Eukaryotic DNA diverges at a long and complex pyrimidine.purine tract that can adopt altered conformations.

Fowler, Richard F.; Skinner, Dorothy M.

doi:10.1016/s0021-9258(19)84479-4

Cited by 35 publications

(7 citation statements)

References 55 publications

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“…Similarly, a negative superhelical density of only 0.02 to 0.03 has been observed for the Si nuclease cleavage of the TTAA region of crab satellite DNA. However, in this case, the altered structure was strongly pH dependent (10), which is in contrast to the JCV Mad-1 sequence. P1 nuclease at neutral pH showed a fine-mapping profile in the TATA box similar to that found with Si nuclease.…”

Section: Discussioncontrasting

confidence: 59%

Unusual DNA structure in the regulatory region of the human papovavirus JC virus

Amirhaeri

Wohlrab

Major

et al. 1988

J Virol

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The human papovavirus JC virus (JCV) was analyzed for the presence of unusual DNA conformations. Recombinant plasmids containing 60% of the JCV prototype Mad-1 strain DNA were constructed and analyzed with both enzymatic and chemical probes. Fine-mapping studies revealed that the most prominent S1 nuclease-sensitive and bromoacetaldehyde-modified sites were located within the TATA boxes of each 98-base-pair tandem repeat. Further studies revealed that the S1 nuclease-sensitive site in the first TATA box (proximal to the origin) was approximately 50-fold stronger than the site in the second TATA box (distal from the origin). Deletion of the first TATA box drastically reduced the extent of bromoacetaldehyde modification in the second TATA box, whereas deletion of the second TATA box had little or no effect on the reactivity at the first TATA box. Hence, the biological and conformational role of the second TATA box remains unclear. No supercoil-induced relaxation was found, and reactions with the probes were not pH dependent. Also, fragments containing this regulatory region did not appear to be bent, although the A+T-rich segment contained a tract of eight consecutive A's. We conclude that the regulatory region of JCV contains non-B, but right-handed, DNA conformations which account for this behavior.

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Section: Discussioncontrasting

confidence: 59%

Unusual DNA structure in the regulatory region of the human papovavirus JC virus

Amirhaeri

Wohlrab

Major

et al. 1988

J Virol

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“…A d(C)22 tract closely neighbored by d(CCT)15 and d-(CGCAC)5 sequences at its 5' and 3' ends, respectively, in Bermuda land crab DNA can adopt two different types of altered conformations under the influence of negative super-1 Abbreviations: C-C+, base pair of two cytosines with a shared proton; • , Watson-Crick base pair of adenine and thymine; CD, circular dichroism; NMR, nuclear magnetic resonance. helicity and decreased pH (Fowler & Skinner, 1986). Finally, d(C4A4C4A4C4) sequences at the ends of macronuclear DNA molecules of the protozoan Oxytricha nova are essential for coherence into an unusual structure (Oka & Thomas, 1987).…”

mentioning

confidence: 99%

Circular dichroism spectra of DNA oligomers show that short interior stretches of C.cntdot.C+ base pairs do not form in duplexes with A.cntdot.T base pairs

Edwards¹,

Ratliff²,

Gray³

1988

Biochemistry

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Circular dichroism (CD) experiments were carried out on a series of DNA oligomers to determine if short internal stretches of protonated cytosine-cytosine (C.C+) base pairs could coexist with adenine-thymine (A.T) base pairs. (1) C.C+ base pairs did form in the absence of A.T base pairs in the individual oligomers d(AACC)5 and d(CCTT)5, as indicated by the appearance of a long-wavelength CD band centered at 282-284 nm, when the pH was lowered to 6 or 5 at 0.5 M Na+. A comparison of measured with calculated spectra showed that d(CCTT)5 at pH 5, 0.5 M Na+, 20 degrees C, likely adopted a structure with a central core of stacked C.C+ base pairs and looped-out thymines. Under the same conditions, it appeared that C.C+ base pairs also formed in d(AACC)5, but with the adenines remaining intrahelical. Each of these oligomers showed a cooperative transition for formation of C.C+ base pairs as the temperature was lowered, with C.C+ base pairs forming at a higher temperature in d(CCTT)5 than in d(AACC)5. A.T base formed in equimolar mixtures of d(AACC)5 plus d(CCTT)5 as monitored by an increase in the negative magnitude of the 250-nm CD band. However, a large increase did not appear at about 285 nm in CD spectra of the mixtures, showing that there were no stacked C.C+ base pairs in the d(AACC)5.d(CCTT)5 duplex even though they formed under the same conditions in the individual strands. Thus, in this duplex, A.T base pairs prevented the formation of neighboring internal C.C+ base pairs. (2) CD measurements were also made of d(A10C4T10).(ABSTRACT TRUNCATED AT 250 WORDS)

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“…Hydrolysis was catalyzed at sites of 5'-C*Gand 5'-G*Cin both d(CG)6 and d(GC)6. The possibility that a redundant sequence such as d(CG)6 may form a non-B, non-Z conformation cannot be directly addressed in this study (Suggs & Wagner, 1986;Fowler & Skinner, 1986;Evans & Efstratiadis, 1986). However, this is not required to explain the action of S-l on these oligonucleotides.…”

Section: Discussionmentioning

confidence: 99%

“…The anomalous behavior of alternating copolymers also persisted when such sequences were inserted into plasmids (Suggs & Wagner, 1986;Evans & Efstratiadis, 1986). Redundant sequences in nature, often found near the beginning of certain genes, may similarly adopt an equilibrium of conformations (Hentschel, 1982;Mace et al, 1983;Weintraub, 1983;Fowler & Skinner, 1986). A pronounced feature of these regions is their unexpectedly high sensitivity to S-1 and other nucleases (Elgin, 1989).…”

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confidence: 99%

Facile interconversion of duplex structures formed by copolymers of d(CG)

Rokita¹,

Romero-Fredes²

1989

Biochemistry

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Correlations between DNA sequence and reactivity have often been drawn with an implicit or explicit connection to duplex structure. An in vitro model using oligonucleotides of defined sequences has been developed to characterize a potential source of the hypersensitivity that naturally occurring regions of redundant sequence exhibit with many nucleases. S-1 nuclease was used here to diagnose the unusual hybridization of copolymeric DNA, d(CG)6, and related oligomers, through product and kinetic analysis. Fully complementary but redundant sequences reacted with this enzyme almost an order of magnitude faster than did heterogeneous fragments of DNA. Hydrolysis products of the copolymers indicated that conformations with unpaired termini were the sole substrates under these studies, and only a facile equilibrium between aligned and extended structures was required to explain the heightened reactivity of this DNA. For example, d(CG)6 was converted to d(CG)5 and d(CG)4 whereas d(CG)4C was initially processed to an octamer and then only later to a hexamer. Catalysis by S-1 exhibited no other substrate or product specificity; even the disordered bases in the loop region of a hairpin structure, d(CG)3T4(CG)3, did not provide sites of enhanced enzyme action. The rate of DNA consumption under standard conditions was proportional to the expected concentration of overhanging sequences rather than the absolute amount of DNA present. All initial attempts to saturate enzyme activity failed, and therefore, the rate of substrate formation through strand slippage was always faster than the catalytic depletion of unpaired bases. Only a low-energy transition state(s) must then separate the various hybridized species since this structural equilibration proceeded readily under conditions of 10 mM potassium phosphate, pH 7, 100 mM NaCl, and 22 degrees C.

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Eukaryotic DNA diverges at a long and complex pyrimidine.purine tract that can adopt altered conformations.

Cited by 35 publications

References 55 publications

Unusual DNA structure in the regulatory region of the human papovavirus JC virus

Unusual DNA structure in the regulatory region of the human papovavirus JC virus

Circular dichroism spectra of DNA oligomers show that short interior stretches of C.cntdot.C+ base pairs do not form in duplexes with A.cntdot.T base pairs

Facile interconversion of duplex structures formed by copolymers of d(CG)

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