An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies
نویسندگان
چکیده
منابع مشابه
Fluorescent nucleic acid base analogues.
The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the na...
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Many enzymes that repair or modify bases in double-stranded DNA gain access to their substrates by base flipping. Although crystal structures provide stunning snap shots, biochemical approaches addressing the dynamics have proven difficult, particularly in complicated multi-step reactions. Here, we use protein-DNA crosslinking and potassium permanganate reactivity to explore the base-flipping s...
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Base flipping is the movement of a DNA base from an intrahelical, base-stacked position to an extrahelical, solvent-exposed position. As there are favorable interactions for an intrahelical base, both hydrogen bonding and base stacking, base flipping is expected to be energetically prohibitive for an undamaged DNA duplex. For damaged DNA bases, however, the energetic cost of base flipping may b...
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Although change and adaptation are key to life, nature is reluctant to abandon old inventions. Even today when the hypothetical RNA world of our ancestors has been supplanted by the richer possibilities offered by proteins, we still find key processes catalyzed by RNA. Perhaps the oldest discovery was the unique power of base pairing to enable replication. This must have been key to the develop...
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Deoxyribonucleic acid-deoxyribonucleic acid reassociation and deoxyribonucleic acid-ribosomal ribonucleic acid cistron similarity studies showed that the anaerobic, gram-positive cocci comprise a rather heterogeneous group of bacteria. The deoxyribonucleic acid-ribosomal ribonucleic acid hybridization studies distinguished seven groups. Groups 1 and 2 consisted of Peptostreptococcus magnus and ...
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ژورنال
عنوان ژورنال: Journal of Chemical Theory and Computation
سال: 2009
ISSN: 1549-9618,1549-9626
DOI: 10.1021/ct9001575