Scientists demonstrate that an i-motif and a partially folded structure coexist in the C-rich human ILPR oligonucleotides

Soma N Dhakal in JACS

Scientists from Kent State University have demonstrated that an i-motif and a partially folded structure coexisted in the C-rich human ILPR oligonucleotides using laser tweezers. 

This discovery has recently been published as an article titled ‘Coexistence of an ILPR I-Motif and a Partially Folded Structure with Comparable Mechanical Stability Revealed at the Single-Molecule Level" in JACS.’ Here, ILPR stands for Insulin Linked Polymorphic Region which is human insulin gene. The ILPR region is known to regulate the production of insulin, a hormone which is responsible for the metabolism of glucose. When the control of insulin level fails it causes diabetes. Any stable DNA secondary structure formed in ILPR region may affect the transcription regulation of insulin gene causing insulin related health problems. This clarifies the importance of understanding the stability of DNA secondary structure. According to the main author of the article, Soma N Dhakal, a PhD student at Kent State University chemistry department, they have pioneered the mechanical stability of the tetraplex DNA secondary structure called i-motif formed by the cytosine-rich DNA sequence from the human ILPR.

The mechanical stability of i-motif was investigated in single molecule level which was supported by other bulk methods such as CD, UV and footprinting. In case of single-molecule study the DNA molecule containing the region of interest (one of the most prevalent variant of human ILPR sequence) was tethered between two surface-functionalized polystyrene beads (~ 2 um in diameters) which are trapped in two laser focuses. One of the laser focuses was stationary and another was moved apart to create tension in the molecule. This allowed to unfold the i-motif formed in the region of interest. The unfolding force and contour length change were recorded for individual molecule. 

Although the single molecular methods like laser tweezers take a while for data collection, it is very impressive in terms of studying individual molecules which is not possible in any bulk techniques like Circular Dichroism (CD), NMR, electrophoresis etc. This is one of the biggest advantages of single molecular methods.

The formation of an i-motif is decreased with increasing pH, while that of partially folded structure is pH independent. Both the i-motif and the partially folded structure have unfolding forces higher than the stall forces of RNA polymerases, suggesting either of the structure can stop transcription from a mechanical perspective alone. Authors have claimed that this is the first time that single molecular investigation on i-motif structures has been done.