trovirdine, MKC-442, and AZT against the drug-sensitive HIV-1 strain HTLV(IIIB), it was also 50-100 times more effective than delavirdine or nevirapine and twice as effective as our recently reported lead compound N-[2-(2-fluorophenethyl)]-N'-[2-(5-bromopyridyl)]-thiourea (HI-240) against the NNI-resistant Y181C mutant HIV-1 strain A17. Most importantly, HI-236 was highly effective against the multidrug-resistant HIV-1 strain RT-MDR with multiple mutations involving the RT residues 74V, 41L, 106A, and 215Y. The activity of HI-236 against RT-MDR was superior to that of other anti-HIV agents tested, which are listed in the following order: HI-236 (IC50: 5 nM) > HI-240 (IC50: 6 nM) > trovirdine (IC50: 20 nM) > AZT (IC50: 150 nM) > MKC-442 (IC50: 300 nM) > delavirdine (IC50: 400 nM) > nevirapine (IC50: 5 microM).

Anti-HIV Agents↗

Molecular interaction of Agouti protein and Agouti-related protein with human melanocortin receptors.

Agouti protein and the Agouti-related protein (AGRP) are antagonists of the melanocortin-3 receptor and melanocortin-4 receptor. Both proteins contain 10 cysteines in the C-terminal domain arranged in five disulfide bonds. One possible arrangement of the disulfide bonds predicts an octapeptide loop, and the chemical properties of four residues within this loop (residues 111-114 in human AGRP) bear striking resemblance to those of several melanocortin peptides, including alpha-MSH, MT-II, and SHU-9119. We showed that cyclic synthetic octapeptides based on the sequence of this loop from Agouti protein or human AGRP are functional antagonists of the human melanocortin-4 receptor. All peptides had a lower affinity for the melanocortin-3 receptor than for the melanocortin-4 receptor. Substitution of serines for cysteines resulted in linear peptides which had reduced binding affinities for both receptors. Mutational analysis of human AGRP indicated that its C-terminal domain is functionally equivalent to the intact human AGRP. The RFF111-113 triplet appears to be the most critical portion of AGRP in determining the binding affinity for both melanocortin-3 and melanocortin-4 receptors. These data strongly suggest that the loop defined by Cys-110 and Cys-117 is critical in determining the antagonist activity of human AGRP. Our data provide indirect evidence for the suggestion that the Cys-110 to Cys-117 octapeptide loop of human AGRP mimics the conformation of alpha-MSH, MT-II, and SHU-9119.

Agouti Signaling Protein↗

A nanomechanical device based on the B-Z transition of DNA.

The assembly of synthetic, controllable molecular mechanical systems is one of the goals of nanotechnology. Protein-based molecular machines, often driven by an energy source such as ATP, are abundant in biology. It has been shown previously that branched motifs of DNA can provide components for the assembly of nanoscale objects, links and arrays. Here we show that such structures can also provide the basis for dynamic assemblies: switchable molecular machines. We have constructed a supramolecular device consisting of two rigid DNA 'double-crossover' (DX) molecules connected by 4.5 double-helical turns. One domain of each DX molecule is attached to the connecting helix. To effect switchable motion in this assembly, we use the transition between the B and Z forms of DNA. In conditions that favour B-DNA, the two unconnected domains of the DX molecules lie on the same side of the central helix. In Z-DNA-promoting conditions, however, these domains switch to opposite sides of the helix. This relative repositioning is detected by means of fluorescence resonance energy transfer spectroscopy, which measures the relative proximity of two dye molecules attached to the free ends of the DX molecules. The switching event induces atomic displacements of 20-60 A.

Biomechanical Phenomena↗

A disrupted homologue of the human CLN3 or juvenile neuronal ceroid lipofuscinosis gene in Saccharomyces cerevisiae: a model to study Batten disease.

1. In order to investigate the biological function of the human CLN3 gene that is defective in Batten disease, we created a yeast strain by PCR-targeted disruption of the yeast gene (YHC3), which is a homologue of the human CLN3 gene. 2. The phenotypic characterization revealed that the yhc3 delta mutants are more sensitive to combined heat and alkaline stress than the wild-type strains as determined by inhibition of cell proliferation. 3. This suggests that the yhc3 delta mutant is a good model to investigate the biological function of human CLN3 gene in mammalian cells and to understand the pathophysiology of juvenile Batten disease.

Alkalosis↗

Polymorphisms of the endothelial nitric oxide synthase gene - no consistent association with myocardial infarction in the ECTIM study.

BACKGROUND: Our aim in the present study was to determine whether endothelial NO synthase gene (ecNOS) polymorphisms are associated with myocardial infarction (MI). METHODS: Forty chromosomes from patients with MI were screened for polymorphisms of the ecNOS gene using polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis and sequencing. Ten polymorphisms were detected: three in the 5' flanking sequence at positions -1474, -924 and -788, two in coding sequences 774C --> T (silent) and G894 --> T (Glu-298 --> Asp) and five in introns 2, 11, 12, 22 and 23. Five hundred and thirty-one patients with MI and 610 control subjects recruited in France and Northern Ireland in the ECTIM study were genotyped for these polymorphisms. RESULTS: Glu-298 homozygotes were more frequent among patients with MI than in control subjects in the French population [OR = 1.47 (1.03-1.97), P < 0.009], but no such difference was observed in Northern Ireland. No significant difference between cases and control subjects was detected for the other polymorphisms. Our search for a possible association of the combination of ecNOS polymorphisms with MI by logistic regression analysis was also negative. CONCLUSIONS: We have explored a set of polymorphisms of the ecNOS gene in a large case-control study of MI and found that the polymorphisms were not consistently associated with MI.

Adult↗

Intraventricular haemorrhage and its prognosis, prevention and treatment in term infants.

The purpose of this study was to investigate the prognosis of intraventricular haemorrhage (IVH) in term infants and its prevention and treatment. The authors diagnosed IVH in full-term newborns by using computerized tomography (CT) or cranial ultrasonography (US). The results of CT or US were reviewed and the grade of haemorrhage was determined by an independent radiologist using Papile's criteria. All the infants were examined on the first day of their life by a paediatrician and judged to be full term. Survivors were examined between age 2 and 10 years at the Child Development Clinic by a Developmental Paediatrician using the Gesell scales and a standard neurologic examination. The results showed that three of 36 infants (8 per cent) died; complications of pregnancy were present in 17 mothers (47 per cent); nine women tested negative for platelet antigen 1 and their infants exhibited alloimmune thrombocytopenia. Age at diagnosis ranged from in utero to 28 days. Clinical presentation included feeding intolerance, irritability, jaundice, fever, and restlessness. Of the nine children with grade IV IVH, three died and six survivors were severely handicapped. Overall, 22 (67 per cent) of 33 survivors had no or mild handicap. The results of this study suggest that severity of haemorrhage was of prognostic value. Perinatal alloimmune thrombocytopenia turned out to be the single most important cause of severe haemorrhage and poor outcome. Identification and treatment of these infants must begin in utero if we are to prevent IVH and its complications in this group of patients.

Cerebral Hemorrhage↗

A quantitative assessment of how Canadian intensivists believe they utilize oxygen in the intensive care unit.

OBJECTIVES: To investigate attitudes and practices regarding oxygen therapy in intensive care units (ICUs) and to devise quantitative descriptive indices. SETTING: Canadian university-affiliated adult ICUs. PARTICIPANTS: Fifty-two medical directors of ICUs in 48 institutions. INTERVENTION: Structured postal questionnaire returned by 48 participants. MEASUREMENTS AND MAIN RESULTS: Attitudes, beliefs, and stated practices relating to oxygen use in ICUs were determined. Novel descriptors S-50min (minutes of oxygen saturation [Sao2] acceptable to >50% of respondents), F-50max (maximum F(IO)2 above which <50% of respondents would increase F(IO)2), and F-50min (minimum F(IO)2 below which <50% of respondents would decrease F(IO)2) were determined. All respondents believed that oxygen toxicity was a concern. Twenty-nine percent of respondents indicated that they did not always assess tissue oxygenation in critical cases. A stepwise reduction in acceptance of progressive desaturation and increasing duration of hypoxemia was found. Presented with a stable patient with Sao2 of 98%, the maximum level of F(IO)2 above which respondents stated that they would not increase the F(IO)2 was 0.41+/-0.17 (mean +/- SD). For stable patients with Sao2 of 85%, the minimum F(IO)2 below which respondents would not reduce F(IO)2 was 0.59+/-0.23 (mean +/- SD). F-50max was 0.8 vs. 0.5 for Sao2 of 80%-85% vs. 85%-90%, respectively; F-50min was 0.6 vs. 0.21 for Sao2 of 90%-95% vs. 95%-100%, respectively. CONCLUSIONS: Considerable variation exists in the attitudes, beliefs, and stated practices relating to the management of oxygen therapy in the ICU. These data are amenable to quantitative description and illustrate the necessity for documentation of actual practice and development of support systems for decision-making in this and similar areas.

Adult↗

Structure-based design of non-nucleoside reverse transcriptase inhibitors of drug-resistant human immunodeficiency virus.

A computer model of reverse transcriptase (RT) from human immunodeficiency virus type 1 (HIV-1) was used to design thiourea compounds that were predicted to inhibit RT. The RT model was used to approximate how changes in binding pocket shape, volume and chemical properties resulting from residue mutations would affect inhibitor binding. Our lead compound, N-[2-(2,5-dimethoxyphenylethyl)]-N'-[2-(5-bromopyridyl)]-thi ourea (HI-236) was tested against clinically observed non-nucleoside inhibitor (NNI)-resistant mutated strains of HIV. HI-236 was more potent than trovirdine, MKC-442 and zidovudine against the drug-sensitive HIV-1 strain IIIB, 50-100 times more effective than delavirdine or nevirapine and twice as effective as our recently reported lead compound N-[2-(2-fluorophenethyl)]-N'-[2-(5-bromopyridyl)]-thiourea (HI-240) against the NNI-resistant Y181C mutant HIV-1 strain A17. HI-236 was highly effective against the multidrug-resistant HIV-1 strain RT-MDR containing multiple mutations involving the RT residues 74V, 41L, 106A and 215Y. In general, thiourea compounds such as HI-236 and HI-240 showed better inhibition of drug-resistant strains of HIV-1 than thioalkylbenzyl-pyrimidine compounds such as HI-280 and HI-281. The improved activity of thioureas against RT mutants is consistent with a structural analysis of the NNI binding pocket model of RT. The activity of HI-236 against RT-MDR was superior to that of other anti-HIV agents tested, in the following order, from high to low activity; HI-236 (IC50 5 nM), HI-240 (IC50 6 nM), trovirdine (IC50 20 nM), zidovudine (IC50 150 nM), MKC-442 (IC50 300 nM), delavirdine (IC50 400 nM) and nevirapine (IC50 5 microM).

Alanine↗

[Improvement in affinity of phage antibodies against HBsAg by light chain shuffling].

OBJECTIVE: We had cloned an Fd gene of human antibody against HBsAg previously. The objective of this experiment is to improve the affinity phage antibody by chain-shuffling. METHODS: Human antibody light chain gene repertoire was generated by RT-PCR from human peripheral blood lymphocyte, and then phage antibody sublibrary was constructed by inserting the repertoire into the phagmid which contained the Fd gene. The matched gene of light chain was selected by biopaning. RESULTS: After three rounds of selection, eight clones with higher absorbance than that of original clone at 490 nm in ELISA were obtained. DNA sequencing showed three of the five VL genes were kappa type, and the other two were lambda type. CONCLUSION: The results indicated that the affinity of chain shuffled phage antibodies(phab) were improved. The specificity of the selected phab was also confirmed.

Antibody Affinity↗

Structure-based design of specific inhibitors of Janus kinase 3 as apoptosis-inducing antileukemic agents.

A novel homology model of the kinase domain of Janus kinase (JAK) 3 was used for the structure-based design of dimethoxyquinazoline compounds with potent and specific inhibitory activity against JAK3. The active site of JAK3 in this homology model measures roughly 8 A x 11 A x 20 A, with a volume of approximately 530 A3 available for inhibitor binding. Modeling studies indicated that 4-(phenyl)-amino-6,7-dimethoxyquinazoline (parent compound WHI-258) would likely fit into the catalytic site of JAK3 and that derivatives of this compound that contain an OH group at the 4' position of the phenyl ring would more strongly bind to JAK3 because of added interactions with Asp-967, a key residue in the catalytic site of JAK3. These predictions were consistent with docking studies indicating that compounds containing a 4'-OH group, WHI-P131 [4-(4'-hydroxyphenyl)-amino-6,7-dimethoxyquinazoline], WHI-P154 [4-(3'-bromo-4'-hydroxylphenyl)-amino-6,7-dimethoxyquinazoline], and WHI-P97 [4-(3',5'-dibromo-4'-hydroxylphenyl)-amino-6,7-dimethoxyquinazolin e], were likely to bind favorably to JAK3, with estimated K(i)s ranging from 0.6 to 2.3 microM. These compounds inhibited JAK3 in immune complex kinase assays in a dose-dependent fashion. In contrast, compounds lacking the 4'-OH group, WHI-P79 [4-(3'-bromophenyl)-amino-6,7-dimethoxyquinazoline], WHI-P111 [4-(3'-bromo-4'-methylphenyl)-amino-6,7-dimethoxyquinazoline], WHI-P112 [4-(2',5'-dibromophenyl)-amino-6,7-dimethoxyquinazoline], WHI-P132 [4-(2'-hydroxylphenyl)-amino-6,7-dimethoxyquinazoline], and WHI-P258 [4-(phenyl)-amino-6,7-dimethoxyquinazoline], were predicted to bind less strongly, with estimated K(i)s ranging from 28 to 72 microM. These compounds did not show any significant JAK3 inhibition in kinase assays. Furthermore, the lead dimethoxyquinazoline compound, WHI-P131, which showed potent JAK3-inhibitory activity (IC50 of 78 microM), did not inhibit JAK1 and JAK2, the ZAP/SYK family tyrosine kinase SYK, the TEC family tyrosine kinase BTK, the SRC family tyrosine kinase LYN, or the receptor family tyrosine kinase insulin receptor kinase, even at concentrations as high as 350 microM. WHI-P131 induced apoptosis in JAK3-expressing human leukemia cell lines NALM-6 and LC1;19 but not in melanoma (M24-MET) or squamous carcinoma (SQ20B) cells. Leukemia cells were not killed by dimethoxyquinazoline compounds that were inactive against JAK3. WHI-P131 inhibited the clonogenic growth of JAK3-positive leukemia cell lines DAUDI, RAMOS, LC1;19, NALM-6, MOLT-3, and HL-60 (but not JAK3-negative BT-20 breast cancer, M24-MET melanoma, or SQ20B squamous carcinoma cell lines) in a concentration-dependent fashion. Potent and specific inhibitors of JAK3 such as WHI-P131 may provide the basis for the design of new treatment strategies against acute lymphoblastic leukemia, the most common form of childhood cancer.

Antineoplastic Agents↗

Expression of dominant-negative Ikaros isoforms in T-cell acute lymphoblastic leukemia.

Ikaros, a zinc finger-containing DNA-binding protein, is required for normal lymphocyte development. Germ-line mutant mice that express only non-DNA binding dominant-negative "leukemogenic" Ikaros isoforms lacking critical NH2-terminal zinc fingers develop an aggressive form of T-cell leukemia. We studied Ikaros gene expression in leukemic cells from 18 children with T-cell acute lymphoblastic leukemia (T-ALL). In each of the 18 T-ALL cases as well as JK-E6-1 and MOLT-3 cell lines, we found high-level expression of dominant-negative isoforms of Ikaros with abnormal subcellular compartmentalization patterns. Nuclear extracts from these cells failed to bind to the IKAROS-specific binding sequence in DNA. PCR cloning and sequencing confirmed that JK-E6-1 and MOLT-3 cell lines as well as leukemic cells from 9 of 10 patients with T-ALL expressed dominant-negative Ikaros isoforms Ik-4, Ik-7, and Ik-8 that lack critical NH2-terminal zinc fingers. In 6 of 10 patients, we detected a specific mutation leading to an in-frame deletion of 10 amino acids (delta KSSMPQKFLG) upstream to the transcription activation domain and adjacent to the COOH-terminal zinc fingers of Ik-2, Ik-4, Ik-7, and Ik-8. Thus, children with T-ALL express high levels of dysfunctional dominant-negative Ikaros isoforms.

Adult↗

[Selection of human phage antibodies against HAV and DNA sequence analysis].

OBJECTIVE: To obtain the anti-HAV antibodies. METHODS: The antibody-capturing antigen strategy was used in panning antibody library with impure antigen. The HAV-binding activity and specificity of phage antibodies were assayed by sandwich ELISA and competitive inhibition ELISA. RESULTS: Phage antibodies(Fab) against HAV were screened from a human immunoglobulin combinatorial library. Fd and light chain genes were sequenced. Comparison of the Fd gene and light chain gene with KABAT database showed that the heavy chain belonged to IgG1 subclass, and its variable region was derived from rearranged germ-line gene of DP88, D3-3 and JH5; while the light chain was a member of V kappa III family, the germ-line gene was DP kappa 22 and J kappa 4. CONCLUSION: Phage antibodies against HAV were selected from the antibody library by using the antibody-capturing antigen strategy. The result also suggested that the antibody library was constructed successfully.

Amino Acid Sequence↗

Specificity of alpha-cyano-beta-hydroxy-beta-methyl-n-[4-(trifluoromethoxy)phe nyl]-propenamide as an inhibitor of the epidermal growth factor receptor tyrosine kinase.

The epidermal growth factor receptor (EGFR) tyrosine kinase has an essential function for the survival of human breast cancer cells. In a systematic effort to design potent and specific inhibitors of this receptor family protein tyrosine kinase (PTK) as antibreast cancer agents, we recently reported the construction of a three-dimensional homology model of the EGFR kinase domain. In this model, the catalytic site is defined by two beta-sheets that form an interface at the cleft between the NH2-terminal and COOH-terminal lobes of the kinase domain. Our modeling studies revealed a distinct, remarkably planar triangular binding pocket within the kinase domain with approximate dimensions of 15 A x 12 A x 12 A, and the thickness of the binding pocket is approximately 7 A with an estimated volume of approximately 600 A3 available for inhibitor binding. Molecular docking studies had identified alpha-cyano-beta-hydroxy-beta-methyl-N-[4-(trifluoromethoxy)phenyl]-p ropenamide (LFM-A12) as our lead inhibitor, with an estimated binding constant of 13 microM, which subsequently inhibited EGFR kinase in vitro with an IC50 value of 1.7 microM. LFM-A12 was also discovered to be a highly specific inhibitor of the EGFR. Even at very high concentrations ranging from 175-350 microM, this inhibitor did not affect the enzymatic activity of other PTKs, including the Janus kinases JAK1 and JAK3, the Src family kinase HCK, the Tec family member Bruton's tyrosine kinase, SYK kinase, and the receptor family PTK insulin receptor kinase. This observation is in contrast to the activity of a quinazoline inhibitor tested as a control, 4-(3-bromo, 4-hydroxyanilino)-6,7-dimethoxyquinazoline, which was shown to inhibit EGFR and other tyrosine kinases such as HCK, JAK3, and SYK.

Aniline Compounds↗

Structure-based design of potent inhibitors of EGF-receptor tyrosine kinase as anti-cancer agents.

In a systematic effort to design inhibitors of the epidermal growth factor receptor (EGFR) family protein tyrosine kinases (PTK) as anti-cancer agents, we have constructed a three-dimensional homology model of the EGFR kinase domain and used molecular modeling methods for the structure-based design of analogs of the active metabolite of leflunomide (LFM) with potent and specific inhibitory activity against EGFR. These docking studies identified alpha-cyano-beta-hydroxy-beta-methyl-N-[4-(trifluoromethoxy)phenyl]-p ropenamide (LFM-A12) as our lead compound, which was predicted to bind to the EGFR catalytic site in a planar conformation. LFM-A12 inhibited the proliferation (IC50 = 26.3 microM) and in vitro invasiveness (IC50 = 28.4 microM) of EGFR positive human breast cancer cells in a concentration-dependent fashion. Similarly, the model of the EGFR binding pocket was used in combination with docking procedures to predict the favorable placement of chemical groups with defined sizes at multiple modification sites on another class of EGFR inhibitors, the 4-anilinoquinazoline. This approach has led to the successful design of a dibromo quinazoline derivative, WHI-P97, which had an estimated Ki value of 0.09 microM from modeling studies and a measured IC50 value of 2.5 microM in EGFR kinase inhibition assays. WHI-P97 effectively inhibited the in vitro invasiveness of EGFR-positive human cancer cells in a concentration-dependent manner. However, unlike LFM-A12, the quinazoline compounds are not specific for EGFR.

Antineoplastic Agents↗

Therapeutic effect of abstinence capsule on withdrawal symptoms of heroin addicts.

435 heroin addicts were treated for 10 days to evaluate the therapeutic effectiveness of abstinence capsule on heroin withdrawal symptoms and its main adverse actions. Lofexidine was applied in a control group of 48 addicts. The single blind method and some determination methods used internationally were employed to evaluate the therapeutic effectiveness and adverse actions of the drugs. The results showed that the abstinence capsule has better therapeutic effectiveness, with less adverse actions, wider safety range, longer time of action and less cost than lofexidine.

Adolescent↗

Sequence dependence of branch migratory minima.

The Holliday junction is a central intermediate in the process of genetic recombination. The position of its branch-point can relocate through an isomerization known as branch migration. This migration occurs because the branch-point is flanked by homologous symmetry. All attempts at modeling the kinetics of branch migration have relied on the assumption that branch migration minima are sequence-independent. We have tested that assumption here, using a competition assay based on symmetric immobile branched junctions; these are junctions that cannot undergo branch migration, despite the fact that they are flanked by homology. The assay used is predicated on the non-association of strands displaced in the assay; we have tested this assumption, and have performed our experiments under conditions where we know that it is true. We have measured the free energy of relocating a branched junction from a fixed non-homologous sequence to all possible dimeric symmetric sequences. We find that the assumption of sequence-independence is often valid, but that it is not universally true. We find that the flanking sequences can have a marked effect on the free energy measured, both for extensions of symmetry and for reversals of flanking nucleotides. We have varied the temperature in our experiments, and have derived both enthalpies and entropies for the different sequences. The entropies are largely unfavorable, whereas the enthalpies are largely favorable; regardless of the signs of these quantities, we see that this is another system where enthalpy-entropy compensation is operative.

Base Sequence↗