Kinetics of proflavin binding to bacteriophages T2L and T4D

McCall, Philip; Bloomfield, Victor A.

doi:10.1002/bip.1976.360151202

Cited by 19 publications

(10 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These effects explain the contradictory findings of Ref. 8. Implications for the structure, function, and practical uses of T4 are discussed.…”

mentioning

confidence: 80%

“…Phosphate buffer was the pH 7.6 buffer from Ref. 8. T o store DNA, NET buffer was used: O.1M NaC1, 0.01M Tris C1, 0.001M EDTA.…”

Section: Buffers and Reagentsmentioning

confidence: 99%

“…The effects on k* of phosphate explain the otherwise paradoxical observation [ P. J. McCall and V. A. Bloomfield (1976) Biopolymers 15, 2323-23361 that in a phosphate buffer the permeabilities of T4wt and T40s41 are the same. …”

mentioning

confidence: 94%

See 2 more Smart Citations

Variation of the permeability of bacteriophage T4: Analysis by use of a protein‐specific probe for the T4 interior

Griess¹,

Khan²,

Serwer³

1991

Biopolymers

View full text Add to dashboard Cite

The permeability of bacteriophage T4 and the change in T4 permeability caused by mutation to osmotic shock resistance are investigated here by quantification of the kinetics with which both a DNA-specific probe (ethidium) and a protein-specific probe [1,1'-bi(4-anilino)naphthalene-5,5'-di-sulfonic acid, or bis-ANS)] bind to T4. In the case of an osmotic shock-resistant mutant, T40s41, both ethidium and bis-ANS bind with first order kinetics. The first-order rate constant (k*) for both bis-ANS and ethidium is a function of anion type and concentration. Adenosine triphosphate, phosphate, bisulfite, sulfate, and acetate anions all reduce k* below the k* observed when chloride is the only anion. When chloride is the only anion at 25 degrees C, k* values for binding to T40s41 are orders of magnitude above k* values for binding to wild-type T4 (T4wt). At 25 degrees C, k* for T4wt is too small to measure but k* for T4wt increases at 50-55 degrees C to values approaching those measured for T40s41, without inactivating T4wt, when chloride is the only anion; during heating, T4wt is stabilized by both ethidium and bis-ANS. Binding to T4wt is reversible at 50-55 degrees C, but not at 25 degrees C. Equilibrium binding of bis-ANS to T40s41 reveals 112 +/- 24 sites per T4 capsid. Equilibrium binding of ethidium to T40s41 reveals both high- and low-affinity sites previously observed in the packaged DNA of other bacteriophages. The ATP-induced decrease in k* is not accompanied by a decrease in equilibrium binding. The following hypotheses are presented to explain the above data: (a) All detected bis-ANS binding sites on T4 are interior to the outer surface of T4. (b) The value of k* for both bis-ANS and ethidium is controlled at the port(s) of passage through the outer shell of the T4 capsid. (c) The anions present control k* values at the port(s) of entry, probably by controlling the size of this port. The effects on k* of phosphate explain the otherwise paradoxical observation [P. J. McCall and V. A. Bloomfield (1976) Biopolymers 15, 2323-2336] that in a phosphate buffer the permeabilities of T4wt and T40s41 are the same.

show abstract

“…These effects explain the contradictory findings of Ref. 8. Implications for the structure, function, and practical uses of T4 are discussed.…”

mentioning

confidence: 80%

“…Phosphate buffer was the pH 7.6 buffer from Ref. 8. T o store DNA, NET buffer was used: O.1M NaC1, 0.01M Tris C1, 0.001M EDTA.…”

Section: Buffers and Reagentsmentioning

confidence: 99%

See 1 more Smart Citation

Variation of the permeability of bacteriophage T4: Analysis by use of a protein‐specific probe for the T4 interior

Griess¹,

Khan²,

Serwer³

1991

Biopolymers

View full text Add to dashboard Cite

show abstract

“…3 In this latter study, nonintercalative binding was not distinguished from intercalative binding. In a preliminary study9 of the intercalative binding of ethidium to DNA packaged in bacteriophage T7, a similar deviation from simple psuedo-first-order kinetics was observed.…”

Section: Introductionmentioning

confidence: 95%

Kinetics of ethidium's intercalation in packaged bacteriophage T7 DNA: Effects of DNA packing density

et al. 1986

View full text Add to dashboard Cite

SynopsisThe kinetics of ethidium's intercalative binding to DNA packaged in bacteriophage T7 and two T7 deletion mutants have been determined, using enhancement of fluorescence to quantitate binding. At a constant ethidium concentration. the results can be described as first-order binding with two different rate constants, k: ( = k, + k 1 ) and k; (= k, -C k .,). The larger rate constant (k:) was at least four orders of magnitude smaller than the comparable first-order forward rate constant for binding to DNA released from its capsid. At 25°C values of k; decreased as the amount of DNA packaged per internal volume increased. This latter observation indicates that the rate of ethidium's binding to packaged T7 DNA is limited by an event that occurs inside of the DNA-containing region of T7, not by the crossing of T7 capsid's outer shell. Arrhenius plots of k; are biphasic, indicating a transition for packaged DNA at a temperature of 20°C. The data indicate that k:s are limited by either sieving of ethidium during its passage through the packaged DNA or subsequent hindered intercalation.

show abstract

“…At low nucleotide/dye ratios, there is a blue shift in the visible spectrum of the dye which is attributed to stacking of dye aggregates along the sugar-phosphate backbone (1). The published optical studies include a quantitative analysis of the binding of proflavine to polynucleotides and transfer RNA (3,4), to DNA (5,6), and to bacteriophage (7,8).…”

mentioning

confidence: 99%

Sequence specificity of mutagen-nucleic acid complexes in solution: Intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes

Patel¹,

Canuel²

1977

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The complex formed between the mutagen proflavine and the dC-dC-dC-dG and dG-dG-dC-dC self-complementary tetranucleotide duplexes has been monitored by proton high resolution nuclear magnetic resonance spectroscopy in 0.1 M phosphate solution at high nucleotide/drug ratios. The large upfield shifts (0.5 to 0.85 ppm) observed at all the proflavine ring nonexchangeable protons on complex formation are consistent with intercalation of the mutagen betweenbase pairs of the tetranucleotide duplex. We have proposed an ap roximate overlap geometry between the proflavine ring and nearest neighbor base pairs at the intercalation site from a comparison between experimental shifts and those calculated for various stacking orientations. We have compared the binding of actinomycin D, propidium diiodide, and proflavine to self-complementary tetranucleotide sequences dC-dC-dG-dG and dGdC-dC-dC by UV absorbance changes in the drug bands between 400 and 500 nm. Actinomycin D exhibits a pronounced specificity for sequences with dG-dC sites (dG-dG-dC-dC), while propidium diiodide and proflavine exhibit a specificity for sequences with dC-dG sites (dC-dC-dG-dG). Actinomycin D binds more strongly than propidium diiodide and proflavine to dCdG-dC-dG (contains dC-dG and dG-dC binding sites), indicative of the additional stabilization from hydrogen bonding and hydrophobic interactions between the pentapeptide lactone rings of actinomycin D and the base pair edges and sugar-phosphate backbone of the tetranucleotide duplex. The cationic acridine dyes form two types of complexes with nucleic acids dependent on the nucleotide to dye ratio (1). At high nucleotide/dye ratios, there is a red shift which has been attributed to intercalation of the dye between nucleic acid base pairs (2). At low nucleotide/dye ratios, there is a blue shift in the visible spectrum of the dye which is attributed to stacking of dye aggregates along the sugar-phosphate backbone (1). The published optical studies include a quantitative analysis of the binding of proflavine to polynucleotides and transfer RNA (3, 4), to DNA (5, 6), and to bacteriophage (7, 8).The 2:2 complexes of 9-aminoacridine with the dinucleoside phosphates adenylyl-(3'-5')-uridine (9) and 5-iodocytidylyl-(3'-5')-guanosine (10) have been solved by x-ray crystallography. The adenine bases form Hoogsteen type hydrogen bonds to the uracil bases in the former crystal structure (9), and the base pairs are stacked parallel to each other with the 9-aminoacridine sandwiched between them. The cytosine-bases form Watson-Crick type hydrogen bonds to the guanosine bases in the latter crystals (10), with one 9-aminoacridine stacked on the exterior and the other molecule intercalated into the dinucleoside duplex.Alden and Arnott have put forward a model based on stereochemical principles for the intercalation of proflavine (Fig. 1) into B-DNA (11). The model proposes a change in the torsion angles about C4'-C5' and 04-P backbone bonds to a trans conformation and a change in sugar pucker to C3' endo-(3...

show abstract

Kinetics of proflavin binding to bacteriophages T2L and T4D

Cited by 19 publications

References 31 publications

Variation of the permeability of bacteriophage T4: Analysis by use of a protein‐specific probe for the T4 interior

Variation of the permeability of bacteriophage T4: Analysis by use of a protein‐specific probe for the T4 interior

Kinetics of ethidium's intercalation in packaged bacteriophage T7 DNA: Effects of DNA packing density

Sequence specificity of mutagen-nucleic acid complexes in solution: Intercalation and mutagen-base pair overlap geometries for proflavine binding to dC-dC-dG-dG and dG-dG-dC-dC self-complementary duplexes

Contact Info

Product

Resources

About