Sequence Dependence of DNA Conformation, Dynamics and Interactions in Solution

Patel, Dinshaw J.; Kozlowski, Sharon A.; Pardi, Arthur; Bhatt, R. K.; Ikuta, Satoshi; Itakura, Keiichi

doi:10.1007/978-94-009-6457-0_8

Cited by 44 publications

(77 citation statements)

References 60 publications

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“…Furthermore, Taq DNA polymerase extension of a 3′ mismatched primer is more efficient for T-G and G-T mismatches than other mismatches at low dNTP concentrations (35). NMR and X-ray crystallography analysis of the structure of aberrant base pairs in duplex DNA oligonucleotide have indicated that G-T, A-C and G-A pairs existed as 'wobble' structures which differ slightly in dimensions from a normal Watson-Crick base pair (36,37). It was suggested that a well-stacked wobble pair may result in a more stable structure than a poorly stacked base pair approximating Watson-Crick geometry more closely.…”

Section: (3′-t) Lp3′t Was the Discriminating Oligonucleotide T-a (♦)mentioning

confidence: 99%

Improving the Fidelity of Thermus Thermophilus DNA Ligase

Luo

Bergstrom

Barany

1996

Nucleic Acids Research

103

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The DNA ligase from Thermus thermophilus (Tth DNA ligase) seals single-strand breaks (nicks) in DNA duplex substrates. The specificity and thermostability of this enzyme are exploited in the ligase chain reaction (LCR) and ligase detection reaction (LDR) to distinguish single base mutations associated with genetic diseases. Herein, we describe a quantitative assay using fluorescently labeled substrates to study the fidelity of Tth DNA ligase. The enzyme exhibits significantly greater discrimination against all single base mismatches on the 3′-side of the nick in comparison with those on the 5′-side of the nick. Among all 12 possible single base pair mismatches on the 3′-side of the nick, only T-G and G-T mismatches generated a quantifiable level of ligation products after 23 h incubation. The high fidelity of Tth DNA ligase can be improved further by introducing a mismatched base or a universal nucleoside analog at the third position of the discriminating oligonucleotide. Finally, two mutant Tth DNA ligases, K294R and K294P, were found to have increased fidelity using this assay.

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Section: (3′-t) Lp3′t Was the Discriminating Oligonucleotide T-a (♦)mentioning

confidence: 99%

Improving the Fidelity of Thermus Thermophilus DNA Ligase

Luo

Bergstrom

Barany

1996

Nucleic Acids Research

103

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“…Extensive nuclear magnetic resonance (NMR) data was available documenting the conformation and dynamics of this mismatch in B-DNA in solution (69,(78)(79)(80)(81)(82), and single crystal X-ray structures have been solved for G-T mispairs in A (83, 84), B (85), and Z-DNA (85,86). In every case, the G-T mismatch has been found to adopt the wobble conformation anticipated by Crick (66), which is stabilized by two imino proton-carbonyl hydrogen bonds.…”

Section: G-t and A-c Transition Mismatchesmentioning

confidence: 99%

“…The dynamics of the G-T wobble pair have been addressed in the elegant studies of Patel and coworkers (78)(79)(80)(81), who used NMR methods to examine the solution behavior of the B-form heteroduplex formed by the self complementary dodecamer d(C-G-T-G-A-A-T-T-C-G-C-G). Thermal depen dence of I�hemical shifts for nonexchangeable base protons revealed a common melting transition for the 10 nonterminal base pairs within the heteroduplex (52°C in 0.…”

Section: That the Enthalpy Of Melting Of The G-t Heteroduplex Formed mentioning

confidence: 99%

DNA Mismatch Correction

Modrich¹

1987

Annual Review of Biochemistry

106

135

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“…Additionally, characteristic cross peaks for Watson-Crick base pairing are observed for G8 and G2 in the 2D NOESY correlation of the unmodified RNA oligomer (not shown). While the chemical shifts of G7 and U4 are characteristic for a G -U base pair [20] [29], we do not observe an NOE cross peak for this base pair in the unmodified sample, but only a strong exchange peak with the solvent. This is in agreement with findings by Allain and Varani [20] for the UUCG hairpin in the PI helix of the spliceosome.…”

Section: )mentioning

confidence: 57%

“…This is expected from work in DNA where only at pH 5 cytidines become protonated and form C + . U base pairs [26] [29]. In contrast to the fluorinated hairpin, no strong intranucleotide H-C(s),H-C(l') cross peak could be observed, indicating an anti orientation of the base G7 in the duplex conformation.…”

Section: ') Cos(n 'J(h-c(y)f-c(2')) 24')mentioning

confidence: 99%