# Investigation of energetics of sharp DNA bending

> **NIH NIH R01** · GEORGIA INSTITUTE OF TECHNOLOGY · 2023 · $200,000

## Abstract

Genetic information is carried by DNA, a polymeric molecule governed by the laws of physics. Strongly bent and
twisted DNA is associated with many genomic processes including packaging, transcription, repair, and editing,
which suggests that these processes are aided by the intrinsic deformability of DNA. Hence, altered deformability
of DNA due to damage or mutation can perturb the regulatory state of the genome, thus increasing the
susceptibility to disease. Understanding how deformability of DNA changes with base sequence can thus provide
a missing link between genetic variation and cell physiology. DNA is a double helical ladder of base pair steps
with the major and minor grooves. This groove asymmetry confers DNA with asymmetric bendability and bend-
twist coupling, properties truly unique to DNA, but these properties have not been thoroughly investigated by
experimental means. Extreme bending or twisting of a single base pair step can lead to large changes in the
three-dimensional DNA conformation, but the thermodynamics and sequence dependence of extreme
bendability and twistability remain largely unknown due to the lack of experimental methods. Deformed base pair
steps will likely affect how enzymes and transcription factors interact with DNA, but testing this idea requires fine
control of base-pair step deformation.
The PI has investigated the thermodynamics of strong DNA bending by the combined use of short DNA with
sticky ends and surface-based single-molecule assays. During the first funding period of this R01, looping and
unlooping rates were measured from DNA molecules of different lengths and base sequences including
mismatched bases. The results from these studies elucidated the kinetics of loop formation and helped us to
design new approaches to quantifying asymmetric bendability and bend-twist coupling of DNA. Furthermore,
they revealed DNA loop geometries that enable measurement of the bending and twist stiffness of individual
base pair steps.
Building upon these key results and insights from the first R01, this proposal will measure extreme deformability
of DNA and investigate its consequence on the kinetics of a DNA targeting protein. The experimental approach
is to combine singe-molecule FRET with small DNA loops of different geometries. Four specific aims are
proposed: Aim 1, quantifying the bending asymmetry and bend-twist coupling of DNA; Aim 2, quantifying bending
stiffness of mismatched base pairs at different bending angles; Aim 3, measuring coaxial stacking and unstacking
rates of individual base pair steps; and Aim 4, measuring the reaction kinetics of Cas12, an RNA-guided DNA
targeting protein of the CRISPR system, on curved and twisted DNA substrates. These studies will shed light on
the generic mechanics-function relationship of DNA.

## Key facts

- **NIH application ID:** 10796243
- **Project number:** 3R01GM112882-09S1
- **Recipient organization:** GEORGIA INSTITUTE OF TECHNOLOGY
- **Principal Investigator:** Harold D Kim
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $200,000
- **Award type:** 3
- **Project period:** 2015-03-06 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10796243

## Citation

> US National Institutes of Health, RePORTER application 10796243, Investigation of energetics of sharp DNA bending (3R01GM112882-09S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10796243. Licensed CC0.

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