Southern molecular hybridization experiments with parallel complementary DNA probes

Tchurikov, Nickolai A.; Shchyolkina, Anna K.; Borissova, O.F.; Chernov, B. K.

doi:10.1016/0014-5793(92)80545-r

Cited by 22 publications

(22 citation statements)

References 13 publications

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“…Sequences with a propensity to form parallel DNAs have been found in specific chromosome regions [10–12], and they could have an evolutionary role [13]. Moreover, certain types of parallel-stranded DNA can be excellent templates for the formation of triplexes, and so they can be used to develop more powerful antisense oligonucleotides [14, 15].…”

Section: Introductionmentioning

confidence: 99%

Structural Properties of G,T‐Parallel Duplexes

Aviñó

Cubero

Gargallo

et al. 2010

Journal of Nucleic Acids

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The structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.

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Section: Introductionmentioning

confidence: 99%

Structural Properties of G,T‐Parallel Duplexes

Aviñó

Cubero

Gargallo

et al. 2010

Journal of Nucleic Acids

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“…were specially synthesized to obtain antiparallel (I-II), parallel (I-III) decaduplexes and antiparallel (IV-V), parallel (IV-VI) 40-duplexes [6].…”

Section: Methodsmentioning

confidence: 99%

“…The possibility of antiparallel 7-nucleotide duplex formation of (I) and (III) strands instead of parallel decanucleotide formation was excluded by the annealing procedure [6]. The specialized fluorescent techniques [7,9] permitted us to check the formation of perfect antiparallel I-II and parallel I-III decaduplexes.…”

Section: 1 Decaduplexesmentioning

confidence: 99%

“…The measured times of rotational relaxation of AF and ethidium bromide complexes with (IV-V) and (IV-VI) oligonucleotides are the same &c = 88 f 4 ns) and testify to the absence of hairpins or other unusual structures in the parallel 40nucleotide duplex [6]. The absence of mismatches and unpaired nucleotides in parallel 40-duplex was checked by the 'r-method' [9].…”

Section: -Nucleotide Duplexesmentioning

confidence: 99%

“…The parallel complementary probes of normal nucleotide content can be used for molecular hybridization experiments, suggesting the stability of GCcontaining parallel DNA [6]. Thus, more direct experi-mental evidences are needed for understanding the GCpairing in parallel DNA.…”

Section: Introductionmentioning

confidence: 99%

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Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence

et al. 1993

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The low-cooperative melting of parallel DNA formed by a natural 40 bp long sequence from Drosophila:that possesses a normal nucleotide content was studied by using the special method of measuring the fluorescence of its complex with acriflavine as well as by conventional thermal denaturation. Acriflavine allows discrimination of the melting of AT and GC pairs because its fluorescence is quenched by neighbouring G bases. We have observed that about 40% of AT pairs melt at 14°C while the remainder melt at 42°C. The GC pairs remain stable up to -40°C and melt at 54°C. The higher stability of GC pairs suggests the formation of cis Watson-Crick pairs in parallel DNA.Parallel stranded DNA; Stability of GC pairs

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Parallel-stranded duplex DNA containing dA · dU base pairs

Förtsch¹,

Fritzsche²,

Birch-Hirschfeld³

et al. 1998

Biopolymers

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DNA oligonucleotides with dA and dU residues can form duplexes with trans d(A · U) base pairing and the sugar‐phosphate backbone in a parallel‐stranded orientation, as previously established for oligonucleotides with d(A · T) base pairs. The properties of such parallel‐stranded DNA (ps‐DNA) 25‐mer duplexes have been characterized by absorption (uv), CD, ir, and fluorescence spectroscopy, as well as by nuclease sensitivity. Comparisons were made with duplex molecules containing (a) dT in both strands, (b) dU in one strand and dT in the second, and (c) the same base combinations in reference antiparallel‐stranded (aps) structures. Thermodynamic analysis revealed that total replacement of deoxythymine by deoxyuridine was accompanied by destabilization of the ps‐helix (reduction in Tm by −13°C in 2 mM MgGl2, 10 mM Na‐cacodylate). The U‐containing ps‐helix (U1 · U2) also melted 14°C lower than the corresponding aps‐helix under the same ionic conditions; this difference was very close to that observed between ps and aps duplexes with d(A · T) base pairs. Force field minimized structures of the various ps and aps duplexes with either d(A · T) or d(A · U) base pairs ps/aps and dT/dU combinations are presented. The energy‐minimized helical parameters did not differ significantly between the DNAs containing dT and dU. © 1996 John Wiley & Sons, Inc.

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Southern molecular hybridization experiments with parallel complementary DNA probes

Cited by 22 publications

References 13 publications

Structural Properties of G,T‐Parallel Duplexes

Structural Properties of G,T‐Parallel Duplexes

Relative stability of AT and GC pairs in parallel DNA duplex formed by a natural sequence

Parallel-stranded duplex DNA containing dA · dU base pairs

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