Closing the lid on DNA end-to-end stacking interactions

Li Li; Suzette A. Pabit; Jessica S. Lamb; Hye Yoon Park; Lois Pollack

doi:10.1063/1.2937402

Closing the lid on DNA end-to-end stacking interactions

Li Li, Suzette A. Pabit, Jessica S. Lamb, Hye Yoon Park, Lois Pollack

Research output: Contribution to journal › Article › peer-review

31 Scopus citations

Abstract

Recent experiments suggest that short DNA strands associate by end-to-end stacking. Here, we report interactions between DNAs with modified ends. DNA duplexes, 20 bp long, were capped with short T₄ loops at 2, 1 or 0 ends, and were placed in solutions containing 20 mM Mg²⁺. Association was observed only in constructs with one or more uncapped ends. DNA-DNA interactions were characterized by measuring variations in small angle x-ray scattering (SAXS) curves at the lowest scattering angles. Second virial coefficients were computed from the SAXS data. Our results confirm that end-to-end stacking plays an important role in short strand DNA-DNA interactions.

Original language	English (US)
Article number	223901
Journal	Applied Physics Letters
Volume	92
Issue number	22
DOIs	https://doi.org/10.1063/1.2937402
State	Published - 2008
Externally published	Yes

Bibliographical note

Funding Information:
We thank K. Finkelstein for experimental assistance and D. Burke for suggesting the dumbbell construct. This research is funded by the NSF through MCB-0347220 and the Cornell NBTC, and by NIH through P01-GM066275. CHESS is supported by NSF and NIH/NIGMS under Grant No DMR-9713424.

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abstract = "Recent experiments suggest that short DNA strands associate by end-to-end stacking. Here, we report interactions between DNAs with modified ends. DNA duplexes, 20 bp long, were capped with short T4 loops at 2, 1 or 0 ends, and were placed in solutions containing 20 mM Mg2+. Association was observed only in constructs with one or more uncapped ends. DNA-DNA interactions were characterized by measuring variations in small angle x-ray scattering (SAXS) curves at the lowest scattering angles. Second virial coefficients were computed from the SAXS data. Our results confirm that end-to-end stacking plays an important role in short strand DNA-DNA interactions.",

author = "Li Li and Pabit, {Suzette A.} and Lamb, {Jessica S.} and Park, {Hye Yoon} and Lois Pollack",

note = "Funding Information: We thank K. Finkelstein for experimental assistance and D. Burke for suggesting the dumbbell construct. This research is funded by the NSF through MCB-0347220 and the Cornell NBTC, and by NIH through P01-GM066275. CHESS is supported by NSF and NIH/NIGMS under Grant No DMR-9713424. ",

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doi = "10.1063/1.2937402",

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AU - Li, Li

AU - Pabit, Suzette A.

AU - Lamb, Jessica S.

AU - Park, Hye Yoon

AU - Pollack, Lois

N1 - Funding Information: We thank K. Finkelstein for experimental assistance and D. Burke for suggesting the dumbbell construct. This research is funded by the NSF through MCB-0347220 and the Cornell NBTC, and by NIH through P01-GM066275. CHESS is supported by NSF and NIH/NIGMS under Grant No DMR-9713424.

PY - 2008

Y1 - 2008

N2 - Recent experiments suggest that short DNA strands associate by end-to-end stacking. Here, we report interactions between DNAs with modified ends. DNA duplexes, 20 bp long, were capped with short T4 loops at 2, 1 or 0 ends, and were placed in solutions containing 20 mM Mg2+. Association was observed only in constructs with one or more uncapped ends. DNA-DNA interactions were characterized by measuring variations in small angle x-ray scattering (SAXS) curves at the lowest scattering angles. Second virial coefficients were computed from the SAXS data. Our results confirm that end-to-end stacking plays an important role in short strand DNA-DNA interactions.

AB - Recent experiments suggest that short DNA strands associate by end-to-end stacking. Here, we report interactions between DNAs with modified ends. DNA duplexes, 20 bp long, were capped with short T4 loops at 2, 1 or 0 ends, and were placed in solutions containing 20 mM Mg2+. Association was observed only in constructs with one or more uncapped ends. DNA-DNA interactions were characterized by measuring variations in small angle x-ray scattering (SAXS) curves at the lowest scattering angles. Second virial coefficients were computed from the SAXS data. Our results confirm that end-to-end stacking plays an important role in short strand DNA-DNA interactions.

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Closing the lid on DNA end-to-end stacking interactions

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