scholarly journals A study of the alkaline hydrolysis of fractionated reticulocyte ribosomal ribonucleic acid and its relevance to secondary structure

1968 ◽  
Vol 106 (3) ◽  
pp. 733-741 ◽  
Author(s):  
R A Cox ◽  
Hannah J. Gould ◽  
K Kanagalingam
Keyword(s):  
Secondary Structure ◽  
Phosphate Buffer ◽  
Potassium Hydroxide ◽  
Chain Scission ◽  
Average Chain Length ◽  
Guanidinium Chloride ◽  
Stable Species ◽  
Hairpin Loops ◽  
Ribosomal Ribonucleic Acid ◽  
Hydrolysis Of

1. RNA isolated from the sub-units of rabbit reticulocyte ribosomes was hydrolysed by 0·4n-potassium hydroxide at 20°. The probability of main-chain scission was calculated from the number-average chain length, which was obtained from S25,w in 0·01m-phosphate buffer. 2. The fraction, f, of the original secondary structure that the fragments re-formed at neutral pH in 4m-guanidinium chloride, as well as in 0·01m- and 0·1m-phosphate buffer, was derived from changes in extinction over the range 220–310mμ on thermal denaturation. 3. The secondary structure of RNA is regarded as an assembly of hairpin loops each of 2N+b residues on average, where N is the number of base-paired residues and b is the number of unpaired residues. 4. If chain scission takes place at random then 2N+b=logf/log(1–p). 5. For RNA from the smaller sub-unit 2N+b was estimated as 25±5 residues, compared with 30±5 residues for the less stable species and 35±5 residues for the more stable species of hairpin loop of RNA from the larger sub-unit.

scholarly journals A spectrophotometric study of the denaturation of deoxyribonucleic acid in the presence of urea or formaldehyde and its relevance to the secondary structure of single-stranded polynucleotides

1968 ◽  
Vol 108 (4) ◽  
pp. 599-610 ◽  
Author(s):  
R A Cox ◽  
K Kanagalingam
Keyword(s):  
Secondary Structure ◽  
Rat Liver ◽  
Ribosomal Rna ◽  
Phosphate Buffer ◽  
Sodium Phosphate ◽  
Double Helix ◽  
Spectrophotometric Study ◽  
Guanidinium Chloride ◽  
Base Pairs ◽  
Sodium Phosphate Buffer

1. The thermal denaturation of DNA from rat liver was studied spectrophotometrically. In sodium phosphate buffers denaturation led to a single-stranded form having, at 25°, about 25% of the hypochromism of the intact double helix. 2. The hypochromism of the denatured form was the same in 1mm- as in 10mm-sodium phosphate buffer and was scarcely affected by reaction with formaldehyde. The hypochromism was decreased by about 40% in the presence of 8m-urea. 3. The hypochromism of denatured DNA at low ionic strengths was about the same as that of fragments of reticulocyte ribosomal RNA that were too short to form double-helical secondary structure and about the same as that of RNA after reaction with formaldehyde. 4. The spectrum of DNA was slightly affected by the presence of 8m-urea or 4m-guanidinium chloride. The differences in the spectrum of the native and denatured forms of DNA in 0·1m-sodium phosphate buffer, in 8m-urea–10mm-sodium phosphate buffer and in 4m-guanidinium chloride–10mm-sodium phosphate buffer, pH7·6, were similar but not identical. 5. Denatured rat liver DNA appears to have no double-helical character at 25° in 10mm-sodium phosphate buffer, pH7·6; increasing the buffer concentration to 0·1m leads to a more compact form in which about 40% of the residues form base pairs.

scholarly journals Hydrolysis of polynucleotides and the characterization of their secondary structure. A theoretical study

1968 ◽  
Vol 106 (3) ◽  
pp. 725-731 ◽  
Author(s):  
R A Cox
Keyword(s):  
Secondary Structure ◽  
Theoretical Study ◽  
Linear Polymers ◽  
Hairpin Loop ◽  
Base Pairs ◽  
Phosphate Bond ◽  
Hairpin Loops ◽  
Hydrolysis Of

1. Single-stranded RNA may be regarded as an assembly of L hairpin loops each stabilized by N base pairs and each containing b unpaired residues; one loop is connected to another by c residues. 2. A theory based on the statistics of the random degradation of linear polymers was developed to relate N, b and c with the probability, p, of hydrolysing a diesterified phosphate bond. 3. The number of residues per hairpin loop, which is 2N+b, is related to the fraction, f, of the original loops remaining intact by the equation: 2N+b=logf/log(1–p). 4. The theory was extended to show that the number of residues per loop may be evaluated by fractionating the RNA after hydrolysis and examining the secondary structure of each fraction. Fragments that are shorter than the hairpin loop cannot reproduce the original secondary structure. The probability that a fragment will form an intact loop increases most rapidly for fragments of between 2N+b and 2(2N+b)+c residues. 5. The probability of producing a fragment capable of forming one, and only one, hairpin loop was related to N, b and c.

scholarly journals Effect of Enzymic Hydrolysis of the Scissile Bond on the Secondary Structure of a Dimeric Globular Protein

1986 ◽  
Vol 18 (2) ◽  
pp. 103-109 ◽  
Author(s):  
Tomoko Komiyama ◽  
Takayasu Mori ◽  
Hajime Omata ◽  
Makoto Miwa
Keyword(s):  
Secondary Structure ◽  
Globular Protein ◽  
Enzymic Hydrolysis ◽  
Scissile Bond ◽  
Hydrolysis Of

Hidrolisis minyak biji asam jawa (tamarindus indica linn) menjadi asam lemaknya dan uji aktivitas antibakteri

2021 ◽  
Vol 2 (2) ◽  
pp. 100-104
Author(s):  
Arnanda Dhafin Rizky ◽  
Sutrisno Sutrisno ◽  
Parlan Parlan
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Fatty Acid ◽  
Potassium Hydroxide ◽  
Seed Oil ◽  
Acid Number ◽  
Moderate Intensity ◽  
Tamarindus Indica ◽  
Tamarind Seed ◽  
Hydrolysis Of

Saponification tamarind seed oil used potassium hydroxide and acidification with hydrochloric acid is produced fatty acid in the form of soft white solid, has melting point 50-55 degrees celcius. The result of this hydrolysis positive test of unsaturation. It has an acid number of 115.36, saponification number of 114.80, and iodine number of 53.34. The success of hydrolysis of oil into fatty acid is characterized by identification of IR spectra showing O-H vibration with moderate intensity and widening, C=O vibration of carboxylic acid with strong intensity. Fatty acids of tamarind seed have the potential as antibacterial to test bacteria Staphylococcus aureus and Escherichia coli with diameter respectively 7.31 mm and 7.58 mm. Minyak biji asam jawa yang disaponifikasi menggunakan kalium hidroksida dan pengasaman dengan asam klorida dihasilkan asam lemak berupa padatan lunak berwana putih, memiliki titik lebur 50-55 derajat celcius. hasil hidrolisis ini positif uji ketidakjenuhan, bilangan asam 115,36, bilangan penyabunan 114,80, dan bilangan iod 53,34. Keberhasilan hidrolisis minyak menjadi asam lemak ditandai dari identifikasi spektrum IR yang menunjukkan vibrasi ulur O-H dengan intensitas sedang dan melebar serta vibrasi ulur C=O asam karboksilat dengan intensitas kuat. Asam lemak biji asam jawa berpotensi sebagai antibakteri terhadap bakteri uji Staphylococcus aureus dan Escherichia coli dengan zona hambat masing-masing 7,31 mm dan 7,58 mm.

scholarly journals Processing of RNA Containing 8-Oxo-7,8-Dihydroguanosine (8-oxoG) by the Exoribonuclease Xrn-1

2021 ◽  
Vol 8 ◽  
Author(s):  
Cheyenne N. Phillips ◽  
Shawn Schowe ◽  
Conner J. Langeberg ◽  
Namoos Siddique ◽  
Erich G. Chapman ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Conformational Changes ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Spatial Constraints ◽  
Phase Synthesis ◽  
Naturally Occurring ◽  
Processive Enzyme ◽  
Moving Band ◽  
Hydrolysis Of

Understanding how oxidatively damaged RNA is handled intracellularly is of relevance due to the link between oxidized RNA and the progression/development of some diseases as well as aging. Among the ribonucleases responsible for the decay of modified (chemically or naturally) RNA is the exonuclease Xrn-1, a processive enzyme that catalyzes the hydrolysis of 5′-phosphorylated RNA in a 5′→3′ direction. We set out to explore the reactivity of this exonuclease towards oligonucleotides (ONs, 20-nt to 30-nt long) of RNA containing 8-oxo-7,8-dihydroguanosine (8-oxoG), obtained via solid-phase synthesis. The results show that Xrn-1 stalled at sites containing 8-oxoG, evidenced by the presence of a slower moving band (via electrophoretic analyses) than that observed for the canonical analogue. The observed fragment(s) were characterized via PAGE and MALDI-TOF to confirm that the oligonucleotide fragment(s) contained a 5′-phosphorylated 8-oxoG. Furthermore, the yields for this stalling varied from app. 5–30% with 8-oxoG located at different positions and in different sequences. To gain a better understanding of the decreased nuclease efficiency, we probed: 1) H-bonding and spatial constraints; 2) anti-syn conformational changes; 3) concentration of divalent cation; and 4) secondary structure. This was carried out by introducing methylated or brominated purines (m1G, m6,6A, or 8-BrG), probing varying [Mg2+], and using circular dichroism (CD) to explore the formation of structured RNA. It was determined that spatial constraints imposed by conformational changes around the glycosidic bond may be partially responsible for stalling, however, the results do not fully explain some of the observed higher stalling yields. We hypothesize that altered π-π stacking along with induced H-bonding interactions between 8-oxoG and residues within the binding site may also play a role in the decreased Xrn-1 efficiency. Overall, these observations suggest that other factors, yet to be discovered/established, are likely to contribute to the decay of oxidized RNA. In addition, Xrn-1 degraded RNA containing m1G, and stalled mildly at sites where it encountered m6,6A, or 8-BrG, which is of particular interest given that the former two are naturally occurring modifications.

Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F

1990 ◽  
Vol 10 (3) ◽  
pp. 1134-1144 ◽  
Author(s):  
F Rozen ◽  
I Edery ◽  
K Meerovitch ◽  
T E Dever ◽  
W C Merrick ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Translation Initiation ◽  
Direct Evidence ◽  
Rna Helicase ◽  
Initiation Factor ◽  
Helicase Activity ◽  
Ribosome Binding ◽  
Initiation Factors ◽  
Translation Initiation Factors ◽  
Hydrolysis Of

The mechanism of ribosome binding to eucaryotic mRNAs is not well understood, but it requires the participation of eucaryotic initiation factors eIF-4A, eIF-4B, and eIF-4F and the hydrolysis of ATP. Evidence has accumulated in support of a model in which these initiation factors function to unwind the 5'-proximal secondary structure in mRNA to facilitate ribosome binding. To obtain direct evidence for initiation factor-mediated RNA unwinding, we developed a simple assay to determine RNA helicase activity, and we show that eIF-4A or eIF-4F, in combination with eIF-4B, exhibits helicase activity. A striking and unprecedented feature of this activity is that it functions in a bidirectional manner. Thus, unwinding can occur either in the 5'-to-3' or 3'-to-5' direction. Unwinding in the 5'-to-3' direction by eIF-4F (the cap-binding protein complex), in conjunction with eIF-4B, was stimulated by the presence of the RNA 5' cap structure, whereas unwinding in the 3'-to-5' direction was completely cap independent. These results are discussed with respect to cap-dependent versus cap-independent mechanisms of ribosome binding to eucaryotic mRNAs.

Spectrophotometric Determination of Carbaryl in Grains

1982 ◽  
Vol 65 (1) ◽  
pp. 32-34
Author(s):  
Kalapanda M Appaiah ◽  
Rasamsetti Ramakrishna ◽  
Kadari R Subbarao ◽  
Omprakash Kapur
Keyword(s):  
Spectrophotometric Determination ◽  
Absorption Maximum ◽  
Potassium Hydroxide ◽  
Oxidizing Agent ◽  
Spectrophotometric Measurement ◽  
The Relationship ◽  
Hydrolysis Of

Abstract A method has been developed for determining carbaryl (1-naphthyl N-methyl carbamate) in grains, based on hydrolysis of carbaryl with methanolic potassium hydroxide to 1-naphthol, reaction with 4-aminophenazone in the presence of alkaline oxidizing agent, and spectrophotometric measurement at the absorption maximum at 475 nm. The relationship between absorbance and concentration is linear in the range of 0.5-20 μg/mL. The method can be applied to levels as low as 0.3 ppm carbaryl in grains.

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