Stacking geometry between two sheared Watson-Crick basepairs: Computational chemistry and bioinformatics based prediction

BackgroundMolecular modeling of RNA double helices is possible using most probable values of basepair parameters obtained from crystal structure database. The A:A w:wC non-canonical basepair, involving Watson-Crick edges of two Adenines in cis orientation, appears quite frequently in database. Bimodal distribution of its Shear, due to two different H-bonding schemes, introduces the confusion in assigning most the probable value. Its effect is pronounced when the A:A w:wC basepair stacks on Sheared wobble G:U W:WC basepairs.MethodsWe employed molecular dynamics simulations of three possible double helices with GAG, UAG and GAU sequence motifs at their centers and quantum chemical calculation for non-canonical A:A w:wC basepair stacked on G:U W:WC basepair.ResultsWe noticed stable structures of GAG motif with specifically negative Shear of the A:A basepair but stabilities of the other motifs were not found with A:A w:wC basepairing. Hybrid DFT-D and MP2 stacking energy analyses on dinucleotide step sequences, A:A w:wC::G:U W:WC and A:A w:wC::U:G W:WC reveal that viable orientation of A:A::G:U prefers one of the H-bonding modes with negative Shear, supported by crystal structure database. The A:A::U:G dinucleotide, however, prefers structure with only positive Shear.ConclusionsThe quantum chemical calculations explain why MD simulations of GAG sequence motif only appear stable. In the cases of the GAU and UAG motifs “tug of war” situation between positive and negative Shears of A:A w:wC basepair induces conformational plasticity.General significanceWe have projected comprehensive reason behind the promiscuous nature of A:A w:wC basepair which brings occasional structural plasticity.     

Interaction of the high density lipoprotein conversion factor with recombinant discoidal complexes of egg phosphatidylcholine, free cholesterol, and apolipoprotein A-I

An HDL conversion factor which promotes the conversion of HDL3 to populations of larger and smaller particles has recently been identified in human plasma. In the present report a partially purified preparation of this factor has been used to examine the conversion of 79:0:1, 77:5:1, and 74:10:1 (mol:mol:mol) egg phosphatidylcholine-free cholesterol-apolipoprotein A-I (apoA-I) recombinant discoidal complexes. The study was carried out in order to ascertain whether the conversion process is regulated by the concentration of free cholesterol in the complexes. The complexes comprised one major and two minor populations of particles with respective Stokes' diameters of 96 A, 84 A, and 78 A. The 74:10:1 complexes also contained a population of particles 112 A in diameter. The 79:0:1 and 77:5:1 complexes contained two molecules of apoA-I per particle. The 74:10:1 complexes comprised two classes of particles with two or three molecules of apoA-I. When the 74:10:1 complexes were incubated with the conversion factor, the 96 A and 84 A particles were converted to a population of particles 78 A in diameter that contained two apoA-I molecules. In the case of the 79:0:1 and 77:5:1 complexes, the 96 A particles were converted to 78 A particles but the concentration of 84 A particles did not change. The rate of conversion of 96 A particles to 78 A particles was dependent on the concentration of free cholesterol in the complexes. When the 74:10:1 complexes were incubated for 24 hr with the conversion factor, the 96 A particles were completely converted to particles 78 A in diameter. In the case of the 77:5:1 complexes, complete conversion was achieved by 48 hr. Conversion of the 79:0:1 complexes did not proceed to completion, even when the incubation was extended beyond 48 hr. The rate of conversion of 96 A particles to 78 A particles was also dependent on the concentration of the conversion factor in the incubation mixtures. The previous incubations contained equivalent concentrations of apoA-I and conversion factor. When the concentration of the conversion factor relative to apoA-I was reduced, there was a concomitant decrease in the rate of conversion of 96 A particles to 78 A particles. Conversion was not evident when the concentration of the conversion factor was reduced to one-tenth that of apoA-I.(ABSTRACT TRUNCATED AT 400 WORDS)     

中国湖北地区汉族家系补体第四成分（C4）单倍型的检测

用我室仿国际标准C4定型程序改进后建立的方法及羧肽酶B处理后C4分型方法对湖北地区93个无血缘关系的汉族家系进行C4单倍型的检测,对310个C4单倍型分析可见,我国汉族以A3B1频率最高(0.4194),A3B2次之(0.1161),A2B1与A4B2均为0.0903。以下依次是AQOB1(0.0645)、A3BQO(0.0548)、AQOBQO(0.0322)、A2B2(0.0256)、A4B1(0.0161)、A2B92(0.0129)等。从连锁不平衡参数(Δ)的卡方数值可见,A4B2、AQOBQO及A2B92具有极显著意义的阳性△值;而A4B1与AQOB2则具有极显著意义的阴性△值。将我们的结果与日本人、美国及德国白人,南非黑人的资料进行了对比,并进行了一些讨论。     

水稻雄性不育新质源的研究──新型水稻细胞质雄性不育系马协A与野败型珍汕97A不育性的遗传学比较

采用套袋自交结实率和自然结实率为主,花粉育性和田间目测整株育性为辅的综合性状,判定新型细胞质雄性不育系马协Ａ以及它与明恢６３的杂种Ｆ_１、Ｆ_２和ＢＦ_１的植株育性,并以野败型珍汕９７Ａ作对照,比较研究了其不育性的遗传规律。结果表明,马协Ａ与珍汕９７Ａ不育性的遗传均由两对基因控制,但新型细胞质雄性不育系马协Ａ两对基因的作用方式与珍汕９７Ａ不同。前者Ｆ_２群体的育性分离符合９：３：３：１的比例,ＢＦ_１符合１：２：１的比例;后者相应群体则符合１２：３：１和２：１：１的比例,两对基因间表现为显性上位。斯米尔诺夫检验也表明马协Ａ／明恢６３和珍汕９７Ａ／明恢６３的Ｆ_２群体的结实率频率分布差异显著（Ｐ＜０．０１）。并讨论了细胞质雄性不育的遗传机理及分子基础。     

Book Reviews

Book reviewed in this article: Palaeobiology of ammonoids: A review by M. J Benton: Ammonoid Paleobiology. Topics in Geobiology. Vol. 13 . By N. H. Landman, K. Tanabe and R. A. Davis. Reconstructing the tree of life: A review by M. J. Benton: Multicellular Animals: A new approach to the phylogenetic order in nature. Volume I . By P. Ax. Springer The reverse of the medal: A review by A. Minelli: Homoplasy. The Recurrence of Similarity in Evolution . By Michael J. Sanderson and Larry Hufford (Eds.).     

Thermodynamic studies of base pairing involving 2,6-diaminopurine.

The thermal stabilities of oligodeoxyribonucleotide duplexes containing 2,6-diaminopurine (D) matched with each of the four normal DNA bases were determined by optical melting techniques. Comparison of optical melting curves yielded relative stabilities for the D-containing standard base pairs in an otherwise identical base-pair sequence. The D:T pair was found to be more stable than the A:T pair in dC3DG3:dC3TG3, as stable as the A:T in dCT3DT3G:dCA3TA3G, and less stable than the A:T in dCA3DA3G:dCT7G. The order of stabilities for X:Y in the DNA duplex dCA3XA3G:dCT3YT3G is: (A:T) greater than (T:D) congruent to (D:T) greater than or equal to (T:A) greater than (C:D) congruent to (D:A) congruent to (D:G) greater than or equal to (D:C) congruent to (G:D) congruent to (D:D) greater than or equal to (A:D). Implications of these results for design of DNA oligonucleotide probes are discussed.     

Fatty acid composition of lipid A in Pseudomonas fluorescens

The fatty acid composition of lipid A was studied using gas-liquid chromatography (GLC) and GLC-mass spectrometry in Pseudomonas fluorescens strains of biovars A, B, C, i, F and G, the type strain ATCC 13525 (biovar A) inclusive. The following fatty acids were identified as predominant in the composition of lipid A in the strains representing biovars A, B, C, i, F and G: 3-hydroxydecanoic (3-OH C10:0), 2-hydroxydodecanoic (2-OH C12:0), 3-hydroxydodecanoic (3-OH C12:0), dodecanoic (C12:0), hexadecanoic (C16:0), octadecanoic (C18:0), hexadecenoic (C16:1) and octadecenoic (C18:1) acids. Lipid A of a biovar G strain differed noticeably from other strains in its fatty acid composition. Its main components were as follows: 3-hydroxytetradecanoic (3-OH C14:0), 3-hydroxypentadecanoic (3-OH C15:0) and dodecanoic (C12:0) fatty acids. The coefficients of similarity were determined for lipid A specimens isolated from the studied strains of P. fluorescens by calculating their fatty acid composition with a computer.     

NMR studies of G:A mismatches in oligodeoxyribonucleotide duplexes modelled after ribozymes.

The structures of two oligodeoxyribonucleotide duplexes, the base sequences of which were modelled after both a hammerhead ribozyme and a small metalloribozyme, were studied by NMR. Both duplexes contain adjacent G:A mismatches; one has a PyGAPu:PyGAPu sequence and the other a PyGAPy:PuGAPu sequence. It is concluded on the basis of many characteristic NOEs that in both duplexes G:A base pairs are formed in the unique 'sheared' form, where an amino proton instead of an imino proton of G is involved in the hydrogen bonding, and G and A bases are arranged 'side by side' instead of 'head to head'. A photo-CIDNP experiment, which gives unique and independent information on the solvent accessibility of nucleotide bases, also supports G:A base pairing rather than a bulged-out structure of G and A residues. This is the first demonstration that not only the PyGAPu:PyGAPu sequence but also the PyGAPy:PuGAPu sequence can form the unique sheared G:A base pairs. Taking the previous studies on G:A mismatches into account, the idea is suggested that a PyGA:GAPu sequence is a minimum and essential element for the formation of the sheared G:A base pairs. The sheared G:A base pairs in the PyGAPu:PyGAPu sequence are suggested to be more stable than those in the PyGAPy:PuGAPu sequence. This is explained rationally by the idea proposed above.     

Coenzyme Q10 in maternal plasma and milk throughout early lactation

In contrast to other lipophilic antioxidants Coenzyme Q10 originates from food intake as well as from endogenous synthesis. The CoQ10 concentration and lipid content of maternal milk and maternal plasma was investigated during early lactation. Breast milk was obtained from 23 women: A: colostrums (24-48 hours postpartum), B: transitional milk (day 7 pp), C: mature milk (day 14 pp). At the same time capillary blood specimens were collected. Milk and plasma were stored at -84 degrees C until CoQ10 was analysed after hexane extraction by HPLC. The lipid content was determined by PAP-analysis of cholesterol. The plasma content of CoQ10 was the highest soon after delivery (A: 1.29, B:1.20, C:1.07 pmol/microl; Wilcoxon p < 0.05 A vs. C and B vs. C). This tendency was still evident after lipid-adjustment (A:209, B:180, C:175 micromol CoQ10/mol cholesterol; Wilcoxon p < 0.01 A vs. B and C). The level of CoQ10 in milk showed a gradual decline during early lactation (A:0.80, B:0.57, C:0.44 pmol/microl; Wilcoxon p < 0.02 A vs. B and C). After lipid-adjustment this tendency became even more evident (A: 137, B:86, C:67 micromol CoQ10/mol cholesterol; Wilcoxon p < 0.002 A vs. B and C, p < 0.05 B vs. C). The content of CoQ10 in plasma and milk showed a correlation with early milk (Spearman p < 0.005) but not with mature milk. Although lipid content is low the colostrums is a rich source for the lipophilic antioxidant CoQ10.     

Analysis for linkage between F13A and three chromosome 6 marker loci: evidence for 6pter: F13A:HLA:GL01:cen gene order

Summary The results of the present study provide independent support for F13A:HLA linkage and refine the F13A: HLA and F13A: GLO1 linkage relationships. Analysis of the corresponding recombination fractions for the total paternal F13A:HLA and F13A:GLO1 peak lod scores() indicates a locus order of 6pter: F13A:HLA:GLO1:cen. Lod scores between F13A and PLG, a locus recently assigned to chromosome 6, exclude close linkage between these loci.     

A:T --> G:C base pair substitutions occur at a higher rate than other substitution events in Pms2 deficient mouse cells

The mismatch repair pathway involves multiple proteins that are required to correct DNA polymerase generated mismatches before they become mutations. It has been shown recently, that the predominant base-pair substitution events leading to loss of endogenous Aprt activity in Pms2 null mouse cells are A:T --> G:C mutations (Oncogene 21 (2002) 1768, Oncogene 21 (2002) 2840). To determine if this observation could be explained by an increased rate of A:T --> G:C mutations relative to other base-pair substitutions, we developed a reversion assay to examine G:C --> A:T, C:G --> A:T, and A:T --> G:C mutations within mouse Aprt in a Pms2 null mouse kidney cell line. The results demonstrated a 6-50-fold increase in the rate of the A:T --> G:C mutations relative to the other base-pair substitutions. Additional work demonstrated that growth of the Pms2 null cells in antioxidant containing medium reduced the rate of the A:T --> G:C mutations. The results are discussed with regards to the role of mismatch repair proteins in preventing base-pair substitutions, including those induced by oxidative stress.     

Effect of heavy exercise on spectral baroreflex sensitivity, heart rate, and blood pressure variability in well-trained humans

The aim of the study was to assess the instantaneous spectral components of heart rate variability (HRV) and systolic blood pressure variability (SBPV) and determine the low-frequency (LF) and high-frequency baroreflex sensitivity (HF-BRS) during a graded maximal exercise test. The first hypothesis was that the hyperpnea elicited by heavy exercise could entail a significant increase in HF-SBPV by mechanical effect once the first and second ventilatory thresholds (VTs) were exceeded. It was secondly hypothesized that vagal tone progressively withdrawing with increasing load, HF-BRS could decrease during the exercise test. Fifteen well-trained subjects participated in this study. Electrocardiogram (ECG), blood pressure, and gas exchanges were recorded during a cycloergometer test. Ventilatory equivalents were computed from gas exchange parameters to assess VTs. Spectral analysis was applied on cardiovascular series to compute RR and systolic blood pressure power spectral densities, cross-spectral coherence, gain, and alpha index of BRS. Three exercise intensity stages were compared: below (A1), between (A2), and above (A3) VTs. From A1 to A3, both HF-SBPV (A1: 45 +/- 6, A2: 65 +/- 10, and A3: 120 +/- 23 mm2Hg, P < 0.001) and HF-HRV increased (A1: 20 +/- 5, A2: 23 +/- 8, and A3:40 +/- 11 ms2, P < 0.02), maintaining HF-BRS (gain, A1: 0.68 +/- 0.12, A2: 0.63 +/- 0.08, and A3: 0.57 +/- 0.09; alpha index, A1: 0.58 +/- 0.08, A2: 0.48 +/- 0.06, and A3: 0.50 +/- 0.09 ms/mmHg, not significant). However, LF-BRS decreased (gain, A1: 0.39 +/- 0.06, A2: 0.17 +/- 0.02, and A3: 0.11 +/- 0.01, P < 0.001; alpha index, A1: 0.46 +/- 0.07, A2: 0.20 +/- 0.02, and A3: 0.14 +/- 0.01 ms/mmHg, P < 0.001). As expected, once VTs were exceeded, hyperpnea induced a marked increase in both HF-HRV and HF-SBPV. However, this concomitant increase allowed the maintenance of HF-BRS, presumably by a mechanoelectric feedback mechanism.     

Role of cysteine amino acid residues on the RNA binding activity of human thymidylate synthase

The role of cysteine sulfhydryl residues on the RNA binding activity of human thymidylate synthase (TS) was investigated by mutating each cysteine residue on human TS to a corresponding alanine residue. Enzymatic activities of TS:C43A and TS:C210A mutant proteins were nearly identical to wild-type TS, while TS:C180A and TS:C199A mutants expressed >80% of wild-type enzyme activity. In contrast, TS:C195A was completely inactive. Mutant proteins, TS:C195A, TS:C199A and TS:C210A, retained RNA binding activity to nearly the same degree as wild-type human TS. RNA binding activity of TS:C43A was reduced by 30% when compared to wild-type TS, while TS:C180A was completely devoid of RNA binding activity. In vitro translation studies confirmed that mutant proteins TS:C43A, TS:C195A, TS:C199A and TS:C210A, significantly repressed human TS mRNA translation, while TS:C180A was unable to do so. To confirm the in vivo significance of the cysteine sulfhydryl residue, mutant proteins TS:C180A and TS:C195A were each expressed in human colon cancer HCT-C18:TS(–) cells that expressed a functionally inactive TS. A recombinant luciferase reporter gene under the control of a TS-response element was co-transfected into these same cells, and luciferase activity increased in the presence of the TS:C195A mutant TS protein to a level similar to that observed upon expression of wild-type TS protein. In contrast, luciferase activity remained unchanged in cells expressing the TS:C180A mutant protein. Taken together, these findings identify Cys-180 as a critical residue for the in vitro and in vivo translational regulatory effects of human TS.     

Purification and characterization of the two molecular forms of Aspergillus oryzae acid protease.

The isolation and partial characterization of the acid proteases A1 and A2 (EC3.4.23.6) from Aspergillus oryzae grown on solid bran culture are described. The purified preparations were essentially homogeneous by several criteria including sedimentation analysis and polyacrylamide gel electrophoresis. The physiochemical properties of the proteases A1 and A2 were as follows (in the order: A1, A2): molecular weight: 63 000 & 32 000; sedimentation coefficient s20, w: 3.93 and 3.16 S; diffusion constant D20, w, 5.63 - 10(-7) and 8.61 - 10(-7) CM2/S, partial specific volume, v: 0.73 ml/g for both; nitrogen content: 16.30 and 13.42%; E1% 1 cm at 280 nm: 5.9 and 11.1. The two enzymes had the same pH optima in the acid pH range, and both activated bovine pancreatic trypsinogen. The enzymes were essentially of the same amino acid composition and immunologically cross-reacted with each other. The protease A2 contained little or no carbohydrate, whereas the protease A1 was glycoprotein, containing 49% carbohydrate comprising glucose, mannose, and galactose. These results suggest that the protein portion of acid protease A1 is the same as that of acid protease A2.     

Mutations induced by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in the lacZ and cII genes of Muta Mouse

4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) found in chewing tobacco, snuff, cigarettes, and cigars is a tobacco-specific nitrosamine and classified as a possible human carcinogen (Class 2B) by the International Agency for Research on Cancer (IARC). NNK given intraperitoneally was seen to induce lung and liver adenomas. To evaluate the genotoxicity of NNK in vivo, NNK was intraperitoneally administered to Muta Mouse at two concentrations (125 and 250 mg/kg, once a week for 4 weeks) followed by the measurement of mutant frequencies in the lacZ and cII genes from lung and liver in the same mice. Characterization of the types of the mutation was determined by sequencing the cII genes from mutant plaques. The mutant frequencies in both target genes from both organs dose-dependently increased up to 10 times compared to those of the control group. For the types of mutations, the ratio of the G:C to A:T mutation in the total number of mutants was less than the ratio of A:T to T:A and A:T to C:G transversion, contrary to a previous report. The A:T to T:A transversion was the most highly induced mutation both in the lung and liver cII genes. The increasing rate of mutant frequencies in lung and liver over the vehicle control was 55 and 56 times, respectively, while the increasing rate of G:C to A:T transition was only 1.9 and 2.8 times, respectively. These observations show that NNK predominantly induces DNA adducts leading to A:T to T:A and/or A:T to C:G mutations in the transgene.     

Onset of oxidative damage in alpha-crystallin by radical probe mass spectrometry

The early onset oxidative damage within segments of the protein alpha-crystallin is examined by radical probe mass spectrometry by its treatment with reactive oxygen species under low-, moderate-, and high-oxidizing conditions. Five regions comprising the first 11 residues of the N-termini of the A and B subunits (A/B:1-11), central domains from each subunit B:57-69 and A:104-112, and a C-terminal segment of the A subunit A:120-145 were found to be the initial sites of oxidation. The susceptibility of each segment to oxidation and oxidative damage is investigated by subjecting the intact protein to different oxidation conditions within the ion source of an electrospray ionization mass spectrometer. LC-MS of the oxidized protein digests enables the sites and levels of oxidation to be monitored. The onset of oxidative damage and the levels of oxidation observed before damage occurs differ across the protein surface. The regions comprising residues A/B:1-11 and A:104-112 are shown to be more susceptible to oxidative damage than those comprising residues B:57-69 and A:120-145. The results are discussed in the context of available experimental and homology-modeled theoretical structures for the subunits of alpha-crystallin.     

Book Reviews

Book reviewed in this article:
N orth A merica : The Constitution of The Five Nations . A rthur C. P arker .
N orth A merica : Traditional History of The Confederacy of The Six Nations . D uncan C ampbell S cott , F.R.S.C.
N orth A merica : Civil, Religious and Mourning Councils and Ceremonies of Adoption of the New York Indians . R ev . W illiam M. B eauchamp .     

Simian virus 40 mutants carrying two temperature-sensitive mutations.

Five temperature-sensitive mutants of simian virus 40 containing two temperature-sensitive mutations were isolated. The double mutant of the A and D complementation groups, like the D mutants, failed to complement by conventional complementation analysis and did not induce host DNA synthesis at 40 degrees C. However, under conditions that suppressed the D defect, the A:D double mutant expressed only the A defect. Thus, viral DNA replication dropped rapidly after this mutant was shifted from permissive to restrictive temperatures. The A:D double mutant failed to transfrom at the restrictive temperature when subconfluent Chinese hamster lung monolayers were used. Double mutants of A:B, A:C, and A:BC complementation groups, like their A parent, were defective in viral DNA replication, in the induction of host DNA synthesis and in the transformation of secondary Chinese hamster lung cells at the nonpermissive temperature.     

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking.

The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 of the DNA half-site 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results in formation of a sharp DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site. The consensus base-pair T:A at position 6 and the consensus base-pair G:C at position 7 form a T:A/G:C step, which is known to be associated with DNA flexibility. It has been proposed that specificity for T:A at position 6 is a consequence of formation of the DNA kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step on the geometry of DNA kinking, or the energetics of DNA kinking. In this work, we determine crystallographic structures of CAP-DNA complexes having the consensus base-pair T:A at position 6 or the non-consensus base-pair C:G at position 6. We show that complexes containing T:A or C:G at position 6 exhibit similar overall DNA bend angles and local geometries of DNA kinking. We infer that indirect readout in this system does not involve differences in the geometry of DNA kinking but, rather, solely differences in the energetics of DNA kinking. We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence.