TY - JOUR
T1 - Structure of three-way dna junctions. 2. effects of extra bases and mismatches
AU - Shlyakhtenko, Luda S.
AU - Appella, Ettore
AU - Harrington, Rodney E.
AU - Kutyavin, Igor
AU - Lyubchenko, Yuri L.
N1 - Funding Information:
We thank I. Tinoco, Jr., K. Luebke, V. Zhurkin, R. Jernigan, S. Lindsay and B. Jacobs for discussions and encouragement, S. Lindsay, R. Misra and B. Jacobs for the use of equipment in their laboratories, and S. Lindsay for the support (YLL ). This research has been supported by grants from the NIH and the NSF to REH and the Office of Naval Research to SML.
PY - 1994/8
Y1 - 1994/8
N2 - The structure of three-way DNA junctions, containing two linear double helices (arms) and a hairpin as a third arm, was studied by means of a cyclization technique. In addition to branched molecules containing perfect base-paring in helical parts, three-way junctions with mismatches and extra non-complementary nucleotides (bulges) at junction points were studied. Molecules thus designed were ligated at identical conditions and their geometry was compared through the analysis of the efficiency of circle formation. The analysis showed that irregularities in base pairing listed above dramatically change the static and dynamic structural characteristics of the three-way junctions. All mismatches facilitate the kink between linear arms, but quantitatively, the effect depends on the position of the mismatch. The effect is maximal for GG-mismatch placed at the hairpin junction point. The results for bulges are of different kind, and they lead us to conclude that the three-way DNA junction with unpaired nucleotides adopts a T-like geometry with an angle around 90° between arms containing the bulge and two other arms coaxially stacked. Broad distribution of circles indicates that this T-form geometry of bulge-containing junction is more flexible than initial pyramidal structure predominantly due to high mobility of the third arm.
AB - The structure of three-way DNA junctions, containing two linear double helices (arms) and a hairpin as a third arm, was studied by means of a cyclization technique. In addition to branched molecules containing perfect base-paring in helical parts, three-way junctions with mismatches and extra non-complementary nucleotides (bulges) at junction points were studied. Molecules thus designed were ligated at identical conditions and their geometry was compared through the analysis of the efficiency of circle formation. The analysis showed that irregularities in base pairing listed above dramatically change the static and dynamic structural characteristics of the three-way junctions. All mismatches facilitate the kink between linear arms, but quantitatively, the effect depends on the position of the mismatch. The effect is maximal for GG-mismatch placed at the hairpin junction point. The results for bulges are of different kind, and they lead us to conclude that the three-way DNA junction with unpaired nucleotides adopts a T-like geometry with an angle around 90° between arms containing the bulge and two other arms coaxially stacked. Broad distribution of circles indicates that this T-form geometry of bulge-containing junction is more flexible than initial pyramidal structure predominantly due to high mobility of the third arm.
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U2 - 10.1080/07391102.1994.10508092
DO - 10.1080/07391102.1994.10508092
M3 - Article
C2 - 7848563
AN - SCOPUS:0028019454
SN - 0739-1102
VL - 12
SP - 131
EP - 143
JO - Journal of Biomolecular Structure and Dynamics
JF - Journal of Biomolecular Structure and Dynamics
IS - 1
ER -