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1.
Brij Bhushan Uma Shanker Kamaluddin 《Origins of life and evolution of the biosphere》2011,41(5):469-482
Manganese exists in different oxidation states under different environmental conditions with respect to redox potential. Various
forms of manganese oxides, namely, Manganosite (MnO), Bixbyite (Mn2O3), Hausmannite (Mn3O4) and Pyrolusite (MnO2) were synthesized and their possible role in chemical evolution studied. Adsorption studies of ribose nucleotides (5′-AMP,
5′-GMP, 5′-CMP and 5′-UMP) on these manganese oxides at neutral pH, revealed a higher binding affinity to manganosite (MnO)
compared to the other manganese oxides. That manganese oxides having a lower Mn-O ratio show higher binding affinity for the
ribonucleotides indirectly implies that such oxides may have provided a surface onto which biomonomers could have been concentrated
through selective adsorption. Purine nucleotides were adsorbed to a greater extent compared to the pyrimidine nucleotides.
Adsorption data followed Langmuir adsorption isotherms, and X
m
and K
L
values were calculated. The nature of the interaction and mechanism was elucidated by infrared spectral studies conducted
on the metal-oxide and ribonucleotide-metal-oxide adducts. 相似文献
2.
ON Rogacheva BF Shchegolev VE Stefanov GA Zakharov EV Savvateeva-Popova 《Biochemistry. Biokhimii?a》2012,77(5):456-464
Protein-ligand docking and molecular dynamics studies have shown that the key event initiated by 3′:5′-AMP binding to the
A- and B-domains of protein kinase A Iα regulatory subunit is formation of a hydrogen bond between 3′:5′-AMP and A202(A326)
(the residue in parentheses being from the B-domain). The A202(A326) amide group movement associated with the bond formation
leads to reorganization of the phosphate binding cassette (PBC) (the short 310-helix becomes the long α-helix). This process results in L203(L327) displacement and finally causes hinge (B-helix) rotation.
The L203(L327) displacement and packing into the hydrophobic pocket formed by the PBC and β2β3-loop also depends on the β2β3-loop
conformation. The correct conformation is maintained by R, I, E, but not K at position 209(333) of the A- and B-domains. So,
the R209K and R333K mutants have problems with reaching B-conformation. The apo-form of the 3′:5′-AMP-binding domain also
undergoes transition from H- to B-conformation. In this case, the movement of A202(A326) amide group seems to be a result
of reorganization of the PBC into a more stable α-helix. 相似文献
3.
Summary Tobacco chloroplasts were found to contain three species of 5S RNA with different electrophoretic mobility. The nucleotide sequences of two species of the 5S RNA have been determined. The large 5S RNA species (5S RNAL) is composed of 121 nucleotides and the small 5S RNA species (5S RNAs) of 119 nucleotides. The 5S RNAL contains and extra uridine residue at both 5 and 3ends of the 5S RNAs. 相似文献
4.
The intermolecular interaction energies in central guanine triad of telomeric B-DNA were estimated based on ab initio quantum
chemistry calculations on the MP2/aDZ level of theory. The source of structural information was molecular dynamics simulation
of both canonical (AGGGTT) and oxidized (AG8oxoGGTT) telomere units. Our calculations demonstrate that significant stiffness
of central triad occurs if 8oxoG is present. The origin of such feature is mainly due to the increase of stacking interactions
of 8oxoG with neighbouring guanine molecules and stronger hydrogen bonding formation of 8oxoG with cytosine if compared with
canonical guanine. Another interesting observation is the context independence of stacking interactions of 8oxoG. Unlike to
5′-G2/G3-3′ and 5′-G3/G4-3′ sequences which are energetically different, 5′-G2/8oxoG3-3′ and 5′-8oxoG3/G4-3′ sequences are almost iso-energetic. 相似文献
5.
The hammerhead ribozyme is able to cleave RNA in a sequence-specific manner. These ribozymes are usually designed with four
basepairs in helix II, and with equal numbers of nucleotides in the 5′ and 3′ hybridizing arms that bind the RNA substrate
on either side of the cleavage site. Here guidelines are given for redesigning the ribozyme so that it is small, but retains
efficient cleavage activity. First, the ribozyme may be reduced in size by shortening the 5′ arm of the ribozyme to five or
six nucleotides; for these ribozymes, cleavage of short substrates is maximal. Second, the internal double-helix of the ribozyme
(helix II) may be shortened to one or no basepairs, forming a miniribozyme or minizyme, respectively. The sequence of the
shortened helix+loop II greatly affects cleavage rates. With eight or more nucleotides in both the 5′ and the 3′ arms of a
miniribozyme containing an optimized sequence for helix+loop II, cleavage rates of short substrates are greater than for analogous
ribozymes possessing a longer helix II. Cleavage of genelength RNA substrates may be best achieved by miniribozymes. 相似文献
6.
Costanzo G Pino S Botta G Saladino R Di Mauro E 《Origins of life and evolution of the biosphere》2011,41(6):559-562
Nucleic bases are obtained by heating formamide in the presence of various catalysts. Formamide chemistry also allows the
formation of acyclonucleosides and the phosphorylation of nucleosides in every possible position, also affording 2′,3′ and
3′,5′ cyclic forms. We have reported that 3′,5′ cyclic GMP and 3′,5′ cyclic AMP polymerize in abiotic conditions yielding
short oligonucleotides. The characterization of this reaction is being pursued, several of its parameters have been determined
and experimental caveats are reported. The yield of non-enzymatic polymerization of cyclic purine nucleotides is very low.
Polymerization is strongly enhanced by the presence of base-complementary RNA sequences. 相似文献
7.
Tamajusuku AS Carrillo-Sepúlveda MA Braganhol E Wink MR Sarkis JJ Barreto-Chaves ML Battastini AM 《Molecular and cellular biochemistry》2006,289(1-2):65-72
Extracellular nucleotides ATP, ADP, AMP and adenosine are well known signaling molecules of the cardiovascular system that are involved in several physiological processes: cell proliferation, platelet aggregation, inflammatory processes and vascular tonus. The levels of these molecules are controlled by ecto-NTPDases and ecto-5′-nucleotidase/CD73 (ecto-5′-NT/CD73) actions, which are responsible for the complete ATP degradation to adenosine. The thyroid hormones, thyroxine (T4) and triiodothyronine (T3), play important roles in the vascular system promoting vasodilatation. Here we investigated the influence of thyroid hormones on the enzyme cascade that catalyzes the interconversion of purine nucleotides in vascular smooth muscle cells (VSMC). Exposure of VSMCs to 50nM T3 or T4 did not change ATP and ADP hydrolysis significantly. However, the same treatment caused an increase of 75% in AMP hydrolysis, which was time-dependent but dose-independent. Moreover, T3 treatment significantly increased ecto-5′-NT/CD73 mRNA expression, which suggests a genomic effect of this hormone upon ecto-5′-NT/CD73. In addition to the importance of the ecto-5′-NT in cell proliferation and differentiation, its overexpression could result in higher extracellular levels of adenosine, an important local vasodilatator molecule. 相似文献
8.
The functional male sterility controlled by ps gene proved to be a useful tool in hybrid tomato varieties breeding in Poland. The climat conditions such as excessive temperature
and high humidity have a bad effect on the expression and stability of functional male sterility. Using the RAPD methods we
have identified two RAPD markers linked to the ps gene. The markers OPW 131230 and OPAX 10780 were generated by 5′CACAGCGACA 3′ and 5′CCAGGCTGAC 3′ decamers respectively in F2 population of combination 24/29 × G-1. 相似文献
9.
A. M. Varizhuk S. V. Kochetkova N. A. Kolganova E. N. Timofeev V. L. Florentiev 《Russian Journal of Bioorganic Chemistry》2010,36(4):528-531
Oligonucleotide analogues containing one or a few glycine, L-, and D-alanine residues instead of phosphodiester internucleotide linkages were synthesized (C3′-NH-C(O)-CH(X)-NH-C(O)-C4′, where
X = H, (S)-CH3, and (R)-CH3. The stability of the duplexes of modified oligonucleotides with their wild-type complements was studied. The incorporation
of glycine and L-alanine residues into internucleotide linkages was shown to noticeably decrease the stability of modified duplexes as compared
to that of native ones (ΔT
m∼−2°C per modification), whereas analogues containing D-alanine linkers form duplexes with increased stability (ΔT
m∼+2°C per modification). 相似文献
10.
We have studied the activities of 2′,3′-cyclic nucleotide 3′-phosphohydrolase, 1,2-diacylglycerol: CDPethanolamine phosphoethanolamine
transferase (EC 2.7.8.1), and 1,2-diacylglycerol: CDPcholine phosphocholine transferase (EC 2.7.8.2) in developing rat brain
gray matter and white matter. The specific activity of cyclic nucleotide phosphohydrolase was 5–8 fold higher in white matter
than in gray matter at all ages. No significant changes were observed during development. The specific activity of phosphocholine
transferase was 2 to 3 fold higher than phosphoethanolamine transferase at all ages both in gray and white matter. Both phosphocholine
transferase and phosphoethanolamine transferase increased more than 2 fold in specific activity between 14 and 90 days of
age. The total activity of phosphocholine transferase also showed an increase during development. The apparentK
m values for nucleotides and dicaprin were similar in gray matter and white matter. Except for lowK
m values for nucleotides at 14 days of age, no significant changes were observed during development. Changes in rates of glycerophospholipid
synthesis may be partly due to the specific activities of these enzymes but are also determined by the quantities of substrates
and inhibitors and by affinities for the substrates.
Special Issue dedicated to Dr. Eugene Kreps. 相似文献
11.
12.
Adenosine-5′-methylphosphate (MepA) initiates the oligomerization of the 5′-phosphorimidazolide of uridine (ImpU) in the presence
of montmorillonite clay. Longer oligomers form because the 5′-phosphate is blocked with a methyl group that prevents the formation
of cyclic- and pyrophosphate-containing compounds. The MepA initiates 69–84% of the 5–9 charge oligomers, respectively. The
montmorillonite catalyst also provides selectivity in the oligomerization reactions so that the main reaction pathway is MepA
→ MepA3′pU → MepA3′pU2′pU → MepA3′pU2′pU3′pU. MepA did not enhance the oligomerization of ImpA. The relative rates of the reactions were determined from an investigation
of the products in competitive reactions. Selectivity was observed in the reaction of ImpU with equimolar amounts of MepA3′pU and MepA2′pU where the relative reaction rates are 10.3:1, respectively. In the reaction of ImpA with MepA3′pA and MepA2′pA the ImpA reacts 5.2 times faster with MepA3′pA. In the competitive reaction of ImpU and ImpA with MepA3′pA and MepA3′pU the elongation proceeds on MepA3′pA 5.6 times more rapidly than with MepA3′pU. There is no correlation between the extent of binding to the montmorillonite and reaction rates in the formation of longer
oligomers. The formation of more than two sequential 2′,5′-linkages in the oligomer chain proceeds more slowly than the addition
to a single 2′,5′-link or a 3′,5′-link and either chain termination or elongation by a 3′,5′-linage occurs. The central role
that catalysis may have had in the prebiotic formation of biopolymers is discussed.
Note added in proof: There are errors in the high resolution mass spectral data given in Section 4.2.1. The high resolution mass spectrum found
for the cyclic dimer of UpUp (C-UpUp) was 657.02260. C18H21N4O16P2Na2 requires 657.02232. The high resolution mass spectrum found for the cyclic dimer of ApAp (C-ApAp) was 725.05850. C20H22N10O12P2Na3 requires 725.05839. 相似文献
13.
The conformational changes of 3,5,3′-triiodo L-thyronine induced by interaction with phospholipids were analyzed by Raman spectroscopy. The spectra were interpreted in
terms of two conformers of this hormone in equilibrium in the lipid medium, depending on the orientation of the 3′-iodine
with respect to the ring α. Theoretical geometry optimizations on both conformers in vacuo and in different solvents, together with the respective calculated energies support the experimental results. The presence
of only one iodine atom in the phenolic ring allows assumption of a higher flexibility of 3,5,3′-triiodo L-thyronine and a better accommodation into the lipid medium compared to 3,5,3′,5′-tetraiodo L-thyronine. The possible physiological implications of structural differences that appear in membrane models between 3,5,3′-triiodo
L-thyronine and 3,5,3′,5′-tetraiodo L-thyronine are discussed. 相似文献
14.
WU Naihu FANG Xiaohua SHI Xiaomei ZHANG Xiaowu ZHOU Li HUANG Meijuan 《中国科学:生命科学英文版》1999,42(4):383-394
Comparative analysis reveals remarkahle homology between the sequences of bothpsbA gene nucleotides and the inferred amino acids of sorghum, a C4 plant, and those of rice, a C3 plant. The 5′-noncoding region of sorghumpsbA gene contains the conservative promoter elements, “—35” element and “—10” element, like the prokaryote and the promoter element,
TATA box, like the eukaryote. As compared with that of the rice, an extra sequence of 7 bp is found in the leader sequence
of the mRNA in the former. Using anin vitro system, it has been demonstrated that protein factor exists in sorghum chloroplast protein extract which specifically hinds
to the 5′-noncoding region ofpsbA gene. Measurement of the expression of luciferase shows a 2–5 time greater reaction of the expression plasmids pALqs which
contain leader region of sorghumpsbA gene than that of the expression plasmids pALqr which contain leader region of ricepsbA gene inE. coli.
Project supported by the Chinese National “863” and “973” Projects 相似文献
15.
An ORF of 1716 nucleotides, putatively encoding a DNA polymerase, was characterized in the mitochondrial genome of the edible
basidiomycete Agrocybe aegerita. The complete gene, named Aa-polB, and its flanking regions were cloned and sequenced from three overlapping restriction fragments. Aa-polB is located between the SSU rDNA (5′ region) and a gene for tRNAAsn (3′ region), and is separated from these genes by two A+T-rich intergenic regions of 1048 (5′ region) and 3864 (3′ region)
nucleotides, which lack repeated sequences of mitochondrial or plasmid origin. The deduced Aa-POLB protein shows extensive
sequence similarity with the family B DNA polymerases encoded by genomes that rely on protein-primed replication (invertrons).
The domains involved in the 3′→5′ exonuclease (Exo I to III) and polymerase (Pol I to Pol V) activities were localized on
the basis of conserved sequence motifs. The alignment of the Aa-POLB protein (571 amino acids) with sequences of family B
DNA polymerases from invertrons revealed that in Aa-POLB the N-terminal region preceding Exo I is short, suggesting a close
relationship with the DNA polymerases of bacteriophages that have linear DNA. The Aa-polB gene was shown to be present in all wild strains examined, which were collected from a wide range of locations in Europe.
As shown by RT-PCR, the Aa-polB gene is transcribed in the mitochondria, at a low but significant level. The likelihood of the coexistence of Aa-POLB and
Pol γ in the A. aegerita mitochondrion is discussed in the light of recent reports showing the conservation of the nucleus-encoded Pol γ from yeast
to human.
Received: 13 October 1998 / Accepted: 21 December 1998 相似文献
16.
The ovomucoid pre-mRNA has been folded into mini-hairpins adaptable for the RNA recognition motif (RRM) protein binding. The
number of mini-hairpins were 372 for pre-mRNA and 83-86 for mature m RNA The spatial arrangements are, in average, 16 nucleotides
per mini-hairpin which includes 7 nt in the stem, 5.6 nt in the loop and 3.7 nt in the inter-hairpin spacer. The constitutive
splicing system of ovomucoid-pre-mRNA is characterized by preferred order of intron removal of 5/6 > 7/4 > 2/1 > 3. The 5′
splice sites (5′SS), branch point sequences (BPS) and 3′ splice sites (3′SS) were identified and free energies involved have
been estimated in 7 splice sites. Thermodynamic barriers for splice sites from the least (| lowest | -Kcal) were 5,4, 7,6,
2,1, and 3; i.e., −18.7 Kcal, −20.2 Kcal, −21.0 Kcal, −24.0 Kcal, −25.4 Kcal, −26.4 Kcal and −28.2 Kcal respectively. These
are parallel to the kinetic data of splicing order reported in the literature. As a result, the preferred order of intron
removals can be described by a consideration of free energy changes involved in the spliceosomal assembly pathway. This finding
is consistent with the validity of hnRNP formation mechanisms in previous reports. 相似文献
17.
J. E. Tomilova V. V. Kuznetsov M. A. Abdurashitov N. A. Netesova S. Kh. Degtyarev 《Molecular Biology》2010,44(4):606-615
The M1.Bst19I DNA-methyltransferase gene from restriction-modification system Bst19I (recognition sequence 5′-GCATC-3′) in
Bacillus stearothermophilus 19 has been cloned in the expressing vector pJW that carries a tandem of thermo inducible promoters P
R
/P
L
from phage λ. Highly purified enzyme has been isolated by chromatography on various resins from Escherichia coli cells where it is accumulated in a soluble form. The study of M1.Bst19I properties has revealed that the enzyme has a temperature
optimum at 50°C and demonstrates maximal activity at pH 8.0. M1.Bst19I modifies adenine in sequence 5′-GCATC-3′. Kinetic parameters
of M1.Bst19I DNA methylation reaction have been determined as follows: Km for λ DNA is 0.68 ± 0.07 μM, Km for S-adenosyl-L-methionine is 2.02 ± 0.31 μM. Catalytical constant (k
cat) is 1.8 ± 0.05 min−1. Comparative analysis of Target Recognition Domain amino acid sequences for M1.Bst19I and other α-N6-DNA-methyltransferases
has allowed us to suggest the presence of two types of the enzymes containing ATG or ATC triplets in the recognition sequence. 相似文献
18.
The 3′ half molecule of yeast tRNAAla (nucleotides 36–75) was hybridized with a DNA fragment (5′GGAATCGAACC 3′) and the hybrid was then digested withE. coli RNase H (from Boehringer). The enzyme can specifically cleave the 3′ half molecule at the 3′ side of nucleotide Ψ55, thus a fragment C36-Ψ55 was prepared. The 3′-terminal T or TΨ of this fragment was removed by one or two cycles of periodate oxidation and β-elimination.
The products were fragments C36-T54 and C36-G53. Three yeast tRNAAla fragments C56-A76, U55-A76 (with Ψ55 replaced by U), U54-A76 (with T54Ψ55 replaced by UU) were synthesized and ligated with three prepared fragments (C36-Ψ55, C36-T54 and C36-G53) respectively by T4 RNA ligase. The products were further ligated with the 5′ half molecule (nu-cleotides 1–35). Using this
method, one reconstituted yeast tRNAAla (tRNAr) and two yeast tRNAALa analogs: (i) tRNAa with U55 instead of Ψ55; (ii) tRNAb with U54U55 instead of T54Ψ55 were synthesized. The charging and incorporation activities of these three tRNAs were determined. In comparison with the
reconstituted tRNA, the charging activity was 75% for tRNAa and 45% for tRNAb and the incorporation activity was 65% for tRNAa
and 70% for tRNAb. These results suggest that the modified nucleotides T54 and Ψ55 play an important role in yeast tRNAAla function.
Project supported by the National Natural Science Foundation of China. 相似文献
19.
Structural feature of sorghum chloroplastpsbA gene and regulation effects of its 5′-noncoding region
Naihu Wu Xiaohua Fang Xiaomei Shi Xiaowu Zhang Li Zhou Meijuan Huang 《中国科学C辑(英文版)》1999,42(4):383-394
Comparative analysis reveals remarkahle homology between the sequences of bothpsbA gene nucleotides and the inferred amino acids of sorghum, a C4 plant, and those of rice, a C3 plant. The 5′-noncoding region of sorghumpsbA gene contains the conservative promoter elements, “—35” element and “—10” element, like the prokaryote and the promoter element, TATA box, like the eukaryote. As compared with that of the rice, an extra sequence of 7 bp is found in the leader sequence of the mRNA in the former. Using anin vitro system, it has been demonstrated that protein factor exists in sorghum chloroplast protein extract which specifically hinds to the 5′-noncoding region ofpsbA gene. Measurement of the expression of luciferase shows a 2–5 time greater reaction of the expression plasmids pALqs which contain leader region of sorghumpsbA gene than that of the expression plasmids pALqr which contain leader region of ricepsbA gene inE. coli. 相似文献
20.
Siu Wah Wong-Deyrup Youngbae Kim Sonya J. Franklin 《Journal of biological inorganic chemistry》2006,11(1):17-25
The DNA-binding behavior and target sequences of two designed metallopeptides have been investigated with an iterative electrophoresis
mobility shift assay followed by PCR amplification, and by circular dichroism spectroscopy. Peptides P3W and P5b were designed
based on the structural similarity of the helix–turn–helix motif of homeodomains and the EF-hand motifs of calmodulin, as
previously described for P3W. Like P3W, P5b binds both Eu(III) (K
d=12.6±1.9 μM) and Ca(II) (K
d=70±8 μM) with reasonable affinity. Binding selection from a library of randomized 8-mer DNA oligonucleotide sequences identified
one target family for CaP5b [5′-pur-T-pur-G-(G/C)-3′], and two target sites for CaP3W [5′-(A/T)-G-G-G-(T/C)-3′ and 5′-A-T-(G/T)-T-G-3′].
Circular dichroism studies indicate that unlike EuP3W, EuP5b is poorly folded in the absence of DNA. In the presence of DNA
containing target-binding sites for both peptides, both EuP3W and EuP5b increase in helical content, in the latter case significantly.
These results suggest that EuP5b binding to target DNA involves an induced-fit mechanism. These small chimeric metallopeptides
have been found to bind selectively to DNA targets, analogous to natural protein–DNA interactions. This corroborates our earlier
conclusions (J. Am. Chem. Soc. 125:6656, 2003) that sequence-preferential DNA cleavage by Ce(IV)P3W was due to sequence recognition.
Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. 相似文献