Ryan Konik

Publications (3)7.31 Total impact

• Source

  Available from: Zhongbo Yu

  Dataset: 1-s2.0-S0006349512004699-main

  Soma Dhakal, Zhongbo Yu, Ryan Konik, Yunxi Cui, Deepak Koirala, Hanbin Mao
• Source

  Available from: Zhongbo Yu

  Article: G-Quadruplex and i-Motif Are Mutually Exclusive in ILPR Double-Stranded DNA

  Soma Dhakal, Zhongbo Yu, Ryan Konik, Yunxi Cui, Deepak Koirala, Hanbin Mao
  [show abstract] [hide abstract]
  ABSTRACT: G-quadruplex has demonstrated its biological functions in vivo. Although G-quadruplex in single-stranded DNA (ssDNA) has been well characterized, investigation of this species in double-stranded DNA (dsDNA) lags behind. Here we use chemical footprinting and laser-tweezers-based single-molecule approaches to demonstrate that a dsDNA fragment found in the insulin-linked polymorphic region (ILPR), 5 0 -(ACA GGGG TGT GGGG) 2 TGT, can fold into a G-quadruplex at pH 7.4 with 100 mM K þ , and an i-motif at pH 5.5 with 100 mM Li þ . Surprisingly, under a condition that favors the formation of both G-quadruplex and i-motif (pH 5.5, 100 mM K þ), a unique determination of change in the free energy of unfolding (DG unfold) by laser-tweezers experiments provides compelling evidence that only one species is present in each dsDNA. Under this condi-tion, molecules containing G-quadruplex are more stable than those with i-motif. These two species have mechanical stabilities (rupture force R 17 pN) comparable to the stall force of RNA polymerases, which, from a mechanical perspective alone, could justify a regulatory mechanism for tetraplex structures in the expression of human insulin.
  Biophysical Journal 06/2012; 102(11):2575-2584. · 3.65 Impact Factor
• Source

  Available from: Hanbin Mao

  Article: G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA.

  Soma Dhakal, Zhongbo Yu, Ryan Konik, Yunxi Cui, Deepak Koirala, Hanbin Mao
  [show abstract] [hide abstract]
  ABSTRACT: G-quadruplex has demonstrated its biological functions in vivo. Although G-quadruplex in single-stranded DNA (ssDNA) has been well characterized, investigation of this species in double-stranded DNA (dsDNA) lags behind. Here we use chemical footprinting and laser-tweezers-based single-molecule approaches to demonstrate that a dsDNA fragment found in the insulin-linked polymorphic region (ILPR), 5'-(ACA GGGG TGT GGGG)2 TGT, can fold into a G-quadruplex at pH 7.4 with 100 mM K+, and an i-motif at pH 5.5 with 100 mM Li+. Surprisingly, under a condition that favors the formation of both G-quadruplex and i-motif (pH 5.5, 100 mM K+), a unique determination of change in the free energy of unfolding (ΔGunfold) by laser-tweezers experiments provides compelling evidence that only one species is present in each dsDNA. Under this condition, molecules containing G-quadruplex are more stable than those with i-motif. These two species have mechanical stabilities (rupture force≥17 pN) comparable to the stall force of RNA polymerases, which, from a mechanical perspective alone, could justify a regulatory mechanism for tetraplex structures in the expression of human insulin.
  Biophysical Journal 06/2012; 102(11):2575-84. · 3.65 Impact Factor