α- and β-Stilbenosides as base-pair surrogates in DNA hairpins

2006 ◽  
Vol 4 (2) ◽  
pp. 314-322 ◽  
Author(s):  
Ligang Zhang ◽  
Hai Long ◽  
Grant E. Boldt ◽  
Kim D. Janda ◽  
George C. Schatz ◽  
...  
Keyword(s):  
Base Pair ◽  
Dna Hairpins

Spectroscopic and structural impact of a stem base-pair change in DNA hairpins: GTTC-ACA-GAAC versus GTAC-ACA-GTAC

2006 ◽  
Vol 65 (1) ◽  
pp. 84-94 ◽  
Author(s):  
Michèle Lamoureux ◽  
Louis Patard ◽  
Belen Hernandez ◽  
Thierry Couesnon ◽  
Guillaume P.H. Santini ◽  
...  
Keyword(s):  
Base Pair ◽  
Dna Hairpins ◽  
Stem Base ◽  
Structural Impact

Effect of Structural Dynamics and Base Pair Sequence on the Nature of Excited States in DNA Hairpins

2012 ◽  
Vol 116 (37) ◽  
pp. 11447-11458 ◽  
Author(s):  
Sameer Patwardhan ◽  
Stefano Tonzani ◽  
Frederick D. Lewis ◽  
Laurens D. A. Siebbeles ◽  
George C. Schatz ◽  
...  
Keyword(s):  
Excited States ◽  
Structural Dynamics ◽  
Base Pair ◽  
Dna Hairpins ◽  
Pair Sequence

Stabilization of DNA Hairpins by Stilbene Capping of the Terminal Base Pair

2006 ◽  
Vol 53 (6) ◽  
pp. 1501-1507 ◽  
Author(s):  
Ligang Zhang ◽  
Huihe Zhu ◽  
Meledathu C. Sajimon ◽  
Jan A. Rojas Stütz ◽  
Karsten Siegmund ◽  
...  
Keyword(s):  
Base Pair ◽  
Dna Hairpins

Raising the barrier for photoinduced DNA charge injection with a cyclohexyl artificial base pair

2015 ◽  
Vol 185 ◽  
pp. 105-120 ◽  
Author(s):  
Arunoday P. N. Singh ◽  
Michelle A. Harris ◽  
Ryan M. Young ◽  
Stephen A. Miller ◽  
Michael R. Wasielewski ◽  
...  
Keyword(s):  
Base Pair ◽  
Charge Separation ◽  
Charge Recombination ◽  
Hole Injection ◽  
Quantum Yields ◽  
Base Pairs ◽  
Dna Hairpins ◽  
Synthetic Dna ◽  
Photoinduced Charge Separation ◽  
Photoinduced Charge

The effects of an artificial cyclohexyl base pair on the quantum yields of fluorescence and dynamics of charge separation and charge recombination have been investigated for several synthetic DNA hairpins. The hairpins possess stilbenedicarboxamide, perylenediimide, or naphthalenediimide linkers and base-paired stems. In the absence of the artificial base pair hole injection into both adenine and guanine purine bases is exergonic and irreversible, except in the case of stilbene with adenine for which it is slightly endergonic and reversible. Insertion of the artificial base pair renders hole injection endergonic or isoergonic except in the case of the powerful naphthalene acceptor for which it remains exergonic. Both hole injection and charge recombination are slower for the naphthalene acceptor in the presence of the artificial base pair than in its absence. The effect of an artificial base pair on charge separation and charge recombination in hairpins possessing stilbene and naphthalene acceptor linkers and a stilbenediether donor capping group has also been investigated. In the case of the stilbene acceptor–stilbene donor capped hairpins photoinduced charge separation across six base pairs is efficient in the absence of the artificial base pair but does not occur in its presence. In the case of the naphthalene acceptor–stilbene donor capped hairpins the artificial base pair slows but does not stop charge separation and charge recombination, leading to the formation of long-lived charge separated states.

Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamic stability

Biopolymers ◽  
1999 ◽  
Vol 50 (4) ◽  
pp. 425-442 ◽  
Author(s):  
Peter M. Vallone ◽  
Teodoro M. Paner ◽  
Jovencio Hilario ◽  
Michael J. Lane ◽  
Brian D. Faldasz ◽  
...  
Keyword(s):  
Thermodynamic Stability ◽  
Base Pair ◽  
Dna Hairpins ◽  
Loop Sequence

NMR spectroscopic and enzymatic studies of DNA hairpins containing mismatches in the EcoRI recognition site

1998 ◽  
Vol 76 (2-3) ◽  
pp. 391-402 ◽  
Author(s):  
Markus W Germann ◽  
Bernd W Kalisch ◽  
James M Varnum ◽  
Hans J Vogel ◽  
Johan H van de Sande
Keyword(s):  
Restriction Endonuclease ◽  
Base Pair ◽  
Binding Constants ◽  
Recognition Site ◽  
Dna Hairpins ◽  
Phosphodiester Bond ◽  
Dna Oligonucleotides ◽  
Substrate Properties ◽  
Hairpin Structures ◽  
Endonuclease Ecori

We have correlated the structural perturbations caused by DNA mismatches with the enzymatic data of the interaction of the restriction endonuclease EcoRI with DNA. Oligonucleotides d(CGAGAATTCTCA5GAXAATTCT) (X = G, A, T) and d(CGCGAATTYGCGT4CGCXAATTCGCG) (Y = C, X = G, T and Y = A, X = T) containing single mismatches within the EcoRI recognition site were characterized by NMR spectroscopy and by their EcoRI substrate properties. UV melting and gel electrophoresis studies confirm that the oligonucleotides form hairpin structures. The presence of either a CT or a CA mismatch results in markedly lower Tm and van't Hoff enthalpies compared with the fully base paired control. NMR imino proton spectra of these hairpins demonstrate that the perturbation caused by the two mispairs or a noncanonical AT pair is localized and limited to one or two base pairs on either side of the perturbation. The DNA hairpin structures containing single mismatches, and to a lesser extent also sequences with a single noncanonical base pair, are substrates for the restriction endonuclease. In addition to the strand scission at the nonperturbed GpA phosphodiester bond some cleavage is observed at the mismatched position. The interactions of the CA and CT mismatched hairpin with the enzyme are characterized by binding constants that are only 33 and 57 times lower, respectively, than that for the canonical sequence, corresponding to 8-10 kJ·mol-1 less favorable free binding energy. This, taken together with the NMR data, indicates that the CA and CT mismatches have only small effects on the EcoRI recognition of the DNA substrate. We conclude that two out of the three hydrogen bonds that characterize the interaction of EcoRI with the CG base pair in the canonical sequence can still be formed for either the CT or CA mismatched recognition site.Key words: DNA hairpins, EcoRI recognition, mismatches, imino protons.

Detection of the Glanzmann's Thrombasthenia Mutations in Arab and Iraqi-Jewish Patients by Polymerase Chain Reaction and Restriction Analysis of Blood or Urine Samples

1991 ◽  
Vol 66 (04) ◽  
pp. 500-504 ◽  
Author(s):  
H Peretz ◽  
U Seligsohn ◽  
E Zwang ◽  
B S Coller ◽  
P J Newman
Keyword(s):  
Polymerase Chain Reaction ◽  
Base Pair ◽  
Restriction Analysis ◽  
Urine Samples ◽  
Chain Reaction ◽  
Base Pairs ◽  
Glanzmann’S Thrombasthenia ◽  
Glanzmann's Thrombasthenia ◽  
Base Pair Deletion ◽  
Polymerase Chain

SummarySevere Glanzmann's thrombasthenia is relatively frequent in Iraqi-Jews and Arabs residing in Israel. We have recently described the mutations responsible for the disease in Iraqi-Jews – an 11 base pair deletion in exon 12 of the glycoprotein IIIa gene, and in Arabs – a 13 base pair deletion at the AG acceptor splice site of exon 4 on the glycoprotein IIb gene. In this communication we show that the Iraqi-Jewish mutation can be identified directly by polymerase chain reaction and gel electrophoresis. With specially designed oligonucleotide primers encompassing the mutation site, an 80 base pair segment amplified in healthy controls was clearly distinguished from the 69 base pair segment produced in patients. Patients from 11 unrelated Iraqi-Jewish families had the same mutation. The Arab mutation was identified by first amplifying a DNA segment consisting of 312 base pairs in controls and of 299 base pairs in patients, and then digestion by a restriction enzyme Stu-1, which recognizes a site that is absent in the mutant gene. In controls the 312 bp segment was digested into 235 and 77 bp fragments, while in patients there was no change in the size of the amplified 299 bp segment. The mutation was found in patients from 3 out of 5 unrelated Arab families. Both Iraqi-Jewish and Arab mutations were detectable in DNA extracted from blood and urine samples. The described simple methods of identifying the mutations should be useful for detection of the numerous potential carriers among the affected kindreds and for prenatal diagnosis using DNA extracted from chorionic villi samples.

Mutation Spectrum in Patients with Wiskott-Aldrich Syndrome and X-linked Thrombocytopenia: Identification of Twelve Different Mutations in the WASP Gene

1996 ◽  
Vol 75 (04) ◽  
pp. 546-550 ◽  
Author(s):  
Marianne Schwartz ◽  
Albert Békássy ◽  
Mikael Donnér ◽  
Thomas Hertel ◽  
Stefan Hreidarson ◽  
...  
Keyword(s):  
Base Pair ◽  
Hot Spot ◽  
Missense Mutations ◽  
Nucleotide Substitutions ◽  
Exon 2 ◽  
Wiskott Aldrich Syndrome ◽  
Base Pair Deletion ◽  
Reliable Diagnosis ◽  
Wasp Gene ◽  
Detection Of Mutations

SummaryTwelve different mutations in the WASP gene were found in twelve unrelated families with Wiskott-Aldrich syndrome (WAS) or X-linked thrombocytopenia (XLT). Four frameshift, one splice, one nonsense mutation, and one 18-base-pair deletion were detected in seven patients with WAS. Only missense mutations were found in five patients diagnosed as having XLT. One of the nucleotide substitutions in exon 2 (codon 86) results in an Arg to Cys replacement. Two other nucleotide substitutions in this codon, R86L and R86H, have been reported previously, both giving rise to typical WAS symptoms, indicating a mutational hot spot in this codon. The finding of mutations in the WASP gene in both WAS and XLT gives further evidence of these syndromes being allelic. The relatively small size of the WASP gene facilitates the detection of mutations and a reliable diagnosis of both carriers and affected fetuses in families with WAS or XLT.

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